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hyperchem应用-辛烷

hyperchem应用-辛烷

Hyperchem程序应用-辛烷1、画辛烷分子模型：辛烷分子碳碳骨架结构：加氢并模型化：2、用半经验方法CNDO进行优化3、选用从头算计算方法进行单点计算：4、显示原子电荷、显示键长、显示键角、二面角：5、分子性质：6、分子轨道图-最高占据轨道2D、3D图：7、分子轨道图-最低空轨道2D、3D图：8辛烷分子总电荷密度图（2D、3D）：8、辛烷分子2D、3D静电势图、等值面图：9、分子结构模型表示：10、计算输出结果：HyperChem log start -- Mon Dec 13 18:37:31 2010.Geometry optimization, SemiEmpirical, molecule = (untitled).CNDOFletcherReeves optimizerConvergence limit = 0.0001000 Iteration limit = 50Accelerate convergence = YESOptimization algorithm = Fletcher-ReevesCriterion of RMS gradient = 0.1000 kcal/(A mol) Maximum cycles = 345RHF Calculation:Singlet state calculationNumber of electrons = 44Number of Double Occupied Levels = 22Charge on the System = 0Total Orbitals = 44Starting CNDO calculation with 44 orbitalsE=0.0000 Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=1 Diff=14292.75153]E=0.0000 Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=2 Diff=9.35887]E=0.0000 Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=3 Diff=0.54071]E=0.0000 Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=4 Diff=0.03993]E=0.0000 Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=5 Diff=0.00066]E=0.0000 Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=6 Diff=0.00004]E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=1 Diff=115.68581] E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=2 Diff=9.46473] E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=3 Diff=0.86416] E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=4 Diff=0.10244] E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=5 Diff=0.00180] E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=6 Diff=0.00012] E=-5569.6934 Grad=74.633 Conv=NO(0 cycles 1 points) [Iter=7 Diff=0.00001] E=-5516.4321 Grad=113.901 Conv=NO(0 cycles 2 points) [Iter=1 Diff=46.41182] E=-5516.4321 Grad=113.901 Conv=NO(0 cycles 2 points) [Iter=2 Diff=3.63947]E=-5516.4321 Grad=113.901 Conv=NO(0 cycles 2 points) [Iter=3 Diff=0.32064] E=-5516.4321 Grad=113.901 Conv=NO(0 cycles 2 points) [Iter=4 Diff=0.03685] E=-5516.4321 Grad=113.901 Conv=NO(0 cycles 2 points) [Iter=5 Diff=0.00059] E=-5516.4321 Grad=113.901 Conv=NO(0 cycles 2 points) [Iter=6 Diff=0.00003] E=-5613.0083 Grad=6.496 Conv=NO(1 cycles 3 points) [Iter=1 Diff=0.06673] E=-5613.0083 Grad=6.496 Conv=NO(1 cycles 3 points) [Iter=2 Diff=0.00512] E=-5613.0083 Grad=6.496 Conv=NO(1 cycles 3 points) [Iter=3 Diff=0.00050] E=-5613.0083 Grad=6.496 Conv=NO(1 cycles 3 points) [Iter=4 Diff=0.00007] E=-5613.5781 Grad=3.499 Conv=NO(1 cycles 4 points) [Iter=1 Diff=0.06718] E=-5613.5781 Grad=3.499 Conv=NO(1 cycles 4 points) [Iter=2 Diff=0.00516] E=-5613.5781 Grad=3.499 Conv=NO(1 cycles 4 points) [Iter=3 Diff=0.00050] E=-5613.5781 Grad=3.499 Conv=NO(1 cycles 4 points) [Iter=4 Diff=0.00007] E=-5613.6587 Grad=4.830 Conv=NO(1 cycles 5 points) [Iter=1 Diff=0.00755] E=-5613.6587 Grad=4.830 Conv=NO(1 cycles 5 points) [Iter=2 Diff=0.00058] E=-5613.6587 Grad=4.830 Conv=NO(1 cycles 5 points) [Iter=3 Diff=0.00006] E=-5613.6865 Grad=3.874 Conv=NO(2 cycles 6 points) [Iter=1 Diff=0.09278] E=-5613.6865 Grad=3.874 Conv=NO(2 cycles 6 points) [Iter=2 Diff=0.00694] E=-5613.6865 Grad=3.874 Conv=NO(2 cycles 6 points) [Iter=3 Diff=0.00063] E=-5613.6865 Grad=3.874 Conv=NO(2 cycles 6 points) [Iter=4 Diff=0.00008] E=-5613.8223 Grad=3.477 Conv=NO(2 cycles 7 points) [Iter=1 Diff=0.00902] E=-5613.8223 Grad=3.477 Conv=NO(2 cycles 7 points) [Iter=2 Diff=0.00067] E=-5613.8223 Grad=3.477 Conv=NO(2 cycles 7 points) [Iter=3 Diff=0.00006] E=-5613.8574 Grad=2.075 Conv=NO(3 cycles 8 points) [Iter=1 Diff=0.00837] E=-5613.8574 Grad=2.075 Conv=NO(3 cycles 8 points) [Iter=2 Diff=0.00083] E=-5613.8574 Grad=2.075 Conv=NO(3 cycles 8 points) [Iter=3 Diff=0.00010] E=-5613.8574 Grad=2.075 Conv=NO(3 cycles 8 points) [Iter=4 Diff=0.00002] E=-5613.9468 Grad=1.293 Conv=NO(3 cycles 9 points) [Iter=1 Diff=0.00837] E=-5613.9468 Grad=1.293 Conv=NO(3 cycles 9 points) [Iter=2 Diff=0.00083] E=-5613.9468 Grad=1.293 Conv=NO(3 cycles 9 points) [Iter=3 Diff=0.00010] E=-5613.9468 Grad=1.293 Conv=NO(3 cycles 9 points) [Iter=4 Diff=0.00002] E=-5613.9312 Grad=2.539 Conv=NO(3 cycles 10 points) [Iter=1 Diff=0.00351] E=-5613.9312 Grad=2.539 Conv=NO(3 cycles 10 points) [Iter=2 Diff=0.00035] E=-5613.9312 Grad=2.539 Conv=NO(3 cycles 10 points) [Iter=3 Diff=0.00004] E=-5613.9531 Grad=1.581 Conv=NO(4 cycles 11 points) [Iter=1 Diff=0.03067] E=-5613.9531 Grad=1.581 Conv=NO(4 cycles 11 points) [Iter=2 Diff=0.00315] E=-5613.9531 Grad=1.581 Conv=NO(4 cycles 11 points) [Iter=3 Diff=0.00041] E=-5613.9531 Grad=1.581 Conv=NO(4 cycles 11 points) [Iter=4 Diff=0.00007] E=-5614.0254 Grad=1.729 Conv=NO(4 cycles 12 points) [Iter=1 Diff=0.03082] E=-5614.0254 Grad=1.729 Conv=NO(4 cycles 12 points) [Iter=2 Diff=0.00317] E=-5614.0254 Grad=1.729 Conv=NO(4 cycles 12 points) [Iter=3 Diff=0.00041] E=-5614.0254 Grad=1.729 Conv=NO(4 cycles 12 points) [Iter=4 Diff=0.00007] E=-5613.9551 Grad=3.772 Conv=NO(4 cycles 13 points) [Iter=1 Diff=0.03047] E=-5613.9551 Grad=3.772 Conv=NO(4 cycles 13 points) [Iter=2 Diff=0.00314] E=-5613.9551 Grad=3.772 Conv=NO(4 cycles 13 points) [Iter=3 Diff=0.00041]E=-5614.0254 Grad=1.739 Conv=NO(5 cycles 14 points) [Iter=1 Diff=0.10421] E=-5614.0254 Grad=1.739 Conv=NO(5 cycles 14 points) [Iter=2 Diff=0.00961] E=-5614.0254 Grad=1.739 Conv=NO(5 cycles 14 points) [Iter=3 Diff=0.00112] E=-5614.0254 Grad=1.739 Conv=NO(5 cycles 14 points) [Iter=4 Diff=0.00018] E=-5614.0254 Grad=1.739 Conv=NO(5 cycles 14 points) [Iter=5 Diff=0.00000] E=-5614.0059 Grad=2.873 Conv=NO(5 cycles 15 points) [Iter=1 Diff=0.02966] E=-5614.0059 Grad=2.873 Conv=NO(5 cycles 15 points) [Iter=2 Diff=0.00274] E=-5614.0059 Grad=2.873 Conv=NO(5 cycles 15 points) [Iter=3 Diff=0.00032] E=-5614.0059 Grad=2.873 Conv=NO(5 cycles 15 points) [Iter=4 Diff=0.00005] E=-5614.0864 Grad=0.979 Conv=NO(6 cycles 16 points) [Iter=1 Diff=0.00695] E=-5614.0864 Grad=0.979 Conv=NO(6 cycles 16 points) [Iter=2 Diff=0.00061] E=-5614.0864 Grad=0.979 Conv=NO(6 cycles 16 points) [Iter=3 Diff=0.00007] E=-5614.1025 Grad=0.870 Conv=NO(6 cycles 17 points) [Iter=1 Diff=0.00052] E=-5614.1025 Grad=0.870 Conv=NO(6 cycles 17 points) [Iter=2 Diff=0.00005] E=-5614.1055 Grad=0.577 Conv=NO(7 cycles 18 points) [Iter=1 Diff=0.00479] E=-5614.1055 Grad=0.577 Conv=NO(7 cycles 18 points) [Iter=2 Diff=0.00048] E=-5614.1055 Grad=0.577 Conv=NO(7 cycles 18 points) [Iter=3 Diff=0.00006] E=-5614.1069 Grad=0.931 Conv=NO(7 cycles 19 points) [Iter=1 Diff=0.00096] E=-5614.1069 Grad=0.931 Conv=NO(7 cycles 19 points) [Iter=2 Diff=0.00010] E=-5614.1108 Grad=0.447 Conv=NO(8 cycles 20 points) [Iter=1 Diff=0.00213] E=-5614.1108 Grad=0.447 Conv=NO(8 cycles 20 points) [Iter=2 Diff=0.00018] E=-5614.1108 Grad=0.447 Conv=NO(8 cycles 20 points) [Iter=3 Diff=0.00002] E=-5614.1177 Grad=0.476 Conv=NO(8 cycles 21 points) [Iter=1 Diff=0.00213] E=-5614.1177 Grad=0.476 Conv=NO(8 cycles 21 points) [Iter=2 Diff=0.00018] E=-5614.1177 Grad=0.476 Conv=NO(8 cycles 21 points) [Iter=3 Diff=0.00002] E=-5614.1167 Grad=0.939 Conv=NO(8 cycles 22 points) [Iter=1 Diff=0.00085] E=-5614.1167 Grad=0.939 Conv=NO(8 cycles 22 points) [Iter=2 Diff=0.00007] E=-5614.1182 Grad=0.627 Conv=NO(9 cycles 23 points) [Iter=1 Diff=0.02140] E=-5614.1182 Grad=0.627 Conv=NO(9 cycles 23 points) [Iter=2 Diff=0.00201] E=-5614.1182 Grad=0.627 Conv=NO(9 cycles 23 points) [Iter=3 Diff=0.00022] E=-5614.1182 Grad=0.627 Conv=NO(9 cycles 23 points) [Iter=4 Diff=0.00003] E=-5614.1118 Grad=1.125 Conv=NO(9 cycles 24 points) [Iter=1 Diff=0.00758] E=-5614.1118 Grad=1.125 Conv=NO(9 cycles 24 points) [Iter=2 Diff=0.00071] E=-5614.1118 Grad=1.125 Conv=NO(9 cycles 24 points) [Iter=3 Diff=0.00008] E=-5614.1235 Grad=0.266 Conv=NO(10 cycles 25 points) [Iter=1 Diff=0.00049] E=-5614.1235 Grad=0.266 Conv=NO(10 cycles 25 points) [Iter=2 Diff=0.00005] E=-5614.1260 Grad=0.299 Conv=NO(10 cycles 26 points) [Iter=1 Diff=0.00049] E=-5614.1260 Grad=0.299 Conv=NO(10 cycles 26 points) [Iter=2 Diff=0.00005] E=-5614.1245 Grad=0.624 Conv=NO(10 cycles 27 points) [Iter=1 Diff=0.00036] E=-5614.1245 Grad=0.624 Conv=NO(10 cycles 27 points) [Iter=2 Diff=0.00004] E=-5614.1260 Grad=0.339 Conv=NO(11 cycles 28 points) [Iter=1 Diff=0.00379] E=-5614.1260 Grad=0.339 Conv=NO(11 cycles 28 points) [Iter=2 Diff=0.00040] E=-5614.1260 Grad=0.339 Conv=NO(11 cycles 28 points) [Iter=3 Diff=0.00005]E=-5614.1328 Grad=0.318 Conv=NO(11 cycles 29 points) [Iter=2 Diff=0.00040] E=-5614.1328 Grad=0.318 Conv=NO(11 cycles 29 points) [Iter=3 Diff=0.00005] E=-5614.1348 Grad=0.524 Conv=NO(11 cycles 30 points) [Iter=1 Diff=0.01513] E=-5614.1348 Grad=0.524 Conv=NO(11 cycles 30 points) [Iter=2 Diff=0.00160] E=-5614.1348 Grad=0.524 Conv=NO(11 cycles 30 points) [Iter=3 Diff=0.00020] E=-5614.1348 Grad=0.524 Conv=NO(11 cycles 30 points) [Iter=4 Diff=0.00003] E=-5614.1270 Grad=1.092 Conv=NO(11 cycles 31 points) [Iter=1 Diff=0.01436] E=-5614.1270 Grad=1.092 Conv=NO(11 cycles 31 points) [Iter=2 Diff=0.00152] E=-5614.1270 Grad=1.092 Conv=NO(11 cycles 31 points) [Iter=3 Diff=0.00019] E=-5614.1270 Grad=1.092 Conv=NO(11 cycles 31 points) [Iter=4 Diff=0.00003] E=-5614.1348 Grad=0.538 Conv=NO(12 cycles 32 points) [Iter=1 Diff=0.14614] E=-5614.1348 Grad=0.538 Conv=NO(12 cycles 32 points) [Iter=2 Diff=0.01365] E=-5614.1348 Grad=0.538 Conv=NO(12 cycles 32 points) [Iter=3 Diff=0.00158] E=-5614.1348 Grad=0.538 Conv=NO(12 cycles 32 points) [Iter=4 Diff=0.00025] E=-5614.1348 Grad=0.538 Conv=NO(12 cycles 32 points) [Iter=5 Diff=0.00000] E=-5613.9834 Grad=4.088 Conv=NO(12 cycles 33 points) [Iter=1 Diff=0.11050] E=-5613.9834 Grad=4.088 Conv=NO(12 cycles 33 points) [Iter=2 Diff=0.01032] E=-5613.9834 Grad=4.088 Conv=NO(12 cycles 33 points) [Iter=3 Diff=0.00120] E=-5613.9834 Grad=4.088 Conv=NO(12 cycles 33 points) [Iter=4 Diff=0.00019] E=-5613.9834 Grad=4.088 Conv=NO(12 cycles 33 points) [Iter=5 Diff=0.00000] E=-5614.1387 Grad=0.255 Conv=NO(13 cycles 34 points) [Iter=1 Diff=0.00190] E=-5614.1387 Grad=0.255 Conv=NO(13 cycles 34 points) [Iter=2 Diff=0.00021] E=-5614.1387 Grad=0.255 Conv=NO(13 cycles 34 points) [Iter=3 Diff=0.00003] E=-5614.1421 Grad=0.289 Conv=NO(13 cycles 35 points) [Iter=1 Diff=0.00190] E=-5614.1421 Grad=0.289 Conv=NO(13 cycles 35 points) [Iter=2 Diff=0.00021] E=-5614.1421 Grad=0.289 Conv=NO(13 cycles 35 points) [Iter=3 Diff=0.00003] E=-5614.1431 Grad=0.532 Conv=NO(13 cycles 36 points) [Iter=1 Diff=0.00010] E=-5614.1431 Grad=0.532 Conv=NO(13 cycles 36 points) [Iter=2 Diff=0.00001] E=-5614.1431 Grad=0.470 Conv=NO(14 cycles 37 points) [Iter=1 Diff=0.03041] E=-5614.1431 Grad=0.470 Conv=NO(14 cycles 37 points) [Iter=2 Diff=0.00300] E=-5614.1431 Grad=0.470 Conv=NO(14 cycles 37 points) [Iter=3 Diff=0.00038] E=-5614.1431 Grad=0.470 Conv=NO(14 cycles 37 points) [Iter=4 Diff=0.00007] E=-5614.1255 Grad=1.489 Conv=NO(14 cycles 38 points) [Iter=1 Diff=0.01674] E=-5614.1255 Grad=1.489 Conv=NO(14 cycles 38 points) [Iter=2 Diff=0.00165] E=-5614.1255 Grad=1.489 Conv=NO(14 cycles 38 points) [Iter=3 Diff=0.00021] E=-5614.1255 Grad=1.489 Conv=NO(14 cycles 38 points) [Iter=4 Diff=0.00004] E=-5614.1455 Grad=0.166 Conv=NO(15 cycles 39 points) [Iter=1 Diff=0.00113] E=-5614.1455 Grad=0.166 Conv=NO(15 cycles 39 points) [Iter=2 Diff=0.00010] E=-5614.1455 Grad=0.166 Conv=NO(15 cycles 39 points) [Iter=3 Diff=0.00001] E=-5614.1465 Grad=0.312 Conv=NO(15 cycles 40 points) [Iter=1 Diff=0.00011] E=-5614.1465 Grad=0.312 Conv=NO(15 cycles 40 points) [Iter=2 Diff=0.00001] E=-5614.1465 Grad=0.207 Conv=NO(16 cycles 41 points) [Iter=1 Diff=0.00191] E=-5614.1465 Grad=0.207 Conv=NO(16 cycles 41 points) [Iter=2 Diff=0.00016]E=-5614.1465 Grad=0.338 Conv=NO(16 cycles 42 points) [Iter=1 Diff=0.00053]E=-5614.1465 Grad=0.338 Conv=NO(16 cycles 42 points) [Iter=2 Diff=0.00005]E=-5614.1470 Grad=0.118 Conv=NO(17 cycles 43 points) [Iter=1 Diff=0.00009]E=-5614.1475 Grad=0.087 Conv=NO(17 cycles 44 points) [Iter=1 Diff=0.00010]E=-5614.1479 Grad=0.135 Conv=NO(17 cycles 45 points) [Iter=1 Diff=0.00000]E=-5614.1479 Grad=0.125 Conv=NO(18 cycles 46 points) [Iter=1 Diff=0.00045]E=-5614.1479 Grad=0.125 Conv=NO(18 cycles 46 points) [Iter=2 Diff=0.00004]E=-5614.1475 Grad=0.250 Conv=NO(18 cycles 47 points) [Iter=1 Diff=0.00015]E=-5614.1475 Grad=0.250 Conv=NO(18 cycles 47 points) [Iter=2 Diff=0.00001]E=-5614.1479 Grad=0.080 