HyperChem作图

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.。

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。

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。

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。

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。

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？。

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。