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单击此处编辑母版标题样式,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,*,数据形式：,构建分子模型,创建数据方法：,直角坐标,(Cartesian Coordinate),内坐标,(Internal Coordinate or Z-matrix),手工建立,利用工具软件,如,Chem3D,X-ray,衍射晶体数据,数据形式：,直角坐标,(Cartesian Coordinate),例,乙烯的直角坐标文件格式,(*.xyz),6,C 0.000000 0.000000 0.000000,C 0.000000 0.000000 1.335000,H 0.943102 0.000000 -0.544500,H 0.943102 0.000000 1.879500,H -0.943102 0.000000 1.879500,H -0.943102 0.000000 -0.544500,文件格式,(syntax),：,Label,x,y,z,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。,原子标号，原子,1,，键长，原子,2,，键角，原子,3,，二面角,文件格式,(syntax),：,Label,，,Atom 1,，,Bond-length,，,Atom2,，,Bond-angle,，,Atom3,，,Dihedral-angle,(Torsion angle),常见内坐标文件,:,Note:,0,o,Bond-angle 180,o,-180,o,Dihedral-angle,180,o,Gaussian(.,gjf,),Gamess(.inp,),ADF,Mopac(.mop,.,dat,),Gaussian Z-matrix,c,c 1 cc2,h 1 hc3 2 hcc3,h 1 hc3 2 hcc3 3 180.000,h 2 hc3 1 hcc3 3 0.000,h 2 hc3 1 hcc3 3-180.00,cc2 1.400000,hc3 1.089000,hcc3 120.000,Gamess,z-matrix,zmat,angstroms,c,c 1 cc2,h 1 hc3 2 hcc3,h 1 hc3 2 hcc3 3 180.000,h 2 hc3 1 hcc3 3 0.000,h 2 hc3 1 hcc3 3-180.00,variables,cc2 1.400000,hc3 1.089000,hcc3 120.000,constants,end,Mopac,Z-matrix,SYMMETRY,C 0.000000 0 0.000000 0 0.000000 0 0 0 0,C 1.400000 1 0.000000 0 0.000000 0 1 0 0,H 1.089000 1 120.000000 1 0.000000 0 1 2 0,H 1.089000 0 120.000000 0 180.000000 0 1 2 3,H 1.089000 0 120.000000 0 0.000000 0 2 1 3,H 1.089000 0 120.000000 0-180.000000 0 2 1 3,3,1,4,3,2,4,3,1,5,3,2,5,3,1,6,3,2,6,ADF Z-matrix,atoms z-matrix,c,c 1 cc2,h 1 2 hc3 hcc3,h 1 2 3 hc3 hcc3 180.000,h 2 1 3 hc3 hcc3 0.000,h 2 1 3 hc3 hcc3 -180.00,cc2 1.400000,hc3 1.089000,hcc3 120.000,end,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。,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.,#P B3LYP/6-31G*GFINPUT IOP(6/7=3)TEST,Example of NBO bond orders,0 1,C 0.000000 0.665676 0.000000,H 0.919278 1.237739 0.000000,H -0.919239 1.237787 0.000000,C 0.000000 -0.665676 0.000000,H -0.919278 -1.237739 0.000000,H 0.919239 -1.237787 0.000000,Gh,0.700000,0.700000,0.000000,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,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,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.,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.,#HF/6-31G*Massage Test,HF+H2O interaction energy:HF removed,0 1,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,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,Note,：,http:/ 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,
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