Conv=YES(19 cycles 48 points) [Iter=1 Diff=0.00000] ENERGIES AND GRADIENTTotal Energy = -39107.4530564 (kcal/mol)Total Energy = -62.5 (a.u.)Binding Energy = -5614.1480863 (kcal/mol)Isolated Atomic Energy = -33493.3049701 (kcal/mol)Electronic Energy = -151855.7014212 (kcal/mol)Core-Core Interaction = 112748.2483647 (kcal/mol)Heat of Formation = -3584.2860863 (kcal/mol)Gradient = 0.0797574 (kcal/mol/Ang) MOLECULAR POINT GROUPC2VEIGENV ALUES(eV)Symmetry: 1 A1 1 B2 2 A1 2 B2 3 A1 Eigenvalue: -48.228653 -44.921967 -39.969822 -34.146118 -30.883162 Symmetry: 1 B1 4 A1 3 B2 1 A2 5 A1 Eigenvalue: -28.682699 -28.469046 -28.056545 -25.610565 -24.098553 Symmetry: 4 B2 2 B1 5 B2 6 A1 2 A2 Eigenvalue: -23.099024 -21.719042 -20.119864 -18.474934 -18.154465 Symmetry: 7 A1 3 B1 6 B2 3 A2 8 A1 Eigenvalue: -16.890295 -15.730311 -15.627211 -14.505156 -14.398620 Symmetry: 7 B2 4 B1 5 B1 4 A2 9 A1 Eigenvalue: -14.220551 -14.122036 6.037422 6.486364 6.984152 Symmetry: 6 B1 8 B2 10 A1 9 B2 11 A1 Eigenvalue: 7.209129 7.266216 7.494792 7.807704 7.893167 Symmetry: 10 B2 5 A2 12 A1 11 B2 13 A1 Eigenvalue: 8.082231 8.194494 8.242883 8.928360 9.149508 Symmetry: 7 B1 14 A1 6 A2 12 B2 8 B1 Eigenvalue: 9.358259 9.783697 10.395283 10.967291 11.024303 Symmetry: 13 B2 15 A1 16 A1 14 B2Eigenvalue: 11.812114 11.856253 12.302794 12.332813ATOMIC ORBITAL ELECTRON POPULATIONSAO: 1 S C 1 Px C 1 Py C 1 Pz C 2 S C1.017689 0.970367 1.030565 0.973715 0.968621AO: 2 Px C 2 Py C 2 Pz C 3 S C 3 Px C1.012650 1.023395 0.956421 0.974890 1.013266AO: 3 Py C 3 Pz C 4 S C 4 Px C 4 Py C1.016258 0.960073 0.976386 1.014955 1.017676AO: 4 Pz C 5 S C 5 Px C 5 Py C 5 Pz C0.959603 0.974890 1.014978 1.014546 0.960073AO: 6 S C 6 Px C 6 Py C 6 Pz C 7 S C0.968622 1.017895 1.018150 0.956422 1.017688AO: 7 Px C 7 Py C 7 Pz C 8 S H 9 S H1.024900 0.976031 0.973714 1.011286 1.004890AO: 10 S H 11 S H 12 S H 13 S H 14 S H1.004890 1.014996 1.014996 1.015570 1.015570AO: 15 S H 16 S H 17 S H 18 S H 19 S H1.015582 1.015582 1.015570 1.015570 1.014996AO: 20 S H 21 S H 22 S H 23 S H1.014995 1.011287 1.004890 1.004890NET CHARGES AND COORDINATESAtom Z Charge Coordinates(Angstrom) Massx y z1 6 0.007665 1.27026 -2.99875 0.00000 12.011002 6 0.038912 1.22452 -1.53312 0.00000 12.011003 6 0.035512 -0.13502 -0.95607 0.00000 12.011004 6 0.031379 -0.21279 0.51953 0.00000 12.011005 6 0.035513 -1.57806 1.08470 -0.00000 12.011006 6 0.038911 -1.66895 2.55885 0.00000 12.011007 6 0.007667 -3.03551 3.09050 -0.00000 12.011008 1 -0.011286 2.31779 -3.39733 -0.00000 1.008009 1 -0.004890 0.76635 -3.44042 0.89791 1.0080010 1 -0.004890 0.76635 -3.44042 -0.89790 1.0080011 1 -0.014996 1.80141 -1.14693 0.88746 1.0080012 1 -0.014996 1.80141 -1.14693 -0.88746 1.0080013 1 -0.015570 -0.70523 -1.35564 0.88637 1.0080014 1 -0.015570 -0.70523 -1.35564 -0.88637 1.0080015 1 -0.015582 0.35562 0.92145 0.88644 1.0080016 1 -0.015582 0.35562 0.92145 -0.88643 1.0080017 1 -0.015570 -2.14485 0.68030 -0.88638 1.0080018 1 -0.015570 -2.14486 0.68029 0.88636 1.0080019 1 -0.014996 -1.11255 2.97401 0.88746 1.0080020 1 -0.014995 -1.11254 2.97402 -0.88745 1.0080021 1 -0.011287 -3.06212 4.21099 0.00000 1.0080022 1 -0.004890 -3.61989 2.76263 -0.89791 1.0080023 1 -0.004890 -3.61990 2.76263 0.89790 1.00800ATOMIC GRADIENTSAtom Z Gradients(kcal/mol/Angstrom)x y z1 6 -0.23321 0.17204 -0.000102 6 -0.05131 -0.05641 -0.000493 6 -0.12340 0.09713 -0.000494 6 0.05576 0.06527 -0.000275 6 0.07533 -0.18029 0.000046 6 -0.08613 -0.00112 -0.000097 6 0.10150 -0.28460 -0.000148 1 0.04407 0.00197 -0.000029 1 -0.01228 0.07302 0.0311010 1 -0.01224 0.07324 -0.0309911 1 -0.05895 -0.04436 -0.1303212 1 -0.05946 -0.04468 0.1308613 1 0.06288 0.03734 -0.0218714 1 0.06334 0.03765 0.0223715 1 0.05153 0.03609 0.1191916 1 0.05140 0.03583 -0.1189617 1 0.05580 0.04741 0.0218218 1 0.05573 0.04738 -0.0218019 1 -0.06188 -0.04176 -0.1312320 1 -0.06184 -0.04172 0.1312321 1 0.01654 0.04341 -0.0000122 1 0.06347 -0.03639 -0.0327523 1 0.06334 -0.03647 0.03294Dipole (Debyes) x y z TotalPoint-Chg. -0.024 -0.017 -0.000 0.030sp Hybrid 0.011 0.008 -0.000 0.013pd Hybrid 0.000 0.000 0.000 0.000Sum -0.013 -0.009 -0.000 0.016Single Point, AbInitio, molecule = (untitled).Convergence limit = 0.0001000 Iteration limit = 50Accelerate convergence = YESFull MP2 correlation energy is requested.The initial guess of the MO coefficients is from eigenvectors of the core Hamiltonian. Shell Types: S, S=P.RHF Calculation:Singlet state calculationNumber of electrons = 58Number of Doubly-Occupied Levels = 29Charge on the System = 0Total Orbitals (Basis Functions) = 95Primitive Gaussians = 153Starting HyperGauss calculation with 95 basis functions and 153 primitive Gaussians. 2-electron Integral buffers will be 3200 words (double precision) long.Two electron integrals will use a cutoff of 1.00000e-010Regular integral format is used.Computing the one-electron integrals ...Computing 2e integrals (s and p orbitals only): done 0%.Computing 2e integrals (s and p orbitals only): done 10%.Computing 2e integrals (s and p orbitals only): done 20%.Computing 2e integrals (s and p orbitals only): done 30%.Computing 2e integrals (s and p orbitals only): done 40%.Computing 2e integrals (s and p orbitals only): done 50%.Computing 2e integrals (s and p orbitals only): done 60%.Computing 2e integrals (s and p orbitals only): done 70%.Computing 2e integrals (s and p orbitals only): done 80%.Computing 2e integrals (s and p orbitals only): done 90%.5631113 integrals have been produced.Computing the initial guess of the MO coefficients ...Iteration = 1 Difference = 1032.07Iteration = 2 Difference = 1938.56Iteration = 3 Difference = 189.33Iteration = 4 Difference = 632.45Iteration = 5 Difference = 171.79Iteration = 6 Difference = 24.01Iteration = 7 Difference = 2.02Iteration = 8 Difference = 0.35Iteration = 9 Difference = 0.03Iteration = 10 Difference = 0.00Iteration = 11 Difference = 0.0002403903Iteration = 12 Difference = 0.0000084763Computing MP2 energy with 29 occupied and 66 virtual orbitals ... Transfering the 2e integrals from AO to MO: done 0%.Transfering the 2e integrals from AO to MO: done 10%.Transfering the 2e integrals from AO to MO: done 20%.Transfering the 2e integrals from AO to MO: done 30%.Transfering the 2e integrals from AO to MO: done 40%.Transfering the 2e integrals from AO to MO: done 50%.Transfering the 2e integrals from AO to MO: done 60%.Transfering the 2e integrals from AO to MO: done 70%.Transfering the 2e integrals from AO to MO: done 80%.Transfering the 2e integrals from AO to MO: done 90%.Energy=-171223.093981 MP2 Correlation Energy=-414.861844 Symmetry=C2V ENERGIES AND GRADIENT========== SCF RESULTS ==========Total Energy = -171223.0939809 (kcal/mol)Total Energy = -272.0 (a.u.)Electronic Kinetic Energy = 170947.5590687 (kcal/mol)Electronic Kinetic Energy = 272.2 (a.u.)The Virial (-V/T) = 2.0016eK, ee and eN Energy = -367133.0518992 (kcal/mol)Nuclear Repulsion Energy = 195909.9579183 (kcal/mol)======== POST SCF RESULTS ========MP2 Correlation Energy = -414.8618444 (kcal/mol)MP2 Correlation Energy = -0.0 (a.u.)Total Energy (with MP2 energy) = -171637.9558252 (kcal/mol)Total Energy (with MP2 energy) = -273.5224594 (a.u.)Occupied and Virtual Orbitals in MP2 = 29, 66========== SCF RESULTS ==========MOLECULAR POINT GROUPC2VEIGENV ALUES(eV)Symmetry: 1 B2 1 A1 2 B2 2 A1 3 A1 Eigenvalue: -303.674866 -303.674713 -303.631775 -303.630157 -303.627747 Symmetry: 3 B2 4 A1 5 A1 4 B2 6 A1 Eigenvalue: -303.623016 -303.612946 -30.261747 -29.204332 -27.434654 Symmetry: 5 B2 7 A1 8 A1 6 B2 1 B1 Eigenvalue: -25.107853 -22.681458 -21.177843 -21.160900 -17.947813 Symmetry: 1 A2 9 A1 7 B2 2 B1 8 B2 Eigenvalue: -16.982294 -16.493128 -16.444221 -15.528235 -15.090984 Symmetry: 10 A1 2 A2 11 A1 9 B2 3 B1 Eigenvalue: -14.549708 -13.900264 -13.511187 -12.866585 -12.585258 Symmetry: 12 A1 10 B2 3 A2 4 B1 13 A1 Eigenvalue: -12.306542 -12.249912 -11.875375 -11.724080 7.087684 Symmetry: 5 B1 11 B2 14 A1 15 A1 4 A2 Eigenvalue: 7.258967 7.333437 7.768019 8.007830 8.335639 Symmetry: 12 B2 16 A1 13 B2 6 B1 14 B2 Eigenvalue: 8.724559 9.351191 9.442577 9.514703 9.899670 Symmetry: 5 A2 7 B1 17 A1 6 A2 8 B1 Eigenvalue: 10.156153 10.202340 10.277209 10.321597 10.688224 Symmetry: 18 A1 19 A1 15 B2 16 B2 20 A1 Eigenvalue: 11.894808 12.191500 12.239221 13.969515 14.873546 Symmetry: 17 B2 18 B2 21 A1 9 B1 7 A2 Eigenvalue: 14.943412 24.174065 24.497423 25.322130 25.437565 Symmetry: 22 A1 10 B1 19 B2 23 A1 8 A2 Eigenvalue: 25.885952 26.483768 27.062307 27.959761 28.765862 Symmetry: 20 B2 24 A1 21 B2 25 A1 26 A1 Eigenvalue: 28.808775 29.825521 30.151628 30.719355 31.761393 Symmetry: 11 B1 22 B2 9 A2 23 B2 12 B1 Eigenvalue: 31.900881 32.902023 33.776600 33.784996 33.892372 Symmetry: 27 A1 13 B1 10 A2 28 A1 24 B2 Eigenvalue: 33.973347 35.433430 36.171829 36.518166 36.652103Symmetry: 14 B1 11 A2 29 A1 30 A1 15 B1 Eigenvalue: 36.898243 37.728039 37.748863 38.017197 38.224873 Symmetry: 25 B2 31 A1 26 B2 32 A1 27 B2 Eigenvalue: 38.257149 38.725616 38.931732 39.085808 40.204521 Symmetry: 12 A2 28 B2 16 B1 33 A1 29 B2 Eigenvalue: 41.526394 43.364548 49.700970 49.825069 55.635876 Symmetry: 34 A1 30 B2 35 A1 31 B2 36 A1 Eigenvalue: 60.068157 62.722443 64.506859 69.455078 77.091454 ATOMIC ORBITAL ELECTRON POPULATIONSC 1 S C 1 S C 1 Px C 1 Py C 1 Pz1.988309 0.353594 0.528720 0.555717 0.528189C 1 S C 1 Px C 1 Py C 1 Pz C 2 S1.112087 0.573252 0.345988 0.569138 1.989476C 2 S C 2 Px C 2 Py C 2 Pz C 2 S0.348915 0.547487 0.559715 0.527539 1.107065C 2 Px C 2 Py C 2 Pz C 3 S C 3 S0.400466 0.350437 0.582624 1.989604 0.349376C 3 Px C 3 Py C 3 Pz C 3 S C 3 Px0.546579 0.556665 0.525439 1.094947 0.398869C 3 Py C 3 Pz C 4 S C 4 S C 4 Px0.337608 0.578260 1.989672 0.349268 0.546835C 4 Py C 4 Pz C 4 S C 4 Px C 4 Py0.556721 0.525498 1.098025 0.397285 0.340660C 4 Pz C 5 S C 5 S C 5 Px C 5 Py0.579368 1.989603 0.349377 0.546403 0.556843C 5 Pz C 5 S C 5 Px C 5 Py C 5 Pz0.525439 1.094939 0.396197 0.340286 0.578257C 6 S C 6 S C 6 Px C 6 Py C 6 Pz1.989476 0.348915 0.551136 0.556063 0.527539C 6 S C 6 Px C 6 Py C 6 Pz C 7 S1.107065 0.406435 0.344470 0.582624 1.988310C 7 S C 7 Px C 7 Py C 7 Pz C 7 S0.353594 0.551270 0.533168 0.528188 1.112088C 7 Px C 7 Py C 7 Pz H 8 S H 8 S0.376075 0.543161 0.569141 0.455906 0.350817H 9 S H 9 S H 10 S H 10 S H 11 S0.455789 0.354839 0.455790 0.354841 0.454201H 11 S H 12 S H 12 S H 13 S H 13 S0.350338 0.454202 0.350338 0.453928 0.354491H 14 S H 14 S H 15 S H 15 S H 16 S0.453928 0.354490 0.453952 0.354422 0.453952H 16 S H 17 S H 17 S H 18 S H 18 S0.354420 0.453928 0.354491 0.453928 0.354491H 19 S H 19 S H 20 S H 20 S H 21 S0.454202 0.350338 0.454202 0.350338 0.455904H 21 S H 22 S H 22 S H 23 S H 23 S0.350817 0.455789 0.354840 0.455789 0.354840NET CHARGES AND COORDINATESAtom Z Charge Coordinates(Angstrom) Mass (Mulliken) x y z1 6 -0.554993 1. -2. 0.00000244 12.011002 6 -0.413723 1. -1. 0.00000350 12.011003 6 -0.377347 -0. -0. 0.00000361 12.011004 6 -0.383332 -0. 0. 0.00000283 12.011005 6 -0.377344 -1. 1.08469892 -0.00000218 12.011006 6 -0.413724 -1. 2. 0.00000175 12.011007 6 -0.554995 -3.03550863 3.09049869 -0.00000256 12.011008 1 0.193277 2. -3. -0.00000215 1.008009 1 0.189371 0. -3. 0. 1.0080010 1 0.189370 0. -3. -0. 1.0080011 1 0.195461 1. -1. 0. 1.0080012 1 0.195460 1. -1. -0. 1.0080013 1 0.191581 -0. -1. 0. 1.0080014 1 0.191582 -0. -1. -0. 1.0080015 1 0.191626 0. 0. 0. 1.0080016 1 0.191628 0. 0. -0. 1.0080017 1 0.191581 -2. 0. -0. 1.0080018 1 0.191581 -2. 0. 0. 1.0080019 1 0.195461 -1. 2. 0. 1.0080020 1 0.195461 -1. 2. -0. 1.0080021 1 0.193278 -3.06212473 4. 0.00000114 1.0080022 1 0.189371 -3. 2. -0. 1.0080023 1 0.189371 -3. 2. 0. 1.00800Net Charge (Electrons):0.0000Dipole Moment (Debye):X: 0.0374 Y: 0.0265 Z: -0.0000 Ttl: 0.0458 Quadrupole Moment (Debye-Ang):XX: -50.1060 YY: -50.0433 ZZ: -49.0744XY: -0.0137 XZ: -0.0000 YZ: -0.0000Octapole Moment (Debye-Ang^2):XXX: 92.7823 YYY: -33.3817 ZZZ: -0.0002XYY: 30.1231 XXY: -13.8770 XXZ: -0.0000XZZ: 29.0156 YZZ: -12.3621 YYZ: -0.0000 XYZ: -0.0000 Hexadecapole Moment (Debye-Ang^3):XXXX: -913.8107 YYYY: -1448.3551 ZZZZ: -99.1216XXXY: 473.6560 XXXZ: -0.0005 YYYX: 469.1867YYYZ: 0.0004 ZZZX: -0.0003 ZZZY: 0.0004XXYY: -394.9777 XXZZ: -163.0937 YYZZ: -256.2102 XXYZ: 0.0002 YYXZ: -0.0002 ZZXY: 158.8551 HyperChem log stop -- Mon Dec 13 18:51:44 2010.。

