分子模拟综合实验打印版

1、综合实验报告2011301040057化基三班杨丽引言：为了复习本学期所学过的一些分子模拟实验的基本操作，我运用在分子模拟实验课堂上学 习到的理论原理和计算方法试着对Diels-Alder反应进行了理论上的研究。选取的是最常规的乙烯 与丁二烯的D-A反应。通过对D-A反应的从头算模拟，我更加系统的理解和掌握了分子模拟的基 本原理及方法；初步学会了如何应用化学计算软件处理实际化学问题。实验内容：一、反应物和产物的电子结构为了探究乙烯与丁二烯电子结构对反应的影响，我采用了 Chem3D中的“surface”模块对反应物及产物作了分 子轨道模拟、静电势模拟以及总电子密度模拟。结果与分析如下。乙烯GA

2、MESS Job: Minimize (Energy/Geometry) RHF6-31G(d)Finish energy = -48965.597501 Kcal/Mol (-78.031711 Hartrees)ChargesC -0.080 C(1) C -0.080 C(2) H 0.040 H(3)H 0.040 H(4) H 0.040 H(5) H 0.040 H(6)n r l.1HOMO= -17.645 evLUMO= -0.282 evfcM，一玲莒。是v_兰- -wdlw -.ksm M 三搭UIM5total charge density molecular elec

3、trostatic potential1,3-丁 二烯GAMESS Job: Minimize (Energy/Geometry) RHF6-31G(d)Finish energy = -97209.583899 Kcal/Mol (-154.913461 Hartrees)Wire-frameChargesC -0.114 C(1)H 0.038 H(4)H -0.115 H(7)ball-stickcylindrical bondsspacefillingC 0.004 C(2)H 0.039 H(3)H 0.004 H(5)C 0.033 C(6)C 0.033 C(8)H 0.039

4、H(9)H 0.039H(10)HOMO= -15.068 ev嗯国P酊total charge densitymolecular electrostatic potential心部耘旅n氏a:LUMO= -3.719ev环己烯GAMESS Job: Minimize (Energy/Geometry) RHF6-31G(d)Finish energy = -146221.8807 Kcal/Mol (-233.019592 Hartrees)space fillingball-stickcylindrical bondsWire-frameChargesC -0.059 C(1)C -0.0

5、82 C(5)H 0.052 H(9)H 0.040 H(13)峪-10C -0.059 C(2)H 0.030 H(6)H 0.052 H(10)C 0.040 C(14)H -0.073 H(3)H -0.082 H(7)H 0.052 H(11)H 0.040 H(15)C -0.073 C(4)C 0.030 C(8)H 0.052 H(12)H 0.040 H(16)HOMO= -14.895 ev LUMO= 1.618 evtotal charge density molecular electrostatic potential从分子轨道的对称性来看，乙烯的HOMO轨道关于镜面

6、呈对称，LUMO反对称，丁二烯的HOMO反对称，LUMO对称，环己烯HOMO对称，LUMO反对称。如果乙烯提供LUMO，T二烯提供HOMO分子轨道对称性是匹配若乙烯提供HOMO 丁二烯提供LUMO对称性也是匹配的。因此将他们的轨道能量按能级次序排列为：1.618 evLUMO-3.719evHOMO-17.645 evethylene-14.895 ev-15.068 evcyclohexenebutadiene从能级图可以看出乙烯提供LUMO，T二烯提供HOMO是能极差更小，所以更有利于加成反应。理论上环己烯 HOMO的能量应该比1,3-丁二烯的HOMO低但系由于计算误差的存在使得环己烯能级

7、能量稍高，这是由于环己 烯并不是共轭体系，因此在计算兀电子轨道时，并不完全准确，误差很大。从电性上分析，两个反应物分子在相互靠近时电性相同，互相排斥，因此不利于加成反应。综上，乙烯与丁二烯在轨道匹配性上是有利于反应的，但在电学性质上对反应不利。两者综合起来造成了乙烯 与丁二烯间的D-A反应条件比较苛刻。二、构想搜索与分子间长程相互作用为了研究乙烯分子与丁二烯分子靠近时的能量变化我首先进行了建模，再采用Chem3D中的Dihedral driver模块 探究了能量与接触面以及接触面间距离的关系。结果及分析如下。Dihedral Driver ChartConiformaitional Energ

