分子模型的创建

常见内坐标文件: Gaussian (.gjf)
Gamess(.inp)
ADF
Mopac(.mop .dat) Note:
0o < Bond-angle < 180 o
-180o ≤ Dihedral-angle ≤180 o
Gaussian Z-matrix
c c h h h h
Atomic charges with hydrogens summed into heavy atoms: 1 1 C -0.143082 2 H 0.000000 3 H 0.000000 4 C 0.000000 5 H 0.000000 6 H 0.000000 7 Bq 0.143082 Sum of Mulliken charges= 0.00000
文件格式(syntax)：
Label, x, y, z ［例］乙烯的直角坐标文件格式(*.xyz)
6 C 0.000000 C 0.000000 H 0.943102 H 0.943102 H -0.943102 H -0.943102 0.000000 0.000000 0.000000 1.335000 0.000000 -0.544500 0.000000 1.879500 0.000000 1.879500 0.000000 -0.544500
程序将其原子序数为 0
USING GHOST ATOMS
Ghost atoms provide a convenient way to request arbitrary points at which to compute electrostatic properties. These points can be specified directly in Cartesian coordinates in the standard orientation. It is sometimes easier to specify the points in internal coordinates, and, since properties are automatically computed at all nuclear coordinates, ghost atoms can be added to the Z-matrix at points of interest.

内坐标和直角坐标的转换
Molden 读、存 Chem3D Gaussian View
Guassian 计算结果输出
在Link 0 Commands 行加入： ％ kjob L301
其它格式的读取软件
MERCURY DIAMOND Hyperchem MERCURY WLViewerPro4.2 Molview MOLEKEL4.3 *** Amber Babel
#P B3LYP/6-31G* GFINPUT IOP(6/7=3) TEST Example of NBO bond orders
0 1 C 0.000000 H 0.919278 H -0.919239 C 0.000000 H -0.919278 H 0.919239 Gh 0.700000
end
1.400000 1.089000 120.000
虚原子(Dummy Atoms)
Dummy atoms are pure mathematic points, and are useful in defining geometries 表示做：X，xx 等。 程序将其原子序数为 -1 鬼原子(Ghost Atoms) A ghost atom can be useful to specify the location of the off-nucleus basis functions, which have zero nuclear charge and mass. 表示做：Bq，G，Gh 等。
内坐标(Internal Coordinate or Z-matrix)
用键长、键角、二面角等几何参 量来表示分子中原子间的键长和位置 的一种坐标方式。矩阵中的每一行对 应于分子内一个原子的内坐标。
文件格式(syntax)：
原子标号，原子1，键长，原子2，键角，原子3，二面角
Label，Atom 1，Bond-length，Atom2，Bond-angle，Atom3，Dihedral-angle (Torsion angle)
# HF/6-31G* Massage Test
HF + H2O interaction energy: HF removed 01 X H 1 1.0 F 2 rHF 1 90.0 O 2 rHO 1 90.0 3 180.0 H 4 rOH 2 aHOH 1 90.0 H 4 rOH 2 aHOH 5 180.0 rHF 0.9203 rHO 1.8086 rOH 0.94 aHOH 126.4442 1 Nuc 0.0 2 Nuc 0.0
Note： http://zorkov.nease.net/ 量子化学软件中文网
MOLDEN: a pre- and post- processing program for molecular and electronic structures
Interfaced via program output
Gaussian GAMESS-US GAMESS-UK
MOPAC, AMPAC
Interfaced via Molden Format
ADF MOLPRO ACESII MOLCAS JAGUAR DALTON HONDO CADPAC
构建分子模型
数据形式：
直角坐标(Cartesian Coordinate) 内坐标(Internal Coordinate or Z-matrix)
创建数据方法：
X-ray衍射晶体数据 手工建立 利用工具软件, 如Chem3D
数据形式：
直角坐标(Cartesian Coordinate)
3,1, 3,2, 3,1, 3,2, 3,1, 3,2,
ADF Z-matrix
atoms z-matrix c c1 h1 h1 h2 h2 cc2 2 hc3 2 3 hc3 1 3 hc3 1 3 hc3
hcc3 hcc3 hcc3 hcc3
180.000 0.000 -180.00
cc2 hc3 hcc3
0.665676 1.237739 1.237787 -0.665676 -1.237739 -1.237787 0.700000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Total atomic charges: 1 1 C -0.286170 2 H 0.143082 3 H 0.143087 4 C -0.286170 5 H 0.143082 6 H 0.143087 7 Bq 0.000000 Sum of Mulliken charges= 0.00000
1 cc2 1 hc3 1 hc3 2 hc3 2 hc3 2 hcc3 2 hcc3 1 hcc3 1 hcc3
3 180.000 3 0.000 3 -180.00
cc2 hc3 hcc3
1.400000 1.089000 120.000
Gamess z-matrix
zmat angstroms c c 1 cc2 h 1 hc3 2 hcc3 h 1 hc3 2 hcc3 h 2 hc3 1 hcc3 h 2 hc3 1 hcc3 variables cc2 1.400000 hc3 1.089000 hcc3 120.000 constants end
Massage with Ghost amtos
Ghost atoms may also be used for a counterpoise calculation for an estimate of the magnitude of BSSE, counterpoise corrections provide only a crude estimate and not an upper bound on the error). A counterpoise correction can be achieved by specifying the dimer structure with the atomic symbol for one monomer replaced by a ghost atom. Since ghost atoms have no basis functions by default, they must be explicitly added via the ExtraBasis facility or a general basis set. See also the discussion of Massage in the manual.
Fra Baidu bibliotek
3 180.000 3 0.000 3 -180.00
Mopac Z-matrix
SYMMETRY
C C H H H H 0.000000 0 1.400000 1 1.089000 1 1.089000 0 1.089000 0 1.089000 0 4 4 5 5 6 6 0.000000 0 0.000000 0 0 0 0 0.000000 0 0.000000 0 1 0 0 120.000000 1 0.000000 0 1 2 0 120.000000 0 180.000000 0 1 2 3 120.000000 0 0.000000 0 2 1 3 120.000000 0 -180.000000 0 2 1 3
Massage
The Massage keyword requests that the molecule specification and basis set data be modified after it is generated. The standard basis functions are assigned to atoms before Massage alterations take place, while the number of electrons is computed from the atomic numbers after the modifications.