HyperChem软件

HyperChem软件

HyperChem软件中Script的常用语句注解1. 计算方法及参数设定calculation-method item计算方法设定item: MolecularMechanics, SemiEmpirical, AbInitio, DFT molecular-mechanics-method item分子力学方法设定item: mm+, amber, bio+, opls, amber94, charmm22, tndo optim-max-cycles x优化最大迭代次数x设定optim-convergence goal 优化收敛目标goal设定optim-converged返回是否收敛(true/false)optim-algorithm item 优化算法设定item: PolakRibiere, NewtonRaphson, etc.assign-basisset item abinitio计算基组设定item: 3-21G, STO-3G, etc.semi-empirical-method item半经验计算方法设定item: am1, pm3, extendedhuckel, cndo, indo, zindos, mndod, tndo, etc.accelerate-scf-convergence true/false 是否加速SCF收敛scf-convergence goal SCF收敛目标goal设定max-iterations n SCF计算的最大迭代次数n设定2. 计算结果输出omsgs-to-file filename 将信息输出到filename文件append-omsgs-to-file filename 将信息追加到filename文件omsgs-not-to-file 关闭输出文件query-response-has-tag yes/no 提取的信息回显开关query-value HSV提取系统数据结构中的信息并单行输出HSV: current-file-name, coordinates,dipole-moment, dipole-moment-componentstotal-energy, heat-of-formation,scf-binding-energy, scf-core-energy, scf-electronic-energy start-logging HyperChem运行记录开启stop-logging HyperChem运行记录关闭export-property-file filename将分子轨道信息写入filename文件3. 分子结构及其文件操作file-format item定义分子结构文件格式item: hin, mol, zmt, ent, skc, xyz, ml2open-file filename 读入filename分子结构文件write-file filename 将分子结构写入filename文件menu-build-add-hydrogens 给分子加氢menu-build-model-build 给分子加氢并规格化do-optimization 进行优化操作do-single-point 进行单点计算do-molecular-dynamics进行分子动力学操作4. 屏幕显示设置screen-refresh-period n屏幕刷新周期atom-labels item原子标识设定item: none, number, symbol, name, charge, etc.show-hydrogens yes/no 分子中氢显示开关show-multiple-bonds yes/no分子中重键显示开关request string弹出窗口并显示由双引号表达的字符串string 5. 其它read-script filename读取名为filename的script文件exit-script 退出script实例: example.scrcalculation-method molecular-mechanicsmolecular-mechanics-method mm+optim-max-cycles 2048optim-convergence 0.1optim-algorithm PolakRibiereomsgs-to-file results.txtquery-response-has-tag nofile-format molopen-file 000A-0001.molmenu-build-model-builddo-optimizationquery-value total-energyfile-format zmtwrite-file 000A-0001.zmtomsgs-not-to-fileexit-script附: HyperChem State Variables (HSV)abinitio-buffer-size: Variable, Read/Write.Type: integer in range (1 .. 2147483647).Two electron integral buffer size.abinitio-calculate-gradient: Variable, Read/Write.Type:boolean.Enable Ab Initio gradient calculation (Single Point only).abinitio-cutoff: Variable, Read/Write.Type: float in range (0 .. 1e+010).Two electron integral cutoff.abinitio-d-orbitals: Variable, Read/Write.boolean.Type:Either five (False) or six (True).abinitio-direct-scf: Variable, Read/Write.boolean.Type:Enable Ab Initio Direct SCF calculation.abinitio-f-orbitals: Variable, Read/Write.boolean.Type:Either seven (False) or ten (True).abinitio-integral-format: Variable, Read/Write.Type: enum(raffenetti, regular).Either regular or raffenetti.abinitio-integral-path: Variable, Read/Write.string.Type:Path for storing integrals.abinitio-mo-initial-guess: Variable, Read/Write.Type: enum(core-hamiltonian, projected-huckel, projected-cndo, projected-indo).Either core-hamiltonian, projected-huckel, projected-cndo, projected-indo. abinitio-mp2-correlation-energy: Variable, Read/Write.boolean.Type:Enable Ab Initio MP2 correlation energy.abinitio-mp2-frozen-core: Variable, Read/Write.boolean.Type:Enable Ab Initio MP2 frozen core.abinitio-scf-convergence: Variable, Read/Write.Type: float in range (0 .. 100).SCF Convergence for Ab Initio.abinitio-use-ghost-atoms: Variable, Read/Write.boolean.Type:Include or ignore ghost atoms.accelerate-scf-convergence: Variable, Read/Write.Type:boolean.Whether to use DIIS procedure.add-amino-acid: Command.Arg list: string.String-1 gives the name of an amino acid residue to add to the system.add-nucleic-acid: Command.Arg list: string.String-1 names the nucleotide to add to the current system.align-molecule: Command.Arg list: .Align the inertial axes of the molecular system.align-viewer: Command.Arg list: enum(x, y, z, line).Align the viewer's line-of-sight with the indicated axis or LINE.allow-ions: Variable, Read/Write.Type:boolean.Whether to allow excess valence on atoms.alpha-orbital-occupancy: Variable, Read/Write.Type: vector of float.(i) Number of electrons in the i-th MO.alpha-scf-eigenvector: Variable, Read/Write.Type: vector of float-list.(i) Coefficients for the i-th MO.amino-alpha-helix: Command.Arg list: (void).Subsequent additions of amino acid residues are to use alpha-helix torsions. amino-beta-sheet: Command.Arg list: (void).Subsequent additions of amino acid residues are to use beta-sheet torsions. amino-isomer: Variable, Read/Write.Type: enum(l, d).Whether amino acids are l or d.amino-omega: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Omega amino acid backbone angle.amino-phi: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Phi amino acid backbone angle.amino-psi: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Psi amino acid backbone angle.animate-vibrations: Variable, Read/Write.boolean.Type:Whether or not to animate vibrations.annotation-color: Variable, Read/Write.string.Type:Default color for annotations.annotation-filled: Variable, Read/Write.boolean.Type:The circle and rectangle annotations are filledannotation-layer-hidden: Variable, Read/Write.boolean.Type:The annotation layer is hidden andd only molecule layer shows. annotation-layer-in-front: Variable, Read/Write.boolean.Type:The annotation layer is in front of molecule layer.append-dynamics-average: Command.Arg list: string.Add a named selection to dynamics average gathering.append-dynamics-graph: Command.Arg list: string.Add a named selection to dynamics graph display.append-omsgs-to-file: Command.Arg list: string.String-1 gives the name of a file to which o-msgs are to be appended. assign-basisset: Command.Arg list: string.Assign a basis set to a selection or system.atom-basisset: Variable, Read/Write.Type: array of string.(iat, imol) The basis set of atom iat in molecule imol.atom-charge: Variable, Read/Write.(iat, imol) The charge of atom iat in molecule imol.atom-color: Variable, Read/Write.Type: array of enum(ByElement, Black, Blue, Green, Cyan, Red, Violet, Yellow, White).(iat, imol) The current color of the atom.atom-count: Variable, Readonly.Type: vector of integer.(imol) The number of atoms in molecule imol.atom-extra-basisset: Variable, Read/Write.Type: array of string, float.(iat, imol) The basis set of atom iat in molecule imol.atom-info: Variable, Readonly.(unknown).Type:Funny composite to support backends.atom-label-text: Variable, Readonly.Type: array of string.(iat, imol) RO. The text of the current atom label.atom-labels: Variable, Read/Write.Type: enum(None, Symbol, Name, Number, Type, Charge, Spin, Mass, BasisSet, Chirality, RMSGradient, Custom).Label for atoms.atom-mass: Variable, Read/Write.Type: array of float.(iat, imol) The mass of atom iat in molecule imol.atom-name: Variable, Read/Write.Type: array of string.(iat, imol) The name of atom iat in molecule imol.atom-spin-density-at-nucleus: Variable, Read/Write.Type: array of float.(iat, imol) The electron density of nucleus of atom iat in molecule imol.atom-spin-population: Variable, Read/Write.Type: array of float.(iat, imol) The spin density of atom iat in molecule imol.atom-type: Variable, Read/Write.Type: array of string.(iat, imol) The type of atom iat in molecule imol.atomic-number: Variable, Read/Write.(iat, imol) The atomic number of atom iat in molecule imol.atomic-symbol: Variable, Readonly.Type: array of string.(iat, imol) The element symbol of the atom.auxilliary-basis: Variable, Read/Write.Type: integer in range (0 .. 3).1=A1, 2=A2, 3=P1back-clip: Variable, Read/Write.float.Type:Set back clipping plane.backend-active: Variable, Read/Write.boolean.Type:Whether current channel is an active backend.backend-communications: Variable, Read/Write.Type: enum(Local, Remote).Whether to compute on local or remote host.backend-host-name: Variable, Read/Write.string.Type:The name of remote host for backend communications.backend-process-count: Variable, Read/Write.Type: integer in range (1 .. 32).The number of processes to run.backend-user-id: Variable, Read/Write.string.Type:The user id to use on the remote host for backend communications.backend-user-password: Variable, Read/Write.string.Type:The password for user id to use on the remote host for backend communications. balls-highlighted: Variable, Read/Write.boolean.Type:Balls and Balls-and-Cylinders should be highlighted when shaded.balls-radius-ratio: Variable, Read/Write.Type: float in range (0.001 .. 1).Size of the Balls relative to the maximum value.balls-shaded: Variable, Read/Write.boolean.Type:Balls and Balls-and-Cylinders should be shaded.basisset-count: Variable, Readonly.integer.Type:Number of coefficients required to describe a molecular orbital.bend-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.beta-orbital-occupancy: Variable, Read/Write.Type: vector of float.(i) Number of electrons in the i-th MO.beta-scf-eigenvector: Variable, Read/Write.Type: vector of float-list.(i) Coefficients for the i-th MO.bond-color: Variable, Read/Write.Type: enum(ByElement, Black, Blue, Green, Cyan, Red, Violet, Yellow, White).The color used for drawing atoms and bonds.bond-spacing-display-ratio: Variable, Read/Write.Type: float in range (0 .. 1).Bond spacing display ratio.builder-enforces-stereo: Variable, Read/Write.boolean.Type:Whether the model builder implicitly enforces any existing stereochemistry. calculation-method: Variable, Read/Write.Type: enum(MolecularMechanics, SemiEmpirical, AbInitio, DFT).Whether molecular mechanics, semi-empirical, or ab initio.cancel-menu: Variable, Read/Write.Type:boolean.Whether the cancel menu is up, or the normal one.cancel-notify: Command.Arg list: string.String-1 names a variable to stop watching.change-stereochem: Command.Arg list: integer, integer.Immediately change the stereochemistry about (iat, imol).change-user-menuitem: Command.Arg list: integer, string, string.Change the text and procedure associated with the specified user MenuItem. chirality: Variable, Read/Write.Type: array of string.(iat, imol) A, R, S, or ?, for achiral, R, S, or unknown chirality. ci-criterion: Variable, Read/Write.Type: enum(Energy, Orbital).One of: energy, orbital.ci-excitation-energy: Variable, Read/Write.Type: float in range (0 .. 10000).When ci-criterion=energy, maximum excitation energy.ci-occupied-orbitals: Variable, Read/Write.Type: integer in range (0 .. 32767).When ci-criterion=orbital, count of occupied orbitals included. ci-state-to-optimize: Variable, Read/Write.Type: integer in range (0 .. 32767).Which CI state to optimize with conjugate directionsci-unoccupied-orbitals: Variable, Read/Write.Type: integer in range (0 .. 32767).When ci-criterion=orbital, count of unoccupied orbitals included. clip-cursor: Variable, Read/Write.Type: float in range (0 .. 1000).Select Z axis clip cursor tool.clip-icon-step: Variable, Read/Write.Type: float in range (0 .. 1000).Select clip step.color-element: Command.Arg list: integer, enum().Element Int-1 gets color String-2 as its default color.color-selection: Command.Arg list: string.String-1 names a color for the current selection.compile-script-file: Command.Arg list: string, string.Compile file string-1, writing result to string-2 configuration: Variable, Read/Write.integer.Type:The current UV configuration of the system.configuration-interaction: Variable, Read/Write.Type: enum(NoCI, SinglyExcited, Microstate).One of: no-ci, singly-excited, microstate.connectivity-in-pdb-file: Variable, Read/Write.Type:boolean.Whether connectivity information is to be included in a PDB file.constrain-bond-angle: Command.Arg list: float angle in range (-360 .. 360).Float-1 gives the angle constraint for the three currently selected atoms. constrain-bond-down: Command.Arg list: integer, integer, integer, integer.Constrain the bond from (iat1, imol1) to (iat2, imo2) to be down.constrain-bond-length: Command.Arg list: float in range (0 .. 100).Float-1 gives the length constraint for the two currently selected atoms. constrain-bond-torsion: Command.Arg list: float angle in range (-360 .. 360).Float-1 gives the torsion constraint for the four currently selected atoms. constrain-bond-up: Command.Arg list: integer, integer, integer, integer.Constrain the bond from (iat1, imol1) to (iat2, imo2) to be up.constrain-change-stereo: Command.Arg list: integer, integer.Constrain atom (iat, imol) to change the current stereochemistry.constrain-drawing: Variable, Read/Write.boolean.Type:Whether to constrain bond lengths and angles to canonicalize drawing of moleculeconstrain-fix-stereo: Command.Arg list: integer, integer.Constrain atom (iat, imol) to enforce the current stereochemistry.constrain-geometry: Command.Arg list: string.String-1 describes the geometry constraint around the currently selected atom. coordinates: Variable, Read/Write.Type: array of float, float, float.(iat, imol) The x, y, and z coordinates of atom iat in molecule imol. coordination: Variable, Readonly.Type: array of integer.(iat, imol) The coordination number for the specified atom.correlation-functional: Variable, Read/Write.Type: enum(None, Perdew86, VWN, LYP, PZ81, PW91, PBE96, HCTH98).Perdew, LYP, etc.cpk-max-double-buffer-atoms: Variable, Read/Write.Type: integer in range (0 .. 2147483647).Maximum number of double buffered atoms in cpk rendering mode. create-atom: Command.Arg list: integer in range (0 .. 103).Create a new atom at the origin with atomic number nAtno.current-file-name: Variable, Readonly.string.Type:The name of the current file.custom-title: Variable, Read/Write.string.Type:Custom Title string, append string to title.cutoff-inner-radius: Variable, Read/Write.Type: float in range (0 .. 1e+010).The distance (in Angstroms) to begin a switched cutoff.cutoff-outer-radius: Variable, Read/Write.Type: float in range (0 .. 1e+010).The distance (in Angstroms) at which nonbonded interactions become zero. cutoff-type: Variable, Read/Write.Type: enum(None, Switched, Shifted).Electrostatic cutoff to apply to molecular mechanics calculations.cycle-atom-stereo: Command.Arg list: integer, integer.Advance the stereo constraint about atom (iat, imol).cycle-bond-stereo: Command.Arg list: integer, integer, integer, integer.Advance the stereo constraint along the bond (iat1, imol1)--(iat2, imol2). cylinders-color-by-element: Variable, Read/Write.boolean.Type:Color Cylinders using element colors.cylinders-width-ratio: Variable, Read/Write.Type: float in range (0 .. 1).Width of the Cylinders relative to the maximum value.d-orbitals-on-second-row: Variable, Read/Write.Type:boolean.Include D orbitals on second row.declare-float: Command.Arg list: string.Declare a new floating-point variable.declare-integer: Command.Arg list: string.Declare a new integer variable.declare-string: Command.Arg list: string.Declare a new string variable.default-element: Variable, Read/Write.Type: integer in range (0 .. 103).The atomic number of the default element for drawing operations. delete-atom: Command.Arg list: integer, integer.Delete the specified atom.delete-file: Command.Arg list: string.filename to be deleted.delete-named-selection: Command.Arg list: string.Remove the named selection String-1 from the list of named selections. delete-selected-atoms: Command.Arg list: (void).Delete the currently selected atoms.dipole-moment: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Dipolemoment.dipole-moment-components: Variable, Read/Write.Type: float, float, float.Dipole moment components.do-langevin-dynamics: Command.Arg list: (void).Perform a Langevin dynamics computation on the system.do-molecular-dynamics: Command.Arg list: (void).Perform a molecular dynamics computation on the system.do-monte-carlo: Command.Arg list: (void).Perform a Monte Carlo computation on the system.do-optimization: Command.Arg list: (void).Perform a structure optimization on the system.do-qm-calculation: Variable, Read/Write.boolean.Type:For single-point QM calculations, whether to re-compute wave function. do-qm-graph: Variable, Read/Write.boolean.Type:For single-point QM calculations, to graph some data.do-qm-isosurface: Variable, Read/Write.boolean.Type:For single-point QM calculations, to generate iso-surface of results.do-single-point: Command.Arg list: (void).Perform a single-point computation on the system.do-vibrational-analysis: Command.Arg list: (void).Perform a vibrational analysis computation on the system.dot-surface-angle: Variable, Read/Write.Type: float angle in range (-90 .. 90).Dot surface angle.double-buffered-display: Variable, Read/Write.boolean.Type:Whether display operations are double-buffered.dynamics-average-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Computation results from dynamics run.dynamics-bath-relaxation-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Bath relaxation time for dynamics.dynamics-collection-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Dynamics data collection interval.dynamics-constant-temp: Variable, Read/Write.boolean.Type:Whether to keep temperature fixed at dynamics-simulation-temp. dynamics-cool-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Time taken to change from dynamics-simulation-temp to dynamics-final-temp. dynamics-final-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).Temperature to cool back to when annealing.dynamics-friction-coefficient: Variable, Read/Write.Type: float in range (0 .. 1000000).Friction coefficient for Langevin dynamics.dynamics-heat-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Time taken to change from dynamics-starting-temp ->dynamics-simulation-temp.dynamics-info-elapsed-time: Variable, Readonly.Type: float in range (0 .. 1e+010).Elapsed time in dynamics run.dynamics-info-kinetic-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-info-last-update: Variable, Readonly.boolean.Type:Last update from dynamics run.dynamics-info-potential-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-info-temperature: Variable, Readonly.Type: float in range (0 .. 1e+010).Computation results from dynamics run.dynamics-info-total-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-playback: Variable, Read/Write.Type: enum(none, playback, record).Playback a recorded dynamics run.dynamics-playback-end: Variable, Read/Write.Type: integer in range (0 .. 32767).End playback of recorded dynamics run.dynamics-playback-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Dynamics playback interval.dynamics-playback-start: Variable, Read/Write.Type: integer in range (0 .. 32767).Start playback of recorded dynamics run.dynamics-restart: Variable, Read/Write.boolean.Type:Use saved velocities.dynamics-run-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Total integration time at dynamics-simulation-temp. dynamics-seed: Variable, Read/Write.Type: integer in range (-32768 .. 32767).Seed for dynamics initialization random number generator. dynamics-simulation-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).High temperature for the dynamics run.dynamics-snapshot-filename: Variable, Read/Write.string.Type:Name file of to store dynamics run.dynamics-snapshot-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Set recording interval of dynamics run.dynamics-starting-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).Starting temperature for the dynamics run.dynamics-temp-step: Variable, Read/Write.Type: float in range (0 .. 1e+010).Step size (K) by which temperature is changed.error: Variable, Read/Write.string.Type:The current error.errors-are-not-omsgs: Command.Arg list: (void).Specifies that error messages are to appear in message boxes. errors-are-omsgs: Command.Arg list: (void).Specifies that error messages should be treated like o-msgs. estatic-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.exchange-functional: Variable, Read/Write.Type: enum(None, Hartree-Fock, Slater, Becke88, PW91, Gill96, PBE96, HCTH98, B3-LYP, B3-PW91, EDF1, Becke97).Slater, Becke88, etc.excited-state: Variable, Read/Write.boolean.Type:False for lowest state, true for next-lowest state.execute-client: Command.Arg list: string.Run a client application.execute-hyperchem-client: Command.Arg list: string.Run a client application. App can reliably connect to instance of HyperChem. execute-string: Command.Arg list: string.Execute the string variable as a script.exit-script: Command.Arg list: (void).Exit the current script.explicit-hydrogens: Variable, Read/Write.boolean.Type:Whether hydrogens are to be drawn explicitly.export-dipole: Variable, Read/Write.boolean.Type:Whether or not to export dipole moment data to .EXT file.export-ir: Variable, Read/Write.boolean.Type:Whether or not to export IR data to .EXT file.export-orbitals: Variable, Read/Write.boolean.Type:Whether or not to export orbital data to .EXT file.export-property-file: Command.Arg list: string.Writes properties to the named file.export-uv: Variable, Read/Write.boolean.Type:Whether or not to export UV data to .EXT file.factory-settings: Command.Arg list: (void).Reset chem to its out-of-the-box state.field-direction: Variable, Read/Write.Type: integer in range (1 .. 3).direction (X,Y or Z) of the static electric field applied to the systemfield-strength: Variable, Read/Write.Type: float in range (-1000 .. 1000).strength (a.u.) of the static electric field applied to the systemfile-diff-message: Command.Arg list: string, string, string, string.Compare file1 to file2; if they are the same say string3, else say string4.file-format: Variable, Read/Write.string.Type:The molecule file format.file-needs-saved: Variable, Read/Write.Type:boolean.Whether the current system needs to be saved.formal-charge: Variable, Read/Write.Type: array of integer.(iat, imol) Positive or negative formal charge on atom used by model builder. front-clip: Variable, Read/Write.float.Type:Set front clipping plane.global-inhibit-redisplay: Variable, Readonly.Type:boolean.Whether redisplay of the system is inhibited (readonly)gradient-x: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the X directiongradient-y: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the Y directiongradient-z: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the Z directiongradients: Variable, Read/Write.Type: array of float, float, float.(iat, imol) The x, y, and z gradients of atom iat in molecule imol.graph-beta: Variable, Read/Write.boolean.Type:If true and UHF, graph beta-spin orbitals instead of alpha.graph-contour-increment: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Increment between contour lines.graph-contour-increment-other: Variable, Read/Write.boolean.Type:Whether to use graph-increment-other (true) or use defaults (false).graph-contour-levels: Variable, Read/Write.Type: integer in range (1 .. 32767).The number of contour levels to plot.graph-contour-start: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Value for first contour line.graph-contour-start-other: Variable, Read/Write.boolean.Type:Whether to use graph-contour-start (true) or use defaults (false).graph-data-row: Variable, Readonly.Type: vector of float-list.(i) The values on the i-th row of graph data.graph-data-type: Variable, Read/Write.Type: enum(electrostatic, charge-density, orbital, orbital-squared, spin-density).The type of wavefunction data to plot.graph-horizontal-grid-size: Variable, Read/Write.Type: integer in range (2 .. 8192).Number of data grid points for plotting in the horizontal direction.graph-orbital-offset: Variable, Read/Write.Type: integer in range (0 .. +Inf).Display orbital offset.graph-orbital-selection-type: Variable, Read/Write.Type: enum(lumo-plus, homo-minus, orbital-number).Display orbital type.graph-plane-offset: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Offset along viewer's Z axis of the plane of the data to plot.graph-vertical-grid-size: Variable, Read/Write.Type: integer in range (2 .. 8192).Number of data grid points for plotting in the vertical direction.grid-max-value: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).The isosurface maximum grid value.grid-min-value: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).The isosurface minimum grid value.hbond-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.heat-of-formation: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Heat of formation.help: Command.Arg list: string.Give help on topic String-1.hide-errors: Variable, Read/Write.boolean.Type:Whether to display error messages on the screen (channel specific). hide-messages: Variable, Read/Write.boolean.Type:Whether to display MESSAGE value on the screen.hide-toolbar: Variable, Read/Write.boolean.Type:Command to toggle the toolbar.hide-warnings: Variable, Read/Write.boolean.Type:Whether to display warning messages on the screen (channel specific). huckel-constant: Variable, Read/Write.Type: float in range (0 .. 10).Extended Huckel constant.huckel-scaling-factor: Variable, Read/Write.Type: float in range (0 .. 100000).Extended Huckel scaling factor.huckel-weighted: Variable, Read/Write.boolean.Type:Extended Huckel weighting factor.。

HyperChem软件

HyperChem软件

HyperChem软件中Script的常用语句注解1. 计算方法及参数设定calculation-method item计算方法设定item: MolecularMechanics, SemiEmpirical, AbInitio, DFT molecular-mechanics-method item分子力学方法设定item: mm+, amber, bio+, opls, amber94, charmm22, tndo optim-max-cycles x优化最大迭代次数x设定optim-convergence goal 优化收敛目标goal设定optim-converged返回是否收敛(true/false)optim-algorithm item 优化算法设定item: PolakRibiere, NewtonRaphson, etc.assign-basisset item abinitio计算基组设定item: 3-21G, STO-3G, etc.semi-empirical-method item半经验计算方法设定item: am1, pm3, extendedhuckel, cndo, indo, zindos, mndod, tndo, etc.accelerate-scf-convergence true/false 是否加速SCF收敛scf-convergence goal SCF收敛目标goal设定max-iterations n SCF计算的最大迭代次数n设定2. 计算结果输出omsgs-to-file filename 将信息输出到filename文件append-omsgs-to-file filename 将信息追加到filename文件omsgs-not-to-file 关闭输出文件query-response-has-tag yes/no 提取的信息回显开关query-value HSV提取系统数据结构中的信息并单行输出HSV: current-file-name, coordinates,dipole-moment, dipole-moment-componentstotal-energy, heat-of-formation,scf-binding-energy, scf-core-energy, scf-electronic-energy start-logging HyperChem运行记录开启stop-logging HyperChem运行记录关闭export-property-file filename将分子轨道信息写入filename文件3. 分子结构及其文件操作file-format item定义分子结构文件格式item: hin, mol, zmt, ent, skc, xyz, ml2open-file filename 读入filename分子结构文件write-file filename 将分子结构写入filename文件menu-build-add-hydrogens 给分子加氢menu-build-model-build 给分子加氢并规格化do-optimization 进行优化操作do-single-point 进行单点计算do-molecular-dynamics进行分子动力学操作4. 屏幕显示设置screen-refresh-period n屏幕刷新周期atom-labels item原子标识设定item: none, number, symbol, name, charge, etc.show-hydrogens yes/no 分子中氢显示开关show-multiple-bonds yes/no分子中重键显示开关request string弹出窗口并显示由双引号表达的字符串string 5. 其它read-script filename读取名为filename的script文件exit-script 退出script实例: example.scrcalculation-method molecular-mechanicsmolecular-mechanics-method mm+optim-max-cycles 2048optim-convergence 0.1optim-algorithm PolakRibiereomsgs-to-file results.txtquery-response-has-tag nofile-format molopen-file 000A-0001.molmenu-build-model-builddo-optimizationquery-value total-energyfile-format zmtwrite-file 000A-0001.zmtomsgs-not-to-fileexit-script附: HyperChem State Variables (HSV)abinitio-buffer-size: Variable, Read/Write.Type: integer in range (1 .. 2147483647).Two electron integral buffer size.abinitio-calculate-gradient: Variable, Read/Write.Type:boolean.Enable Ab Initio gradient calculation (Single Point only).abinitio-cutoff: Variable, Read/Write.Type: float in range (0 .. 1e+010).Two electron integral cutoff.abinitio-d-orbitals: Variable, Read/Write.boolean.Type:Either five (False) or six (True).abinitio-direct-scf: Variable, Read/Write.boolean.Type:Enable Ab Initio Direct SCF calculation.abinitio-f-orbitals: Variable, Read/Write.boolean.Type:Either seven (False) or ten (True).abinitio-integral-format: Variable, Read/Write.Type: enum(raffenetti, regular).Either regular or raffenetti.abinitio-integral-path: Variable, Read/Write.string.Type:Path for storing integrals.abinitio-mo-initial-guess: Variable, Read/Write.Type: enum(core-hamiltonian, projected-huckel, projected-cndo, projected-indo).Either core-hamiltonian, projected-huckel, projected-cndo, projected-indo. abinitio-mp2-correlation-energy: Variable, Read/Write.boolean.Type:Enable Ab Initio MP2 correlation energy.abinitio-mp2-frozen-core: Variable, Read/Write.boolean.Type:Enable Ab Initio MP2 frozen core.abinitio-scf-convergence: Variable, Read/Write.Type: float in range (0 .. 100).SCF Convergence for Ab Initio.abinitio-use-ghost-atoms: Variable, Read/Write.boolean.Type:Include or ignore ghost atoms.accelerate-scf-convergence: Variable, Read/Write.Type:boolean.Whether to use DIIS procedure.add-amino-acid: Command.Arg list: string.String-1 gives the name of an amino acid residue to add to the system.add-nucleic-acid: Command.Arg list: string.String-1 names the nucleotide to add to the current system.align-molecule: Command.Arg list: .Align the inertial axes of the molecular system.align-viewer: Command.Arg list: enum(x, y, z, line).Align the viewer's line-of-sight with the indicated axis or LINE.allow-ions: Variable, Read/Write.Type:boolean.Whether to allow excess valence on atoms.alpha-orbital-occupancy: Variable, Read/Write.Type: vector of float.(i) Number of electrons in the i-th MO.alpha-scf-eigenvector: Variable, Read/Write.Type: vector of float-list.(i) Coefficients for the i-th MO.amino-alpha-helix: Command.Arg list: (void).Subsequent additions of amino acid residues are to use alpha-helix torsions. amino-beta-sheet: Command.Arg list: (void).Subsequent additions of amino acid residues are to use beta-sheet torsions. amino-isomer: Variable, Read/Write.Type: enum(l, d).Whether amino acids are l or d.amino-omega: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Omega amino acid backbone angle.amino-phi: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Phi amino acid backbone angle.amino-psi: Variable, Read/Write.Type: float angle in range (-360 .. 360).The Psi amino acid backbone angle.animate-vibrations: Variable, Read/Write.boolean.Type:Whether or not to animate vibrations.annotation-color: Variable, Read/Write.string.Type:Default color for annotations.annotation-filled: Variable, Read/Write.boolean.Type:The circle and rectangle annotations are filledannotation-layer-hidden: Variable, Read/Write.boolean.Type:The annotation layer is hidden andd only molecule layer shows. annotation-layer-in-front: Variable, Read/Write.boolean.Type:The annotation layer is in front of molecule layer.append-dynamics-average: Command.Arg list: string.Add a named selection to dynamics average gathering.append-dynamics-graph: Command.Arg list: string.Add a named selection to dynamics graph display.append-omsgs-to-file: Command.Arg list: string.String-1 gives the name of a file to which o-msgs are to be appended. assign-basisset: Command.Arg list: string.Assign a basis set to a selection or system.atom-basisset: Variable, Read/Write.Type: array of string.(iat, imol) The basis set of atom iat in molecule imol.atom-charge: Variable, Read/Write.(iat, imol) The charge of atom iat in molecule imol.atom-color: Variable, Read/Write.Type: array of enum(ByElement, Black, Blue, Green, Cyan, Red, Violet, Yellow, White).(iat, imol) The current color of the atom.atom-count: Variable, Readonly.Type: vector of integer.(imol) The number of atoms in molecule imol.atom-extra-basisset: Variable, Read/Write.Type: array of string, float.(iat, imol) The basis set of atom iat in molecule imol.atom-info: Variable, Readonly.(unknown).Type:Funny composite to support backends.atom-label-text: Variable, Readonly.Type: array of string.(iat, imol) RO. The text of the current atom label.atom-labels: Variable, Read/Write.Type: enum(None, Symbol, Name, Number, Type, Charge, Spin, Mass, BasisSet, Chirality, RMSGradient, Custom).Label for atoms.atom-mass: Variable, Read/Write.Type: array of float.(iat, imol) The mass of atom iat in molecule imol.atom-name: Variable, Read/Write.Type: array of string.(iat, imol) The name of atom iat in molecule imol.atom-spin-density-at-nucleus: Variable, Read/Write.Type: array of float.(iat, imol) The electron density of nucleus of atom iat in molecule imol.atom-spin-population: Variable, Read/Write.Type: array of float.(iat, imol) The spin density of atom iat in molecule imol.atom-type: Variable, Read/Write.Type: array of string.(iat, imol) The type of atom iat in molecule imol.atomic-number: Variable, Read/Write.(iat, imol) The atomic number of atom iat in molecule imol.atomic-symbol: Variable, Readonly.Type: array of string.(iat, imol) The element symbol of the atom.auxilliary-basis: Variable, Read/Write.Type: integer in range (0 .. 3).1=A1, 2=A2, 3=P1back-clip: Variable, Read/Write.float.Type:Set back clipping plane.backend-active: Variable, Read/Write.boolean.Type:Whether current channel is an active backend.backend-communications: Variable, Read/Write.Type: enum(Local, Remote).Whether to compute on local or remote host.backend-host-name: Variable, Read/Write.string.Type:The name of remote host for backend communications.backend-process-count: Variable, Read/Write.Type: integer in range (1 .. 32).The number of processes to run.backend-user-id: Variable, Read/Write.string.Type:The user id to use on the remote host for backend communications.backend-user-password: Variable, Read/Write.string.Type:The password for user id to use on the remote host for backend communications. balls-highlighted: Variable, Read/Write.boolean.Type:Balls and Balls-and-Cylinders should be highlighted when shaded.balls-radius-ratio: Variable, Read/Write.Type: float in range (0.001 .. 1).Size of the Balls relative to the maximum value.balls-shaded: Variable, Read/Write.boolean.Type:Balls and Balls-and-Cylinders should be shaded.basisset-count: Variable, Readonly.integer.Type:Number of coefficients required to describe a molecular orbital.bend-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.beta-orbital-occupancy: Variable, Read/Write.Type: vector of float.(i) Number of electrons in the i-th MO.beta-scf-eigenvector: Variable, Read/Write.Type: vector of float-list.(i) Coefficients for the i-th MO.bond-color: Variable, Read/Write.Type: enum(ByElement, Black, Blue, Green, Cyan, Red, Violet, Yellow, White).The color used for drawing atoms and bonds.bond-spacing-display-ratio: Variable, Read/Write.Type: float in range (0 .. 1).Bond spacing display ratio.builder-enforces-stereo: Variable, Read/Write.boolean.Type:Whether the model builder implicitly enforces any existing stereochemistry. calculation-method: Variable, Read/Write.Type: enum(MolecularMechanics, SemiEmpirical, AbInitio, DFT).Whether molecular mechanics, semi-empirical, or ab initio.cancel-menu: Variable, Read/Write.Type:boolean.Whether the cancel menu is up, or the normal one.cancel-notify: Command.Arg list: string.String-1 names a variable to stop watching.change-stereochem: Command.Arg list: integer, integer.Immediately change the stereochemistry about (iat, imol).change-user-menuitem: Command.Arg list: integer, string, string.Change the text and procedure associated with the specified user MenuItem. chirality: Variable, Read/Write.Type: array of string.(iat, imol) A, R, S, or ?, for achiral, R, S, or unknown chirality. ci-criterion: Variable, Read/Write.Type: enum(Energy, Orbital).One of: energy, orbital.ci-excitation-energy: Variable, Read/Write.Type: float in range (0 .. 10000).When ci-criterion=energy, maximum excitation energy.ci-occupied-orbitals: Variable, Read/Write.Type: integer in range (0 .. 32767).When ci-criterion=orbital, count of occupied orbitals included. ci-state-to-optimize: Variable, Read/Write.Type: integer in range (0 .. 32767).Which CI state to optimize with conjugate directionsci-unoccupied-orbitals: Variable, Read/Write.Type: integer in range (0 .. 32767).When ci-criterion=orbital, count of unoccupied orbitals included. clip-cursor: Variable, Read/Write.Type: float in range (0 .. 1000).Select Z axis clip cursor tool.clip-icon-step: Variable, Read/Write.Type: float in range (0 .. 1000).Select clip step.color-element: Command.Arg list: integer, enum().Element Int-1 gets color String-2 as its default color.color-selection: Command.Arg list: string.String-1 names a color for the current selection.compile-script-file: Command.Arg list: string, string.Compile file string-1, writing result to string-2 configuration: Variable, Read/Write.integer.Type:The current UV configuration of the system.configuration-interaction: Variable, Read/Write.Type: enum(NoCI, SinglyExcited, Microstate).One of: no-ci, singly-excited, microstate.connectivity-in-pdb-file: Variable, Read/Write.Type:boolean.Whether connectivity information is to be included in a PDB file.constrain-bond-angle: Command.Arg list: float angle in range (-360 .. 360).Float-1 gives the angle constraint for the three currently selected atoms. constrain-bond-down: Command.Arg list: integer, integer, integer, integer.Constrain the bond from (iat1, imol1) to (iat2, imo2) to be down.constrain-bond-length: Command.Arg list: float in range (0 .. 100).Float-1 gives the length constraint for the two currently selected atoms. constrain-bond-torsion: Command.Arg list: float angle in range (-360 .. 360).Float-1 gives the torsion constraint for the four currently selected atoms. constrain-bond-up: Command.Arg list: integer, integer, integer, integer.Constrain the bond from (iat1, imol1) to (iat2, imo2) to be up.constrain-change-stereo: Command.Arg list: integer, integer.Constrain atom (iat, imol) to change the current stereochemistry.constrain-drawing: Variable, Read/Write.boolean.Type:Whether to constrain bond lengths and angles to canonicalize drawing of moleculeconstrain-fix-stereo: Command.Arg list: integer, integer.Constrain atom (iat, imol) to enforce the current stereochemistry.constrain-geometry: Command.Arg list: string.String-1 describes the geometry constraint around the currently selected atom. coordinates: Variable, Read/Write.Type: array of float, float, float.(iat, imol) The x, y, and z coordinates of atom iat in molecule imol. coordination: Variable, Readonly.Type: array of integer.(iat, imol) The coordination number for the specified atom.correlation-functional: Variable, Read/Write.Type: enum(None, Perdew86, VWN, LYP, PZ81, PW91, PBE96, HCTH98).Perdew, LYP, etc.cpk-max-double-buffer-atoms: Variable, Read/Write.Type: integer in range (0 .. 2147483647).Maximum number of double buffered atoms in cpk rendering mode. create-atom: Command.Arg list: integer in range (0 .. 103).Create a new atom at the origin with atomic number nAtno.current-file-name: Variable, Readonly.string.Type:The name of the current file.custom-title: Variable, Read/Write.string.Type:Custom Title string, append string to title.cutoff-inner-radius: Variable, Read/Write.Type: float in range (0 .. 1e+010).The distance (in Angstroms) to begin a switched cutoff.cutoff-outer-radius: Variable, Read/Write.Type: float in range (0 .. 1e+010).The distance (in Angstroms) at which nonbonded interactions become zero. cutoff-type: Variable, Read/Write.Type: enum(None, Switched, Shifted).Electrostatic cutoff to apply to molecular mechanics calculations.cycle-atom-stereo: Command.Arg list: integer, integer.Advance the stereo constraint about atom (iat, imol).cycle-bond-stereo: Command.Arg list: integer, integer, integer, integer.Advance the stereo constraint along the bond (iat1, imol1)--(iat2, imol2). cylinders-color-by-element: Variable, Read/Write.boolean.Type:Color Cylinders using element colors.cylinders-width-ratio: Variable, Read/Write.Type: float in range (0 .. 1).Width of the Cylinders relative to the maximum value.d-orbitals-on-second-row: Variable, Read/Write.Type:boolean.Include D orbitals on second row.declare-float: Command.Arg list: string.Declare a new floating-point variable.declare-integer: Command.Arg list: string.Declare a new integer variable.declare-string: Command.Arg list: string.Declare a new string variable.default-element: Variable, Read/Write.Type: integer in range (0 .. 103).The atomic number of the default element for drawing operations. delete-atom: Command.Arg list: integer, integer.Delete the specified atom.delete-file: Command.Arg list: string.filename to be deleted.delete-named-selection: Command.Arg list: string.Remove the named selection String-1 from the list of named selections. delete-selected-atoms: Command.Arg list: (void).Delete the currently selected atoms.dipole-moment: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Dipolemoment.dipole-moment-components: Variable, Read/Write.Type: float, float, float.Dipole moment components.do-langevin-dynamics: Command.Arg list: (void).Perform a Langevin dynamics computation on the system.do-molecular-dynamics: Command.Arg list: (void).Perform a molecular dynamics computation on the system.do-monte-carlo: Command.Arg list: (void).Perform a Monte Carlo computation on the system.do-optimization: Command.Arg list: (void).Perform a structure optimization on the system.do-qm-calculation: Variable, Read/Write.boolean.Type:For single-point QM calculations, whether to re-compute wave function. do-qm-graph: Variable, Read/Write.boolean.Type:For single-point QM calculations, to graph some data.do-qm-isosurface: Variable, Read/Write.boolean.Type:For single-point QM calculations, to generate iso-surface of results.do-single-point: Command.Arg list: (void).Perform a single-point computation on the system.do-vibrational-analysis: Command.Arg list: (void).Perform a vibrational analysis computation on the system.dot-surface-angle: Variable, Read/Write.Type: float angle in range (-90 .. 90).Dot surface angle.double-buffered-display: Variable, Read/Write.boolean.Type:Whether display operations are double-buffered.dynamics-average-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Computation results from dynamics run.dynamics-bath-relaxation-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Bath relaxation time for dynamics.dynamics-collection-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Dynamics data collection interval.dynamics-constant-temp: Variable, Read/Write.boolean.Type:Whether to keep temperature fixed at dynamics-simulation-temp. dynamics-cool-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Time taken to change from dynamics-simulation-temp to dynamics-final-temp. dynamics-final-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).Temperature to cool back to when annealing.dynamics-friction-coefficient: Variable, Read/Write.Type: float in range (0 .. 1000000).Friction coefficient for Langevin dynamics.dynamics-heat-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Time taken to change from dynamics-starting-temp ->dynamics-simulation-temp.dynamics-info-elapsed-time: Variable, Readonly.Type: float in range (0 .. 1e+010).Elapsed time in dynamics run.dynamics-info-kinetic-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-info-last-update: Variable, Readonly.boolean.Type:Last update from dynamics run.dynamics-info-potential-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-info-temperature: Variable, Readonly.Type: float in range (0 .. 1e+010).Computation results from dynamics run.dynamics-info-total-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Computation results from dynamics run.dynamics-playback: Variable, Read/Write.Type: enum(none, playback, record).Playback a recorded dynamics run.dynamics-playback-end: Variable, Read/Write.Type: integer in range (0 .. 32767).End playback of recorded dynamics run.dynamics-playback-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Dynamics playback interval.dynamics-playback-start: Variable, Read/Write.Type: integer in range (0 .. 32767).Start playback of recorded dynamics run.dynamics-restart: Variable, Read/Write.boolean.Type:Use saved velocities.dynamics-run-time: Variable, Read/Write.Type: float in range (0 .. 1e+010).Total integration time at dynamics-simulation-temp. dynamics-seed: Variable, Read/Write.Type: integer in range (-32768 .. 32767).Seed for dynamics initialization random number generator. dynamics-simulation-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).High temperature for the dynamics run.dynamics-snapshot-filename: Variable, Read/Write.string.Type:Name file of to store dynamics run.dynamics-snapshot-period: Variable, Read/Write.Type: integer in range (1 .. 32767).Set recording interval of dynamics run.dynamics-starting-temp: Variable, Read/Write.Type: float in range (0 .. 1e+010).Starting temperature for the dynamics run.dynamics-temp-step: Variable, Read/Write.Type: float in range (0 .. 1e+010).Step size (K) by which temperature is changed.error: Variable, Read/Write.string.Type:The current error.errors-are-not-omsgs: Command.Arg list: (void).Specifies that error messages are to appear in message boxes. errors-are-omsgs: Command.Arg list: (void).Specifies that error messages should be treated like o-msgs. estatic-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.exchange-functional: Variable, Read/Write.Type: enum(None, Hartree-Fock, Slater, Becke88, PW91, Gill96, PBE96, HCTH98, B3-LYP, B3-PW91, EDF1, Becke97).Slater, Becke88, etc.excited-state: Variable, Read/Write.boolean.Type:False for lowest state, true for next-lowest state.execute-client: Command.Arg list: string.Run a client application.execute-hyperchem-client: Command.Arg list: string.Run a client application. App can reliably connect to instance of HyperChem. execute-string: Command.Arg list: string.Execute the string variable as a script.exit-script: Command.Arg list: (void).Exit the current script.explicit-hydrogens: Variable, Read/Write.boolean.Type:Whether hydrogens are to be drawn explicitly.export-dipole: Variable, Read/Write.boolean.Type:Whether or not to export dipole moment data to .EXT file.export-ir: Variable, Read/Write.boolean.Type:Whether or not to export IR data to .EXT file.export-orbitals: Variable, Read/Write.boolean.Type:Whether or not to export orbital data to .EXT file.export-property-file: Command.Arg list: string.Writes properties to the named file.export-uv: Variable, Read/Write.boolean.Type:Whether or not to export UV data to .EXT file.factory-settings: Command.Arg list: (void).Reset chem to its out-of-the-box state.field-direction: Variable, Read/Write.Type: integer in range (1 .. 3).direction (X,Y or Z) of the static electric field applied to the systemfield-strength: Variable, Read/Write.Type: float in range (-1000 .. 1000).strength (a.u.) of the static electric field applied to the systemfile-diff-message: Command.Arg list: string, string, string, string.Compare file1 to file2; if they are the same say string3, else say string4.file-format: Variable, Read/Write.string.Type:The molecule file format.file-needs-saved: Variable, Read/Write.Type:boolean.Whether the current system needs to be saved.formal-charge: Variable, Read/Write.Type: array of integer.(iat, imol) Positive or negative formal charge on atom used by model builder. front-clip: Variable, Read/Write.float.Type:Set front clipping plane.global-inhibit-redisplay: Variable, Readonly.Type:boolean.Whether redisplay of the system is inhibited (readonly)gradient-x: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the X directiongradient-y: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the Y directiongradient-z: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Molecular gradient in the Z directiongradients: Variable, Read/Write.Type: array of float, float, float.(iat, imol) The x, y, and z gradients of atom iat in molecule imol.graph-beta: Variable, Read/Write.boolean.Type:If true and UHF, graph beta-spin orbitals instead of alpha.graph-contour-increment: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Increment between contour lines.graph-contour-increment-other: Variable, Read/Write.boolean.Type:Whether to use graph-increment-other (true) or use defaults (false).graph-contour-levels: Variable, Read/Write.Type: integer in range (1 .. 32767).The number of contour levels to plot.graph-contour-start: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Value for first contour line.graph-contour-start-other: Variable, Read/Write.boolean.Type:Whether to use graph-contour-start (true) or use defaults (false).graph-data-row: Variable, Readonly.Type: vector of float-list.(i) The values on the i-th row of graph data.graph-data-type: Variable, Read/Write.Type: enum(electrostatic, charge-density, orbital, orbital-squared, spin-density).The type of wavefunction data to plot.graph-horizontal-grid-size: Variable, Read/Write.Type: integer in range (2 .. 8192).Number of data grid points for plotting in the horizontal direction.graph-orbital-offset: Variable, Read/Write.Type: integer in range (0 .. +Inf).Display orbital offset.graph-orbital-selection-type: Variable, Read/Write.Type: enum(lumo-plus, homo-minus, orbital-number).Display orbital type.graph-plane-offset: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Offset along viewer's Z axis of the plane of the data to plot.graph-vertical-grid-size: Variable, Read/Write.Type: integer in range (2 .. 8192).Number of data grid points for plotting in the vertical direction.grid-max-value: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).The isosurface maximum grid value.grid-min-value: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).The isosurface minimum grid value.hbond-energy: Variable, Readonly.Type: float in range (-1e+010 .. 1e+010).Results from backend computation.heat-of-formation: Variable, Read/Write.Type: float in range (-1e+010 .. 1e+010).Heat of formation.help: Command.Arg list: string.Give help on topic String-1.hide-errors: Variable, Read/Write.boolean.Type:Whether to display error messages on the screen (channel specific). hide-messages: Variable, Read/Write.boolean.Type:Whether to display MESSAGE value on the screen.hide-toolbar: Variable, Read/Write.boolean.Type:Command to toggle the toolbar.hide-warnings: Variable, Read/Write.boolean.Type:Whether to display warning messages on the screen (channel specific). huckel-constant: Variable, Read/Write.Type: float in range (0 .. 10).Extended Huckel constant.huckel-scaling-factor: Variable, Read/Write.Type: float in range (0 .. 100000).Extended Huckel scaling factor.huckel-weighted: Variable, Read/Write.boolean.Type:Extended Huckel weighting factor.。

HyperChem

HyperChem

分子图形与分子模型设计——HyperChem使用简介厦门大学化学系2005年3月HyperChem使用简介HyperChem是HyperCube Inc.的产品，它具有非常强大的综合计算与分析功能，是优秀的分子图形和分子设计的工具软件之一。

HyperChem是运行在Windows系统的分子计算与建模软件，具有量子化学（半经验和从头算）、分子力学、分子动力学、随机动力学、Monte Carlo模拟等计算功能，计算结果可以用三维图形显示。

它还提供用户VB、C/C++和FORTRAN等语言的应用程序接口。

HyperChem 7.5版本已经推出。

图1是HyperChem的工作窗口，最下部是工作状态档。

在菜单下面是常用工具档。

图1 HyperChem的工作窗口HyperChem的操作可以使用鼠标和键盘两种。

在工具档从左开始有8个工具图标，当鼠标点图标之后，鼠标在工作区的形状也改变为该图标的形状：1.绘图工具。

鼠标双击该图标可直接进入缺省元素周期表，选择所要绘制元素。

2.选择工具。

3.xy轴方向旋转工具，也可使用键盘的上下左右光标键进行相同的操作。

4.z轴方向旋转工具，也可使用键盘的Home和End键进行相同的操作。

5.xy轴平移工具，也可使用键盘的Shift+上下左右光标键进行相同的操作。

6.z轴平移工具。

7.缩放工具，也可使用键盘的PgUp和PgDn键进行相同的操作。

8.z轴截片工具。

鼠标操作有较为多样：左点击、右点击、左拖拉、右拖拉、左右拖拉、Shift+左点击、Shift+右点击、双击等。

一般的旋转和平移操作是使用鼠标的左键进行，当完成了某个基团、分子的选择之后，可以使用右键对所选部分进行旋转和平移操作。

HyperChem的详细操作将结合具体的实例进行讲解。

以下通过对HyperChem 5.1的菜单命令的介绍，说明它的主要功能和使用方法。

一、File1.New (Ctrl+N)：新建一个沿尚未命名文件。

谷晓明 物理化学HyperChem

谷晓明 物理化学HyperChem

HyperChem 程序及其应用1、绘制丙二烯分子骨架模型，并测量有关分子构型的几何信息2、指定输出文件File---Start Log。

（1）先用半经验方法进行分子优化，从Setup中选择Semi-empirical…设定参数如下所示（2）选择Options…可设置收敛限和迭代次数，如下所示：(3)从Compute中选择Geometry Optimzation…进行集合构型优化：(4)优化完成之后，在Compute选择Single Point可进行单点计算。

3、采用从头算的方法：（1）Setup中选择Ab Initio…设定参数如下：（2）从Compute中选择Geometry Optimzation…进行集合构型优化：（3）完成集合构型优化后，从Compute选择Single Point可进行单点计算。

4、计算结束后，停止数据输出，从File---Stop Log。

5、分析有关分子的性质并简单分析讨论分子性质（1）采用从头算方法后，分析振动光谱：（该图显示谱线的位置、强度和振动模式）虚振动频率-185.84意味着，此结构不是一个稳定结构，而是一个过渡态。

（2）计算电子光谱最低能量跃迁π-π*在373.90，是禁阻跃迁允许的跃迁是116.84单态π-π*跃迁。

（3）分子偶极矩（4）轨道特征1、最高占据轨道2、最低空轨道（5）绘分子图，测电子光谱从Comput选择Plot Molecular Graphs1、2D图像2、3D图像6、结论与经验1、丙烯分子为一平面型分子，并且其振动频率存在虚频-185.84，意味着此平面结构不是一个稳定结构，而是一个过渡态。

2、半经验算法计算分子总能量为-16180.6852898 (kcal/mol)，从头算方法计算分子总能量为-72576.4084722 (kcal/mol)，所以计算方法的选择很重要。

3、计算分子的电子光谱能够得到该分子最低能量跃迁π-π*在373.90，是禁阻跃迁；允许的跃迁是116.84单态π-π*跃迁。

HyperChem程序及其应用

HyperChem程序及其应用

河北师范大学计算量子化学研究所蔡新华教授量子化学在线教学.100/qc/lzhx-0.htmHyperChem 程序及其应用一、HyperChem 程序的运行环境HyperChem 程序包，用C++写源程序，具有工作站、微机等不同的版本，作为教学示例，我们向大家介绍适用于微机运行的程序版本。

可以通过网络选购HyperChem程序包，也可以免费下载演示版本以供学习只用，现在该公司提供的最新版本为V6.0。

该公司的网址为：该公司与98年诺贝尔奖金得主Pople的关系可以参看其网页有关介绍。

1、软件环境Windows95、Windows98或Windows2000系统。

2、硬件环境486以上的微机，内存应在8M以上，硬盘至少有32M以上自由空间。

为了能够以最佳方式显示分子图像，最好有VGA以上显示器。

3、程序安装使用该程序应注意程序版权（注册）。

安装程序默认子目录为：C:\hyper6安装完成后，该目录可以看到如下文件，其中，绿色烧杯为执行程序图标。

有关该程序的使用说明、参考手册等全套文档均可免费获得。

二、程序基本使用方法我们以演示版本为例，说明该程序的基本使用方法。

1、启动程序在屏幕上，双击绿色烧杯可以得到如下画面：点击 Try进入工作区窗口窗口各部分功能简介标题名称：最大、最小化、退出按钮菜单条：FILE、EDIT、BUILD、SELECT、DISPLAY、DATABASE、SETUP 、COMPUTE、CANCEL、SCRIPT、HELP工具条：工作区：状态行：2、打开已存在的数据文件File-Open选择分子图形的显示方式Display- Labels可以选择原子、化学键等标记方式：Dispay-RenderingRenderings-BallsRendering—Balls and Cylinders3、建立计算分子的数据文件以丁二烯为例：选择Build-Default Element可以显示指定元素的基本性质：选择绘图工具后，得到碳碳骨架。

HyperChem程序及其应用

HyperChem程序及其应用

河北师范大学计算量子化学研究所蔡新华教授量子化学在线教学.100/qc/lzhx-0.htmHyperChem 程序及其应用一、HyperChem 程序的运行环境HyperChem 程序包，用C++写源程序，具有工作站、微机等不同的版本，作为教学示例，我们向大家介绍适用于微机运行的程序版本。

可以通过网络选购HyperChem程序包，也可以免费下载演示版本以供学习只用，现在该公司提供的最新版本为V6.0。

该公司的网址为：该公司与98年诺贝尔奖金得主Pople的关系可以参看其网页有关介绍。

1、软件环境Windows95、Windows98或Windows2000系统。

2、硬件环境486以上的微机，内存应在8M以上，硬盘至少有32M以上自由空间。

为了能够以最佳方式显示分子图像，最好有VGA以上显示器。

3、程序安装使用该程序应注意程序版权（注册）。

安装程序默认子目录为：C:\hyper6安装完成后，该目录可以看到如下文件，其中，绿色烧杯为执行程序图标。

有关该程序的使用说明、参考手册等全套文档均可免费获得。

二、程序基本使用方法我们以演示版本为例，说明该程序的基本使用方法。

1、启动程序在屏幕上，双击绿色烧杯可以得到如下画面：点击 Try进入工作区窗口窗口各部分功能简介标题名称：最大、最小化、退出按钮菜单条：FILE、EDIT、BUILD、SELECT、DISPLAY、DATABASE、SETUP 、COMPUTE、CANCEL、SCRIPT、HELP工具条：工作区：状态行：2、打开已存在的数据文件File-Open选择分子图形的显示方式Display- Labels可以选择原子、化学键等标记方式：Dispay-RenderingRenderings-BallsRendering—Balls and Cylinders3、建立计算分子的数据文件以丁二烯为例：选择Build-Default Element可以显示指定元素的基本性质：选择绘图工具后，得到碳碳骨架。

HyperChem应用 乙烯最低电子激发态的从头计算

HyperChem应用 乙烯最低电子激发态的从头计算

HyperChem应用乙烯最低电子激发态的从头计算优化乙烯的基态通过前面几个例子的学习，你已经对从头计算有了初步的了解，所以下面的一些指令将省略。

用STO-3G基组构造乙烯：1. 在File菜单中选择New，刷新工作区。

2. 确保Explicit Hydrogens没有选择。

3. 从Default Element中选择碳，并画一条C-C单键。

单击碳键中部使它变成双键。

4. 从Build菜单选择Add H和Model Build构造乙烯。

5. 从Setup菜单选择Ab Initio，并选基组为Minimal (STO-3G)。

同时令Total charge = 0，Spin multiplicity = 1，Spin pairing = RHF，Accelerate convergence =Yes，SCF Convergence limit = 0.0001. 按下CI按钮选择CI Method 为None。

优化乙烯基态：1. 选择Compute菜单的Geometry Optimization。

选择Polak-Ribiere方法，RMS gr adient 为0.01。

选择OK关闭对话框。

得到的结果为：C-C bond length：1.31埃，C-H bond length：1.08埃，H-C-H angle：115.7度。

计算相关能：1. 在Setup菜单选择Ab Initio，按下Options按钮并选择MP2 correlation energy。

单击OK回到工作区。

2. 在Compute菜单选择Single Point。

得到结果：SCF能量：-48364.64 kcal/mol ，MP2总能量：-48438.61 kcal/mol，包括-74.97kc al/mol相关能。

具体运算结果可能会与这个值有微小的差别。

乙烯基态轨道观察乙烯的轨道和轨道能量图：1. 从Compute菜单选择Orbitals。

动力学模拟实验详解

动力学模拟实验详解

分子平衡与动态行为的动力学模拟实验详解吴景恒实验目的：（1）掌握Hyperchem中的分子建模方法（2）掌握运用分子力学进行几何优化的方法，能正确设置力场参数及几何优化参数（3）掌握分子动力学、Langevin动力学及Monte Carlo模拟方法， 能正确设置模拟参数（4）通过动力学或Monte Carlo模拟，获取低能量的结构和热力学参数实验注意：（1）穿实验服；实验记录用黑色，蓝色或蓝黑色钢笔或签字笔记录；实验数据记录不需要画表格（2）实验前请先仔细阅读前面的软件使用介绍，然后逐步按照实验步骤所写内容进行操作（3）截图方法：调整视角至分子大小适中，按下键盘上的PrintScreen按键截图，从“Windows开始菜单”打开“画图”工具，按Ctrl+v或“编辑-粘贴”，去掉四周多余部分只留下分子图形，保存图片（4）所有保存的文件全部存在E盘或D盘根目录用自己学号命名的文件夹下，不要带中文命名，实验完毕全部删除，不得在计算用机上使用自己携带的U盘或其他便携存储设备！Hyperchem使用介绍：本次实验用到的工具：Draw：描绘分子工具，在工作区单击画出原子，拖拽画出成键原子，在分子键上单击更改成键类型，双击会出现如下元素周期表用于选择不同原子建立分子Select：选择原子工具，选中的原子或键会呈现绿色，在原子上单击左键选择对应原子/分子（选择模式对应在Select 菜单下Atoms/Moleculars更改），在原子上右击取消选择该原子，在工作区单击选择全部分子，在工作区右击取消全部分子；同时选中（确保Select – Multiple Selections为选中状态）两个原子时在状态栏显示键长（单位为Å），同时选中三个原子显示键角，同时选中四个原子显示二面角Rotate out-of-plane：平面外旋转工具，转换视角用Rotate in-plane：平面内旋转工具，转换视角用Translate：平移工具，转换视角用Mgnify/Shrink：放大镜工具，转换视角用Model Builder：分子建模工具，左三分别用于画C, N, O原子，最右为建立分子模型实验步骤：一、建立丙氨酸两性离子模型（1）根据不同建模方法用下面其中一种方法搭建分子模型：1、在工作区画出丙氨酸两性离子基本构型（氢原子可先不画）2、从Databases – Amino Acids – Ala建立大致模型再添加羟基氧和氨基氢原子（2）分别双击两个C-O键，更改其键型为共轭键；单击工具栏建立分子模型工具（或Build – Add H & Model Build），建立模型后还少一个氢原子的，确认Build – Allow Arbitrary Vsalence为选中状态，手动增加氢原子上去后再点击一次建立分子模型工具或Build – Add H & Model Build：（3）点击Select – Atoms使其为选中状态，选择C-O两个原子记录键长数据；取消选择，选择Cα-C'-O三个原子记录键角数据；取消选择，选择N-Cα-C'-O四个原子记录二面角数据（有两个氧原子，键长和键角只需记录一个，两组二面角都记录）（4）取消选择，Display – Labels选中Charge并确定，请根据建模方法的不同设定不同电荷：1、手工建立模型取消选择，选中两个氧原子，直接画分子的在Build – Set Charge中设置原子电荷为-0.5，然后取消选择，选中氮原子，设置原子电荷为1.0（注意，手工建模的不需要按下面“2、直接从菜单建立丙氨酸模型”所述设置原子电荷）：2、直接从菜单建立丙氨酸模型只需设置新增氧原子与新增氢原子电荷与同类型原子相同，其他原子维持原状（不需对逐个原子进行如图所示电荷设置）：（5）点击Setup – Molecular Mechanics... 选择AMBER力场：点击Options，作如下图的设值：（6）点击Display – Labels – 选中Type并确定，检查是否有原子类型标记为“*”符号；若有，选择未被正确设置的原子，点击Build – Set Atom Type...从弹出窗口为该原子设置为与同类型原子一样的原子类型（如氨基上的氢设为H）（7）再次检查结构，确认已通过单击工具栏建立分子模型工具或Build – Add H & Model Build为原子建好模型；分别点击Display – Labels 选择Charge及Type检查电荷和原子类型是否已正确无误（8）同时选中N-Cα-C'-O四个原子，点击Select – Name Selection...将其命名为ncco（9）点击File – Save As...，在保存类型下拉菜单中选择HyperChem (*.HIN)格式，将其保存为ala.HIN二、丙氨酸两性离子在气相和液相中的几何优化及分子叠合（1）点击Compute – Single Point计算单点能，记录Energy, Gradient两个数值：点击Compute – Geometry Optimization为分子作真空几何优化，“RMS gradient of: ... kcal/mol”设为0.1，“or: … maximum cycles”设为1800（后面所有几何优化按默认设置直接确定即可，不需再作改动），点击OK待至Converged=Yes，记录能量数值以及cycles和points值（后面做几何优化時一样记录cycles和points值）如上测量并记录C-O键长，Cα-C'-O键角，N-Cα-C'-O二面角数值点击File – Save As...，将分子存为ala-gas.HIN文件（2）点击Setup – Periodic Box... 作如下设值：点击OK，丙氨酸离子就被溶于12Å×10Å×12Å的溶剂盒子当中：（3）点击Setup – Molecular Mechanics... - Options作如下设值：同上点击Single Point 和 Geometry Optimization分别进行单点能量及几何优化的计算，分别记录上述能量数值如出现以下提示，请选择“否”并确认Setup – Molecular Mechanics... - Options已如上述完成设定：测量并记录C-O键长，Cα-C'-O键角，N-Cα-C'-O二面角数值（4）液相优化丙氨酸离子后，点击File – Save As...，把分子保存为ala-liq.HIN文件点击Select – Molecules使其为选中状态，单击丙氨酸两性离子使其呈选中状态：然后点击Select – Complement Selection反选周围水分子：按键盘上的Delete键并确定删除水分子，点击Display – Show Periodic Box取消显示盒子边界（5）再次选中液相中优化的丙氨酸离子，点击Display – Color Atoms...在以下选项中选择其中一个给分子上色（尽量选择对比度高易分辨的颜色）：点击File – Merge...选择先前保存的ala-gas.HIN文件合并进工作区，按上述步骤把气相下优化的丙氨酸分子上另一种颜色（6）点击Select – Atoms使其为选中状态，用选择工具分别依次选择两个分子的N, Cα和C’原子（先选择分子一的N原子然后选择分子二的N原子，再选择分子一的Cα原子...如此类推）：点击Display – Overlay叠合两丙氨酸分子：观察叠合结果并写入报告，注意分别标明气相和液相优化的分子为何种颜色；截图，保存图片为Overlay.png；注意不要保存叠合后的分子文件！三、丙氨酸两性离子的分子动力学模拟及蒙特卡罗模拟（1）分子动力学：点击File – Open...点击“否”不保存叠合后的分子文件，然后打开先前保存的ala-liq.HIN文件，点击Compute - Molecular Dynamics...设置如下：点击Averages...把EKIN, EPOT, ETOT, ncco移至最右并点OK；若没有ncco请参照上面第一大点第（8）小点进行设置，下同：点击Proceed，观察分子的运动情况；分子动力学完毕后点击Rescale，如上法截图保存中间结果窗口部分为MD.png，点击Done结束；分别做一次Single Point 和 Geometry Optimization计算记录能量及梯度值，不需保存分子文件（2）Langevin动力学：点击File – Open...打开ala-gas.HIN文件，点击Compute - Langevin Dynamics...作如下设置：同上点击Averages...把EKIN, EPOP, ETOT, ncco移至最右并点OK；点击Proceed，动力学完毕后点击Rescale，截图保存中间结果窗口部分为LD.png；分别做一次Single Point 和 Geometry Optimization计算记录能量及梯度能量值，不需保存分子文件（3）Monte Carlo模拟：点击File – Open...打开ala-liq.HIN文件，点击Compute – Monte Carlo...作如下设置：点击Averages...把ACCR, EPOT, D ACCR, ncco移至最右并点OK：点击Proceed，待动力学完毕后点击Rescale，截图保存中间结果窗口部分为MC.png；分别再做一次Single Point 和 Geometry Optimization计算记录能量及梯度能量值，不需保存分子文件四、记录不同建模方法的实验数据记录邻组建立初始模型后的气相单点计算，气相优化后和液相优化后三个能量值（只需要Energy值）五、结束实验检查下面数据是否已被正确记录：1、丙氨酸离子的初始模型，气相优化和液相优化后的C-O键长，Cα-C'-O键角，N-Cα-C'-O二面角2、丙氨酸离子气相和液相的初始模型及优化后的能量记录（Energy, Gradient, cycles和points）；分子动力学， Langevin动力学和 Monte Carlo模拟后的Single Point 和 Geometry Optimization的能量及梯度值3、丙氨酸离子气相和液相优化结果的分子叠合图；分子动力学， Langevin动力学和 Monte Carlo模拟能量曲线图4、使用不同建模方法法的另一组的能量数据打开”网上邻居-综合 在 Zh00 上-2012-物化计算机实验”，找到以当天日期命名的文件夹，在下面新建以自己学号命名的文件夹，把Overlay.png, MD.png, LD.png, MC.png复制到里面，把原始数据记录取至前台检查签名（原始数据记录请务必写上姓名！），签名后在前台用U盘把自己的实验图片复制下来或发送到自己邮箱里面（教师用计算机学生不得操作！）实验完毕删除自己在用机上所有留下的有关文件，关闭计算机，收拾桌椅并带好个人携带物品离开实验室实验报告：一、实验原始数据记录应附在实验报告的最后，不能直接作为实验报告的内容部分二、实验图片应打印好作为实验报告的内容部分并标上图片标题和注释，不能附在实验报告的最后三、实验报告所有数据必须用表格形式列出，并应对所有已记录的数据进行分析，此外还应包括以下内容：1、分别比较气相和液相下优化的丙氨酸两性离子的结构的异同（观察叠合后的分子），请结合记录的键长键角二面角数据分析异同具体是如何产生的2、试比较分析分子动力学和Monte Carlo模拟后的单点能计算和几何优化结果跟初始模型结果，包括Energy, Gradient, cycles和points数值的比较3、分析在分子动力学模拟和Langevin动力学的模拟的过程中N-Cα-C'-O的变动情况四、思考题（连同给定的书本上的思考题写入实验报告）：1、两种不同建模方法区别在哪里，计算结果又有什么不同？请作具体的分析2、力场设置里面的Dielectric(Epsilon)是什么意思，其下两个选项在气相跟液相优化分别是用的不同设置又是什么意思，设置不同会引起什么差别？（可查阅Hyperchem的使用手册）3、力场设置里面的Cutoffs是什么意思，其下选项在气相跟液相优化分别是用的不同设置又是什么意思，设置不同会引起什么差别？（可查阅Hyperchem的使用手册）4、分子动力学跟Langevin动力学的模拟结果图有什么异同？他们的原理和计算公式具体区别在哪里5、Monte Carlo模拟中为什么没有加入EKIN和ETOT作图，如果对其作图会得到怎样的结果？。

Chemdraw化学结构作图教程

Chemdraw化学结构作图教程

chemdrawChembioOffice 是由CambridgeSoft开发的综合性科学应用软件包。

该软件包是为广大从事化学、生物研究领域的科研人员个人使用而设计开发的产品。

同时，这个产品又可以共享解决方案，给研究机构的所有科技工作者带来效益。

利用ChemBioOffice 你可以方便的进行化学生物结构绘图、分子模型及仿真、可以将化合物名称直接转为结构图，省去绘图的麻烦；也可以对已知结构的化合物命名，给出正确的化合物名称。

一、化学结构的绘制1、键工具（1）.固定键的长度,角度软件对键的长度有一定的限制,在”对象”下拉菜单中，点击“固定键长”或者用键盘上“Ctrl”+“L”，则画出的键长固定。

同样的方法“固定键角”，或直接“Ctrl”+“E”用于固定键的角度，默认值15°为一个单位。

若要改变键的长度或者角度，按下Alt键，同时按动到所需的长度和角度即可。

（2）单键绘制在工具栏里点击工具，在操作页面上单击鼠标左键就画出单键，或者在操作页面上单击鼠标左键并按住旋转,直到要的角度放开左键即画好。

（3）多重键的绘制a．双键的绘制：点击绘制单键上再按动一次即可得到双键。

通过在双键中间（出现光标块）的点击可以改变双键的位置，在上，在下或中间。

也可以单击工具栏中Multiple Bonds拖住鼠标左键会出现键的选择，选择双键，在操作页面单击左键即可出现双键。

b.叁键的绘制：在双键的基础上再次按动左键。

或者在工具栏中Multiple Bonds选择在操作页面单击左键即可。

（4）.楔键工具从工具栏中点击楔键工具, 在操作页面单击鼠标左键并按住旋转,直到要的角度放开左键即画好。

2、环工具环己烷凳环可以用两个方位进行绘制，选择工具，点击即可得到水平方向环，按住shift点击则得到垂直方向环。

除了环己烷凳环外，其他工具在按住Ctril键均会得到不定域共轭结构,如下图：对于苯环，双键可以绘制任意两个方向之一，可以通过按下shift键的同时单击进行切换。

化学软件——HyperChem(分子模拟)介绍

化学软件——HyperChem(分子模拟)介绍

化学软件——HyperChem（分子模拟）介绍HyperChem是一款以高质量，灵活易操作而闻名的分子模拟软件。

通过利用3D对量子化学计算，分子力学及动力学进行模拟动画，HyperChem 为您提供比其它 Windows 软件更多的模拟工具。

图形界面：图形界面，有半经验方法（ AM1 ， PM3 等）， UHF ， RHF 和 CI 和7.0 版新增加的密度泛函。

可进行单点能，几何优化，分子轨道分析，预测可见- 紫外光谱，蒙特卡罗和分子力学计算。

主要功能：1. 结构输入和对分子操作。

2. 显示分子。

3. 化学计算。

用量子化学或经典势能曲面方法，进行单点、几何优化和过渡态寻找计算。

可以进行的计算类型有：单点能，几何优化，计算振动频率得到简正模式，过渡态寻找，分子动力学模拟 Langevin 动力学模拟， Metropolis Monte Carlo 模拟。

支持的计算方法有：从头计算，半经验方法，分子力学，混合计算。

4. 可以用来研究的分子特性有：同位素的相对稳定性；生成热；活化能；原子电荷； HOMO-LUMO能量间隔；电离势；电子亲和力；偶极矩；电子能级； MP2 电子相关能； CI 激发态能量；过渡态结构和能量；非键相互作用能； UV-VIS 吸收谱； IR 吸收谱；同位素对振动的影响；对结构特性的碰撞影响；团簇的稳定性。

5. 支持用户定制的外部程序。

6. 其它模块： RAYTRACE 模块， RMS Fit ， SEQUENCE 编辑器，晶体构造器；糖类构造器，构像搜寻，QSAR 特性，脚本编辑器。

7. 新的力场方法： Amber 2 ， Amber 3 ，用于糖类的 Amber ， Amber 94 ，Amber 96 。

8. ESR 谱。

9. 电极化率。

10. 二维和三维势能图。

11. 蛋白质设计。

12. 电场。

13. 梯度的图形显示。

14. 新增功能：密度泛函理论 (DFT) 计算； NMR 模拟；数据库； Charmm 蛋白质模拟；半经验方法TNDO ；磁场中分子计算；激发态几何优化； MP2 相关结构优化；新的芳香环图；交互式参数控制；增强的聚合物构造功能；新增基组。

利用Hyperchem软件进行分子结构构建及性质计算

利用Hyperchem软件进行分子结构构建及性质计算

利用Hyperchem软件进行分子结构构建及性质计算实验目的1.初步了解分子模型方法的原理和应用。

2.学习使用Hyperchem软件构建简单的分子并使用适当方法优化结构。

3.学习使用Hyperchem软件计算简单分子的几何和电子性质。

实验原理化学的学习使我们认识了许多分子的分子式及二维结构，如何得到分子的三维结构，以及分子在空间的几何特征和电子特征，则可以借助于理论计算的工具和方法去模拟计算。

HyperChem软件是HyperCube公司开发的Windows界面程序。

是常用的分子设计和模拟软件。

它可以应用于构建简单及复杂的分子模型并进行综合计算与分析。

分子构建过程可以通过熟练各个菜单及工具栏的操作来实现，计算和分析需要我们了解常用的计算方法。

在本实验室中我们需要了解一下计算方法，这些方法位于HyperChem的Setup菜单下。

(1)分子力学(Molecular Mechanics)方法：分子力学又叫力场方法，目前广泛地用于计算分子的构象和能量。

适用于超大规模体系，超低精度计算。

分子力学的基本假设：玻恩-奥本海默近似，原子核的运动与电子的运动可以看成是独立的；分子是一组靠各种作用力维系在一起的原子集合。

这些原子在空间上若过于靠近，便相互排斥；但又不能远离，否则连接它们的化学键以及由这些键构成的键角等会发生变化，即出现键的拉伸或压缩、键角的扭变等，会引起分子内部应力的增加。

每个真实的分子结构，都是在上述几种作用达到平衡状态的表现。

分子力学从几个主要的典型结构参数和作用力出发来讨论分子结构，即用位能函数来表示当键长、键角、二面角等结构参数以及非键作用等偏离“理想”值时分子能量的变化。

不同的分子力场方法采用不同的势能函数。

MM+：适用于有机分子的计算。

Amber：适用于有机分子、蛋白质和核酸等大分子的计算。

(2)半经验计算(Semi-empirical)方法：是求解HF(Hartree-Fock)方程时采用各种近似，或者直接使用拟合的经验参数来近似求解自洽场。

HyperChem基本操作 单点计算

HyperChem基本操作 单点计算

HyperChem基本操作单点计算| 网站首页 | 文章资料 | 资源下载 | 图片中心 | 化学论坛 | 雁过留声 ||文章资料首页|新闻公告|专业英语|考研考博|知识点滴|软件教程|实验技术|文献检索|学科专业|化学简史|您现在的位置：积学网 >> 文章资料 >> 软件教程 >> 文章正文用户登录新用户注册HyperChem基本操作单点计算热【字体：小大】HyperChem基本操作单点计算作者：水云间文章来源：本站原创点击数：595 更新时间：2005-11-11HyperChem基本操作单点计算单点计算，仅仅执行势能曲面上的一个单个点的计算。

例如对一个双原子分子来说，这可能是在点a原子间距离R=2.0埃的计算。

单点计算的结果给出系统在当前几何构型的势能，以及那个点的梯度。

在点b，c，d，或e的单点计算可能将给出更高的能量。

如果在关键的部分取足够多的点，利用Origin或者Matlab等数学工具软件，就能描出势能曲线，从而精确算出离解能De和核平衡距离re，利用公式就能得到震动参数ωe。

对多原子系统来说，状况更加复杂，但是本质是一样的。

Orbital中显示的轨道信息Alpha & Beta显示选择的轨道是alpha自旋还是beta自旋。

LUMO+显示选择轨道相对于LUMO的位置关系。

例如，选择能量在LUMO之上的轨道，文本框依次显示+1，+2，+3......；如果选择能量低于LUMO的轨道，文本框显示-1，-2，-3......。

HOMO-显示选择轨道相对于HOMO的位置关系。

例如，选择能量在HOMO之上的轨道，文本框依次显示-1，-2，-3......；如果选择能量低于HOMO的轨道，文本框显示+1，+2，+3......。

Number显示从能量最低轨道开始的选择轨道绝对数值。

对于UHF计算，轨道的alpha和beta 列编号分开显示，对HOMO-和LUMO+选项也是这样。

HyperChem基本操作 画二维草图

HyperChem基本操作 画二维草图

HyperChem基本操作画二维草图1. 双击Drawing工具，打开Element Table对话框。

2. 打开Allow ions，关闭Explicit Hydrogens。

如果关闭Explicit Hydrogens，在画分子的时候，不自动添加氢。

3. 选择碳，接着关闭对话框。

碳设置为缺省元素。

4. 接着按下面操作。

标记原子1. 在Display菜单选择Labels。

2. 在Atoms选项框，选择Symbol。

靠近Symbol的单选按钮会被填充。

3. 左键单击OK。

Labels对话框消失，所有的原子将标注元素符号。

删除原子：1. 左键单击Drawing工具进入绘图模式。

2. 右键单击想要删除的原子，或者想要删除的价键中部。

原子和价键就会消失。

删除多个原子或价键：1. 左键单击Selection工具进入选择模式。

2. 用左右键在工作区拖出选择的目标。

3. 在Edit菜单选择Clear。

4. 在提示框中选择Yes。

Constrain Bond Length对话框Computed没有限制。

由模型决定键长。

Other:输入一个大于0至1000埃的正数。

实用范围是0.75到4埃。

原子类型（Atom Types）在分子动力学计算中，分子中每一个原子都有原子类型。

原子类型代表具有相似化学环境的一系列同类元素原子。

环境参数包括杂化及其它因素。

例如，AMBER原子类型C代表一个sp 2羰基碳，CT代表四面体碳，CH代表一个包括一个氢原子的sp 3碳。

分子动力学计算用相同的方法处理同一类型的所有原子。

每一种力场用于一系列不同类型的原子。

原子类型一般需要分子动力学计算。

但不是半经验计算。

每一种原子类型都有一个不同于其他力场的名称。

力场需要原子类型来获得计算参数。

MM+力场可以处理缺省的原子类型（用未知类型**表示）。

当在画一个新的分子的时候，HyperChem给每个原子一个类型名称**，表示没有指定原子类型。

当在Build菜单选择Model Build或者Calculate Types，或者改变力场（使用Setup菜单的Molecular Mechanics），HyperChem使用Molecular Me chanics Force Field对话框中选择的力场指定恰当的原子类型。

HyperChem

HyperChem

分子图形与分子模型设计——HyperChem使用简介厦门大学化学系2005年3月HyperChem使用简介HyperChem是HyperCube Inc.的产品，它具有非常强大的综合计算与分析功能，是优秀的分子图形和分子设计的工具软件之一。

HyperChem是运行在Windows系统的分子计算与建模软件，具有量子化学（半经验和从头算）、分子力学、分子动力学、随机动力学、Monte Carlo模拟等计算功能，计算结果可以用三维图形显示。

它还提供用户VB、C/C++和FORTRAN等语言的应用程序接口。

HyperChem 7.5版本已经推出。

图1是HyperChem的工作窗口，最下部是工作状态档。

在菜单下面是常用工具档。

图1 HyperChem的工作窗口HyperChem的操作可以使用鼠标和键盘两种。

在工具档从左开始有8个工具图标，当鼠标点图标之后，鼠标在工作区的形状也改变为该图标的形状：1.绘图工具。

鼠标双击该图标可直接进入缺省元素周期表，选择所要绘制元素。

2.选择工具。

3.xy轴方向旋转工具，也可使用键盘的上下左右光标键进行相同的操作。

4.z轴方向旋转工具，也可使用键盘的Home和End键进行相同的操作。

5.xy轴平移工具，也可使用键盘的Shift+上下左右光标键进行相同的操作。

6.z轴平移工具。

7.缩放工具，也可使用键盘的PgUp和PgDn键进行相同的操作。

8.z轴截片工具。

鼠标操作有较为多样：左点击、右点击、左拖拉、右拖拉、左右拖拉、Shift+左点击、Shift+右点击、双击等。

一般的旋转和平移操作是使用鼠标的左键进行，当完成了某个基团、分子的选择之后，可以使用右键对所选部分进行旋转和平移操作。

HyperChem的详细操作将结合具体的实例进行讲解。

以下通过对HyperChem 5.1的菜单命令的介绍，说明它的主要功能和使用方法。

一、File1.New (Ctrl+N)：新建一个沿尚未命名文件。

AquaChem 简要使用说明-05-02-28

AquaChem 简要使用说明-05-02-28
1
AquaChem 简要使用说明
一、 简介
AquaChem 是用于水溶液地球化学数据的分析、作图和模拟的专业软件。由加拿大滑 铁卢水文地质有限公司研制开发。该软件具有完全可以由用户自己定制的地球化学数据和 参数数据库系统，并提供在水文地球化学领域得到广泛应用的多种数据分析和作图工具。
AquaChem 的数据分析功能包括单位转换、电荷平衡、样品混合以及样品相关性分析 和地球化学参数计算等，辅之以广泛应用的水化学数据图形工具，可以更清楚地表示水的 化学特征和质量。AquaChem 的图形工具包括：
三线图 包括 piper（图 1-1a）、Durov（图 1-1b）和简单的三离子三线图（图 1-1c）；
图 1-1a
图 1-1b 图 1-1 AquaChem 中的三线图
图 1-1c
图 1-5 AquaChem 中的地温图
图 1-6 AquaChem 中表示样品位置图
饼图、折线图、放射图 包括饼图（图 1-2a）、折线图（图 1-2b，Schoeller 指印图，图 1-2cStiff 折线图）和放 射图（图 1-2d）； 散点图 包括一般散点图（图 1-3a）和 Ludwig-Langelier 散点图（图 1-3b）； 频率柱状图（图 1-4a）和时间序列图（图 1-4b）； 地温图（图 1-5）； 样品位置图（图 1-6）。 上述水化学数据的各种图示方法均从某一方面提供了对地下水与含水层介质之间复杂 作用的解释。
图 4-4 输入窗口
编辑或改变 Measured Values（实测数据）窗口内的数值后，点按 Save 按钮保存裱画 结果。该窗口右下角的箭头按钮是前进到下一个记录或后退到前一个记录。
4.3 文本窗口
文本窗口显示样品记录列表中一个样品或一组样品的有关信息和（或）计算结果（图 4-5）。要打开该窗口，可以在样品记录列表窗口中选择一个样品记录，然后从主菜单的 Reports 下拉菜单中选择一种类型的文本窗口。

甲醇高斯程序应用

甲醇高斯程序应用

甲醇分子高斯程序应用用HyperChem程序画分子图转化保存格式进行优化进行单点计算进行振动分析进行核磁分析计算结果输出：优化结果Entering Link 1 = C:\E盘学习\G94W_1\G94W\l1.exe PID= 4736.Copyright (c) 1988,1990,1992,1993,1995 Gaussian, Inc.All Rights Reserved.This is part of the Gaussian 94(TM) system of programs. It isbased on the the Gaussian 92(TM) system (copyright 1992Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986Carnegie Mellon University), and the Gaussian 82(TM) system(copyright 1983 Carnegie Mellon University). Gaussian is afederally registered trademark of Gaussian, Inc.This software is provided under written license and may beused, copied, transmitted, or stored only in accord with thatwritten license.The following legend is applicable only to US Governmentcontracts under DFARS:RESTRICTED RIGHTS LEGENDUse, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013.Gaussian, Inc.Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USAThe following legend is applicable only to US Governmentcontracts under FAR:RESTRICTED RIGHTS LEGENDUse, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of theCommercial Computer Software - Restricted Rights clause at FAR 52.227-19.Gaussian, Inc.Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA--------------------------------------------------------------- Warning -- This program may not be used in any manner thatcompetes with the business of Gaussian, Inc. or will provideassistance to any competitor of Gaussian, Inc. The licenseeof this program is prohibited from giving any competitor ofGaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in thebusiness of creating and licensing software in the field ofcomputational chemistry and represents and warrants to thelicensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above.---------------------------------------------------------------Cite this work as:Gaussian 94, Revision E.1,M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill,B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith,G. A. Petersson, J. A. Montgomery, K. Raghavachari,M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres,E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox,J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart,M. Head-Gordon, C. Gonzalez, and J. A. Pople,Gaussian, Inc., Pittsburgh PA, 1995.*********************************************Gaussian 94: x86-Win32-G94RevE.1 23-Nov-199605-Jan-1911*********************************************---------------# HF/6-31G* opt---------------1/18=20,38=1/1,3;2/9=110,12=2,17=6,18=5/2;3/5=1,6=6,7=1,11=9,25=1,30=1/1,2,3;4//1;5/5=2,38=4/2;6/7=2,8=2,9=2,10=2,28=1/1;7//1,2,3,16;1//3(1);99//99;2/9=110/2;3/5=1,6=6,7=1,11=9,25=1,30=1/1,2,3;4/5=5,16=2/1;5/5=2,38=4/2;7//1,2,3,16;1//3(-5);2/9=110/2;3/5=1,6=6,7=1,11=9,25=1,30=1,39=1/1,3;6/7=2,8=2,9=2,10=2,28=1/1;99/9=1/99;----甲醇----Symbolic Z-matrix:Charge = 0 Multiplicity = 1CO 1 R2H 1 R3 2 A3H 1 R4 2 A4 3 D4 0H 1 R4 2 A4 3 -D4 0H 2 R6 1 A6 3 180. 0Variables:R2 1.43R3 1.08926R4 1.08998R6 0.96085A3 109.46629A4 109.45294A6 109.45327D4 120.00764GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radBerny optimization.Initialization pass.----------------------------! Initial Parameters !! (Angstroms and Degrees) !-------------------------------------------------! Name Definition Value DerivativeInfo. !-----------------------------------------------------------------------------! R1 R(2,1) 1.43 estimateD2E/DX2 !! R2 R(3,1) 1.0893 estimateD2E/DX2 !! R3 R(4,1) 1.09 estimateD2E/DX2 !! R4 R(5,1) 1.09 estimateD2E/DX2 !! R5 R(6,2) 0.9609 estimateD2E/DX2 !! A1 A(2,1,3) 109.4663 estimateD2E/DX2 !! A2 A(2,1,4) 109.4529 estimateD2E/DX2 !! A3 A(3,1,4) 109.4891 estimateD2E/DX2 !! A4 A(2,1,5) 109.4529 estimateD2E/DX2 !! A5 A(3,1,5) 109.4891 estimateD2E/DX2 !! A6 A(4,1,5) 109.477 estimateD2E/DX2 !! A7 A(1,2,6) 109.4533 estimateD2E/DX2 !! D1 D(6,2,1,3) 180. estimateD2E/DX2 !! D2 D(6,2,1,4) -59.9924 estimateD2E/DX2 !! D3 D(6,2,1,5) 59.9924 estimateD2E/DX2 !-----------------------------------------------------------------------------Trust Radius=3.00E-01 FncErr=1.00E-07 GrdErr=1.00E-07Number of steps in this run= 25 maximum allowed number of steps= 100.GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radInput orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 .000000 .000000 .0000002 8 .000000 .000000 1.4300003 1 1.027000 .000000 -.3630004 1 -.514000 -.890000 -.3630005 1 -.514000 .890000 -.3630006 1 -.906000 .000000 1.750000----------------------------------------------------------Distance matrix (angstroms):1 2 3 4 51 C .0000002 O 1.430000 .0000003 H 1.089265 2.066296 .0000004 H 1.089984 2.066675 1.779545 .0000005 H 1.089984 2.066675 1.779545 1.780000 .0000006 H 1.970618 .960852 2.863784 2.326055 2.32605566 H .000000Stoichiometry CH4OFramework group CS[SG(CH2O),X(H2)]Deg. of freedom 8Full point group CS NOp 2Largest Abelian subgroup CS NOp 2Largest concise Abelian subgroup CS NOp 2Standard orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 -.050389 .672278 .0000002 8 -.050389 -.757722 .0000003 1 -1.077389 1.035278 .0000004 1 .463611 1.035278 .8900005 1 .463611 1.035278 -.8900006 1 .855611 -1.077722 .000000----------------------------------------------------------Rotational constants (GHZ): 128.2203524 24.6041187 23.7392870Isotopes: C-12,O-16,H-1,H-1,H-1,H-1Standard basis: 6-31G(d) (6D, 7F)There are 28 symmetry adapted basis functions of A' symmetry. There are 10 symmetry adapted basis functions of A" symmetry.Crude estimate of integral set expansion from redundant integrals=1.645. Integral buffers will be 262144 words long.Raffenetti 1 integral format.Two-electron integral symmetry is turned on.38 basis functions 72 primitive gaussians9 alpha electrons 9 beta electronsnuclear repulsion energy 40.1978964472 Hartrees.One-electron integrals computed using PRISM.The smallest eigenvalue of the overlap matrix is 9.720E-03Projected INDO Guess.Initial guess orbital symmetries:Occupied (A') (A') (A') (A') (A') (A") (A') (A') (A")Virtual (A') (A') (A") (A') (A') (A') (A') (A') (A") (A')(A') (A') (A") (A') (A') (A') (A') (A") (A") (A')(A') (A') (A") (A') (A') (A') (A') (A") (A")Requested convergence on RMS density matrix=1.00E-08 within 64 cycles. Requested convergence on MAX density matrix=1.00E-06.Keep R1 integrals in memory in canonical form, NReq= 723889.SCF Done: E(RHF) = -115.033851898 A.U. after 12 cyclesConvg = .2636E-08 -V/T = 2.0024S**2 = .0000********************************************************************* *Population analysis using the SCF density.********************************************************************* *Orbital Symmetries:Occupied (A') (A') (A') (A') (A') (A") (A') (A') (A")Virtual (A') (A') (A') (A") (A') (A') (A") (A') (A') (A")(A') (A') (A') (A") (A') (A') (A') (A") (A') (A")(A') (A') (A") (A') (A") (A') (A') (A') (A')The electronic state is 1-A'.Alpha occ. eigenvalues -- -20.55434 -11.27153 -1.34460 -.92413 -.68075Alpha occ. eigenvalues -- -.61732 -.59095 -.49609 -.44321 Alpha virt. eigenvalues-- .22349 .27737 .32348 .32569 .37628Alpha virt. eigenvalues -- .76644 .77058 .78494 1.05200 1.12991Alpha virt. eigenvalues -- 1.14059 1.18515 1.20649 1.25078 1.27403Alpha virt. eigenvalues -- 1.41400 1.71380 1.76697 1.87870 2.04301Alpha virt. eigenvalues -- 2.37648 2.40437 2.50327 2.68362 2.70514Alpha virt. eigenvalues -- 2.79989 3.15131 4.11997 4.64152 Condensed to atoms (all electrons):1 2 3 4 561 C 4.791384 .212919 .398288 .392755 .392755-.0245972 O .212919 8.375395 -.030829 -.038966-.038966 .2604863 H .398288 -.030829 .515283 -.032341-.032341 .0046014 H .392755 -.038966 -.032341 .578171 -.041056-.0037845 H .392755 -.038966 -.032341 -.041056 .578171-.0037846 H -.024597 .260486 .004601 -.003784-.003784 .331314Total atomic charges:11 C -.1635052 O -.7400383 H .1773394 H .1452205 H .1452206 H .435764Sum of Mulliken charges= .00000Atomic charges with hydrogens summed into heavy atoms:11 C .3042742 O -.3042743 H .0000004 H .0000005 H .0000006 H .000000Sum of Mulliken charges= .00000Electronic spatial extent (au): <R**2>= 84.2067Charge= .0000 electronsDipole moment (Debye):X= 1.5518 Y= 1.1741 Z= .0000 Tot= 1.9459 Quadrupole moment (Debye-Ang):XX= -11.5475 YY= -13.0321 ZZ= -13.6352XY= -2.3623 XZ= .0000 YZ= .0000Octapole moment (Debye-Ang**2):XXX= 1.3589 YYY= -3.6172 ZZZ= .0000 XYY= 2.3711 XXY= -2.1731 XXZ= .0000 XZZ= .6887 YZZ= -.4694 YYZ= .0000 XYZ= .0000Hexadecapole moment (Debye-Ang**3):XXXX= -18.2393 YYYY= -60.7516 ZZZZ= -18.8178 XXXY= -1.2712 XXXZ= .0000 YYYX= -1.8067 YYYZ= .0000 ZZZX= .0000 ZZZY= .0000 XXYY= -11.7011 XXZZ= -6.4998 YYZZ= -13.7628 XXYZ= .0000 YYXZ= .0000 ZZXY= .7975N-N= 4.019789644715E+01 E-N=-3.513712161829E+02 KE=1.147535840525E+02Symmetry A' KE= 1.081533767360E+02Symmetry A" KE= 6.600207316428E+00***** Axes restored to original set *****------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr)Number Number X Y Z-------------------------------------------------------------------1 6 -.010147324 .000000000 .0196469962 8 -.005179200 .000000000 -.0116271013 1 -.005471837 .000000000 .0068112454 1 .003133235 .003215199 -.0034388505 1 .003133235 -.003215199 -.0034388506 1 .014531891 .000000000 -.007953441 ------------------------------------------------------------------- Cartesian Forces: Max .019646996 RMS .007694565Internal Forces: Max .019580541 RMS .008215312GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radBerny optimization.Search for a local minimum.Step number 1 out of a maximum of 25All quantities printed in internal units (Hartrees-Bohrs-Radians) Second derivative matrix not updated -- first step.The second derivative matrix:R1 R2 R3 R4 R5 R1 .40989R3 .00000 .00000 .34815R4 .00000 .00000 .00000 .34815R5 .00000 .00000 .00000 .00000 .55291A1 .00000 .00000 .00000 .00000 .00000A2 .00000 .00000 .00000 .00000 .00000A3 .00000 .00000 .00000 .00000 .00000A4 .00000 .00000 .00000 .00000 .00000A5 .00000 .00000 .00000 .00000 .00000A6 .00000 .00000 .00000 .00000 .00000A7 .00000 .00000 .00000 .00000 .00000D1 .00000 .00000 .00000 .00000 .00000D2 .00000 .00000 .00000 .00000 .00000D3 .00000 .00000 .00000 .00000 .00000A1 A2 A3 A4 A5 A1 .16000A2 .00000 .16000A3 .00000 .00000 .16000A4 .00000 .00000 .00000 .16000A5 .00000 .00000 .00000 .00000 .16000A6 .00000 .00000 .00000 .00000 .00000A7 .00000 .00000 .00000 .00000 .00000D1 .00000 .00000 .00000 .00000 .00000D2 .00000 .00000 .00000 .00000 .00000D3 .00000 .00000 .00000 .00000 .00000A6 A7 D1 D2 D3 A6 .16000D1 .00000 .00000 .01295D2 .00000 .00000 .00000 .01295D3 .00000 .00000 .00000 .00000 .01295Eigenvalues--- .01295 .10346 .10348 .16000 .16000Eigenvalues--- .16000 .16000 .34815 .34815 .34898Eigenvalues--- .40989 .552911000.000001000.000001000.00000RFO step: Lambda=-3.55547630E-03.Linear search not attempted -- first point.Iteration 1 RMS(Cart)= .04261970 RMS(Int)= .00131794Iteration 2 RMS(Cart)= .00101834 RMS(Int)= .00093052Iteration 3 RMS(Cart)= .00003227 RMS(Int)= .00092883Iteration 4 RMS(Cart)= .00000160 RMS(Int)= .00092886TrRot= .000000 .000000 .000000 .000000 .000000 .000000 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total)R1 2.70231 -.01958 .00000 -.04736 -.047362.65495R2 2.05841 -.00743 .00000 -.02107 -.021072.03734R3 2.05977 -.00296 .00000 -.00841 -.008412.05136R4 2.05977 -.00296 .00000 -.00841 -.008412.05136R5 1.81575 -.01635 .00000 -.02938 -.029381.78636A1 1.91055 -.01067 .00000 -.07203 -.071741.83881A2 1.91031 .00780 .00000 .05110 .050231.96055A3 1.91094 -.00120 .00000 -.01416 -.013881.89707A4 1.91031 .00780 .00000 .05110 .050231.96055A5 1.91094 -.00120 .00000 -.01416 -.013881.89707A6 1.91073 -.00252 .00000 -.00181 -.003841.90690A7 1.91032 -.00483 .00000 -.02953 -.029531.88079D1 3.14159 .00000 .00000 .00000 .000003.14159D2 -1.04706 -.00323 .00000 -.03014 -.03203-1.07909D3 1.04706 .00323 .00000 .03014 .032031.07909Item Value Threshold Converged?Maximum Force .019581 .000450 NORMS Force .008215 .000300 NOMaximum Displacement .107894 .001800 NORMS Displacement .042404 .001200 NOPredicted change in Energy=-1.730971E-03GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radInput orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 .023249 .000000 -.6592642 8 .068617 .000000 .7449423 1 1.053113 .000000 -.9781834 1 -.463900 -.885163 -1.0561975 1 -.463900 .885163 -1.0561976 1 -.821846 .000000 1.062231----------------------------------------------------------Distance matrix (angstroms):1 2 3 4 51 C .0000002 O 1.404939 .0000003 H 1.078114 1.984539 .0000004 H 1.085534 2.076341 1.758104 .0000005 H 1.085534 2.076341 1.758104 1.770326 .0000006 H 1.917741 .945302 2.771058 2.323656 2.32365666 H .000000Stoichiometry CH4OFramework group CS[SG(CH2O),X(H2)]Deg. of freedom 8Full point group CS NOp 2Largest Abelian subgroup CS NOp 2Largest concise Abelian subgroup CS NOp 2Standard orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 -.044932 .656800 .0000002 8 -.044932 -.748138 .0000003 1 -1.084557 .942298 .0000004 1 .429146 1.069257 .8851635 1 .429146 1.069257 -.8851636 1 .855312 -1.036507 .000000----------------------------------------------------------Rotational constants (GHZ): 130.5226427 25.385371624.5071898Isotopes: C-12,O-16,H-1,H-1,H-1,H-1Standard basis: 6-31G(d) (6D, 7F)There are 28 symmetry adapted basis functions of A' symmetry.There are 10 symmetry adapted basis functions of A" symmetry.Crude estimate of integral set expansion from redundant integrals=1.645. Integral buffers will be 262144 words long.Raffenetti 1 integral format.Two-electron integral symmetry is turned on.38 basis functions 72 primitive gaussians9 alpha electrons 9 beta electronsnuclear repulsion energy 40.7665395401 Hartrees.One-electron integrals computed using PRISM.The smallest eigenvalue of the overlap matrix is 9.291E-03Initial guess read from the read-write file:Initial guess orbital symmetries:Occupied (A') (A') (A') (A') (A') (A") (A') (A') (A")Virtual (A') (A') (A') (A") (A') (A') (A") (A') (A') (A")(A') (A') (A') (A") (A') (A') (A') (A") (A') (A")(A') (A') (A") (A') (A") (A') (A') (A') (A')Requested convergence on RMS density matrix=1.00E-08 within 64 cycles. Requested convergence on MAX density matrix=1.00E-06.Keep R1 integrals in memory in canonical form, NReq= 723889.SCF Done: E(RHF) = -115.035153141 A.U. after 10 cyclesConvg = .4752E-08 -V/T = 2.0014S**2 = .0000***** Axes restored to original set *****------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr)Number Number X Y Z-------------------------------------------------------------------1 6 .007266277 .000000000 .0053651612 8 -.005827031 .000000000 -.0052195983 1 .001112889 .000000000 -.0046235594 1 -.001002833 -.000587667 .0001408975 1 -.001002833 .000587667 .0001408976 1 -.000546468 .000000000 .004196203 ------------------------------------------------------------------- Cartesian Forces: Max .007266277 RMS .003214952Internal Forces: Max .007035062 RMS .002879612GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radBerny optimization.Search for a local minimum.Step number 2 out of a maximum of 25All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using information from points 1 2Trust test= 7.52E-01 RLast= 1.31E-01 DXMaxT set to 3.94E-01The second derivative matrix:R1 R2 R3 R4 R5 R1 .37445R2 -.00180 .35455R3 -.00107 .00202 .34888R4 -.00107 .00202 .00073 .34888R5-.01800 .00476 .00154 .00154 .54945A1 .00645 .01366 .00509 .00509 .01665A2 .00642 -.00369 -.00128 -.00128-.00077A3 -.01272 -.00486 -.00193 -.00193-.01069A4 .00642 -.00369 -.00128 -.00128-.00077A5 -.01272 -.00486 -.00193 -.00193-.01069A6 .00444 .00293 .00113 .00113 .00497A7 .01976 .01481 .00567 .00567 .02389D1 .00000 .00000 .00000 .00000 .00000D2 .01776 .00991 .00385 .00385 .01805D3 -.01776 -.00991 -.00385 -.00385-.01805A1 A2 A3 A4 A5 A1 .19025A2 -.01063 .16169A3 -.00762 .00530 .15858A4 -.01063 .00169 .00530 .16169A5 -.00762 .00530-.00142 .00530 .15858A6 .00557 -.00273 -.00042 -.00273-.00042A7 .02895 -.01338 -.00320 -.01338-.00320D1 .00000 .00000 .00000 .00000 .00000D2 .01800 -.00961 -.00034 -.00961-.00034D3-.01800 .00961 .00034 .00961 .00034A6 A7 D1 D2 D3 A6 .16074A7 .00413 .18269D1 .00000 .00000 .01295D2 .00208 .01209 .00000 .01839D3 -.00208 -.01209 .00000-.00544 .01839Eigenvalues--- .01295 .10477 .10614 .15061 .16000Eigenvalues--- .16000 .22275 .34815 .34830 .36037Eigenvalues--- .37829 .554911000.000001000.000001000.00000RFO step: Lambda=-2.80021190E-04.Quartic linear search produced a step of -.21618.Iteration 1 RMS(Cart)= .01304810 RMS(Int)= .00021880Iteration 2 RMS(Cart)= .00013827 RMS(Int)= .00018337Iteration 3 RMS(Cart)= .00000171 RMS(Int)= .00018336TrRot= .000000 .000000 .000000 .000000 .000000 .000000 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total)R1 2.65495 -.00123 .01024 -.01677 -.006542.64841R2 2.03734 .00243 .00456 -.00100 .003562.04090R3 2.05136 .00088 .00182 -.00060 .001222.05258R4 2.05136 .00088 .00182 -.00060 .001222.05258R5 1.78636 .00192 .00635 -.00617 .000181.78654A1 1.83881 .00704 .01551 .01461 .029991.86880A2 1.96055 -.00186 -.01086 .00511 -.005601.95495A3 1.89707 -.00127 .00300 -.00769 -.004811.89226A4 1.96055 -.00186 -.01086 .00511 -.005601.95495A5 1.89707 -.00127 .00300 -.00769 -.004811.89226A6 1.90690 -.00055 .00083 -.00955 -.008361.89854A7 1.88079 .00673 .00638 .02356 .029941.91073D1 3.14159 .00000 .00000 .00000 .000003.14159D2 -1.07909 .00179 .00692 .00241 .00971-1.06938D3 1.07909 -.00179 -.00692 -.00241 -.009711.06938Item Value Threshold Converged?Maximum Force .007035 .000450 NORMS Force .002880 .000300 NOMaximum Displacement .030401 .001800 NORMS Displacement .012954 .001200 NOPredicted change in Energy=-2.470957E-04GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radInput orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 .031150 .000000 -.6561522 8 .057923 .000000 .7450723 1 1.057300 .000000 -.9929164 1 -.460574 -.883054 -1.0539025 1 -.460574 .883054 -1.0539026 1 -.827190 .000000 1.077263----------------------------------------------------------Distance matrix (angstroms):1 2 3 4 51 C .0000002 O 1.401480 .0000003 H 1.079996 2.004833 .0000004 H 1.086178 2.070008 1.757113 .0000005 H 1.086178 2.070008 1.757113 1.766108 .0000006 H 1.934289 .945397 2.799454 2.335820 2.33582066 H .000000Stoichiometry CH4OFramework group CS[SG(CH2O),X(H2)]Deg. of freedom 8Full point group CS NOp 2Largest Abelian subgroup CS NOp 2Largest concise Abelian subgroup CS NOp 2Standard orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 -.045943 .655406 .0000002 8 -.045943 -.746075 .0000003 1 -1.078338 .972505 .0000004 1 .438094 1.062477 .8830545 1 .438094 1.062477 -.8830546 1 .845354 -1.061296 .000000----------------------------------------------------------Rotational constants (GHZ): 131.2939911 25.377661124.5091675Isotopes: C-12,O-16,H-1,H-1,H-1,H-1Standard basis: 6-31G(d) (6D, 7F)There are 28 symmetry adapted basis functions of A' symmetry.There are 10 symmetry adapted basis functions of A" symmetry.Crude estimate of integral set expansion from redundant integrals=1.645. Integral buffers will be 262144 words long.Raffenetti 1 integral format.Two-electron integral symmetry is turned on.38 basis functions 72 primitive gaussians9 alpha electrons 9 beta electronsnuclear repulsion energy 40.7755657636 Hartrees.One-electron integrals computed using PRISM.The smallest eigenvalue of the overlap matrix is 9.316E-03Initial guess read from the read-write file:Initial guess orbital symmetries:Occupied (A') (A') (A') (A') (A') (A") (A') (A') (A")Virtual (A') (A') (A') (A") (A') (A') (A") (A') (A') (A")(A') (A') (A') (A") (A') (A') (A') (A") (A') (A")(A') (A") (A') (A') (A") (A') (A') (A') (A')Requested convergence on RMS density matrix=1.00E-08 within 64 cycles. Requested convergence on MAX density matrix=1.00E-06.Keep R1 integrals in memory in canonical form, NReq= 723889.SCF Done: E(RHF) = -115.035412087 A.U. after 10 cyclesConvg = .1335E-08 -V/T = 2.0015S**2 = .0000***** Axes restored to original set *****------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr)Number Number X Y Z-------------------------------------------------------------------1 6 .000251374 .000000000 .0021855712 8 .000950211 .000000000 -.0015626163 1 .000694592 .000000000 -.0003158384 1 -.000440655 -.000610735 -.0002847375 1 -.000440655 .000610735 -.0002847376 1 -.001014867 .000000000 .000262356 ------------------------------------------------------------------- Cartesian Forces: Max .002185571 RMS .000787474Internal Forces: Max .001301258 RMS .000562129GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radBerny optimization.Search for a local minimum.Step number 3 out of a maximum of 25All quantities printed in internal units (Hartrees-Bohrs-Radians)Update second derivatives using information from points 1 2 3Trust test= 1.05E+00 RLast= 4.71E-02 DXMaxT set to 3.94E-01The second derivative matrix:R1 R2 R3 R4 R5 R1 .35392R3 .00540 .00004 .34862R4 .00540 .00004 .00047 .34862R5-.01228 .00395 .00301 .00301 .55392A1 .02601 .00396 -.00515-.00515 .00414A2 .00282-.00218 .00019 .00019 .00074A3 -.01526 -.00312 .00048 .00048-.00710A4 .00282-.00218 .00019 .00019 .00074A5 -.01526 -.00312 .00048 .00048-.00710A6-.00310 .00612 .00335 .00335 .00675A7 .03700 .00529 -.00562-.00562 .00877D1 .00000 .00000 .00000 .00000 .00000D2 .01647 .00975 .00229 .00229 .01492D3 -.01647 -.00975 -.00229 -.00229-.01492A1 A2 A3 A4 A5 A1 .18508A2 -.00903 .16139A3 -.00968 .00535 .15987A4 -.00903 .00139 .00535 .16139A5 -.00968 .00535-.00013 .00535 .15987A6 .01284 -.00401 -.00145 -.00401-.00145A7 .03015 -.01254 -.00717 -.01254-.00717D1 .00000 .00000 .00000 .00000 .00000D2 .02473 -.01047 -.00247 -.01047-.00247D3-.02473 .01047 .00247 .01047 .00247A6 A7 D1 D2 D3 A6 .15800D1 .00000 .00000 .01295D2 .00172 .02065 .00000 .02072D3 -.00172 -.02065 .00000-.00777 .02072Eigenvalues--- .01295 .10452 .10525 .14884 .16000Eigenvalues--- .16017 .22637 .34637 .34815 .35084Eigenvalues--- .37744 .555241000.000001000.000001000.00000RFO step: Lambda=-1.24675649E-05.Quartic linear search produced a step of .03309.Iteration 1 RMS(Cart)= .00157123 RMS(Int)= .00000174Iteration 2 RMS(Cart)= .00000094 RMS(Int)= .00000147TrRot= .000000 .000000 .000000 .000000 .000000 .000000 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total)R1 2.64841 -.00130 -.00022 -.00366 -.003882.64454R2 2.04090 .00076 .00012 .00206 .002182.04308R3 2.05258 .00080 .00004 .00231 .002352.05493R4 2.05258 .00080 .00004 .00231 .002352.05493R5 1.78654 .00104 .00001 .00171 .001721.78826A1 1.86880 .00018 .00099 .00064 .001641.87043A2 1.95495 -.00006 -.00019 -.00002 -.000211.95474A3 1.89226 .00001 -.00016 .00020 .000041.89229A4 1.95495 -.00006 -.00019 -.00002 -.000211.95474A5 1.89226 .00001 -.00016 .00020 .000041.89229A6 1.89854 -.00008 -.00028 -.00094 -.001221.89732A7 1.91073 -.00020 .00099 -.00168 -.000691.91004D1 3.14159 .00000 .00000 .00000 .000003.14159D2 -1.06938 .00010 .00032 .00063 .00095-1.06843D3 1.06938 -.00010 -.00032 -.00063 -.000951.06843Item Value Threshold Converged?Maximum Force .001301 .000450 NORMS Force .000562 .000300 NOMaximum Displacement .002449 .001800 NORMS Displacement .001571 .001200 NOPredicted change in Energy=-6.500622E-06GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG radInput orientation:----------------------------------------------------------Center Atomic Coordinates (Angstroms)Number Number X Y Z----------------------------------------------------------1 6 .034044 .000000 -.6549982 8 .060583 .000000 .7441793 1 1.060784 .000000 -.9936584 1 -.459068 -.883678 -1.0530435 1 -.459068 .883678 -1.0530436 1 -.825656 .000000 1.075955----------------------------------------------------------Distance matrix (angstroms):1 2 3 4 51 C .0000002 O 1.399429 .0000003 H 1.081150 2.005113 .0000004 H 1.087422 2.069041 1.759080 .0000005 H 1.087422 2.069041 1.759080 1.767356 .0000006 H 1.932688 .946306 2.800349 2.334074 2.33407466 H .000000Stoichiometry CH4OFramework group CS[SG(CH2O),X(H2)]Deg. of freedom 8Full point group CS NOp 2Largest Abelian subgroup CS NOp 2Largest concise Abelian subgroup CS NOp 2Standard orientation:----------------------------------------------------------。

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