8、y(1)丁二烯分子绕CCCC二面角转动的构象.O.O.O2.2.J.4 3 2 i oe-.目口占.岛.1卷M.o12.-180-1359Q-45045 9Q 135180CfD C B】Cf4】 fdea reeG稳定构型为 能垒一：E(-180 ) - 11.27 kcal/mol + 52.17 kcal/mol E(-90 ) = 40.90 kcal/mol 能垒二：E(0 ) - 12.80 kcal/mol+52.17 kcal/mol E(90 ) = 39.37 kcal/mol扫描3D势能面初始模型势能面图及表格12345678910122.533.544.555562-1

9、805B.2SS10.QS42.111.8542.15S2.56S2.8172.963/3433-17556.3769.7672.0751.6562.1612.56S2.8152.9573?344-17054BS9S.&342.349l.ffil2.1662.5712.8162.9573.0395-16553.4339.3032.0321.6672.1722.5742.8182.3583/346-16052.S8S9.172.0221.6742.1772.57728192.9593/347-15552.49.1032.02-2.1822.582.B22.9593.04&-15052.589D9

10、B2.0241.6872.1862.5R22.B222.S63.0413-14553.1189.1412.0331.&932.192.5S42.8232,13.0411014053.8979222.O4S1.B9B2.1932.5882.8232.9613.04111-13554.7959192.061.7032.1S52.5872.R242,13.04112-13055.6929.4222.0731.7072.1972.5882.B252.S613.04113-12556.4539182.0851.7092.1SS2.5882.8252.W23.04114-12057.0859.5932.4

11、1.712.1SS2.5SE2.B252.W23.041Ifi-11557.439.S3S2.CSS1.712.1SS2.5SS2.B242.9613.04116-11057.5019.6512.C8S1.72.1S62.5872.R242,13.04117-105572639.6272.0921.7062.1952.5862.B232.S613.04118-1005675S9.5682.0811.7012.1922.5B52,232.963.04119-S556.013S.4792.0661.6952.18S2.5B32.R212.9593.342055,S9.3BS2.04B1.BS92.

12、1852.5812.鸵2.95S3?342154.10192472.027-M2.1812.5782.8192.3583.03953.129 1262.0051.6712.1752.5752B172.9573.03923-75522619.0221.9&4i.rei2.16S2.57128152.9563.03824-7051.62383471.S651.652.1622.56728122.3543.03725-S5513168.9161.S511.6352.1552.5632.E/2.5533.03626加514D28S41.9421.6272.1462.5582.8-372.3513.03

13、527娅51.S499.031341.6142.1372.5522.S-342.553.叫428缺53.0023.1381.9471.M12.1272.5472.M12.9483.033234554.5SBS.4471.9841.5882.1172.542.7582M63.0324。567629.7841.9921.5762.1062.K42.7942.9443.031314559.511102122.031.K42.0342.5272.792.Q3.033262B3S107282.0811.5522；3B22.522.7882.943.02S33-2566.911 3272.1421.542

14、2.072.5132.7K2.9SB3.-D2834-2070.87711SB72.2111.5322.05S2.5052.7792.9363.02735-1575.4712.6S22.2871.5242.0462.4SB2.7752.334,3.02636-10793DS13.3762.3631.5162.0352.4S22.7712.3323.02537-5S4.OM14 0312.4371.&392.0242.4552.7682.S33.024380875114.S142.5051.5032.0142.4792.7652.S2S3.0233959027315.1012.5621.4S72

15、.0052.4742.7622.3273.02240109221615.4782.&3B1.4911.9972.4092.7592.9263.021411593.32515.7412.B421.48S1J9912.4652.7572.S253.021422093JB6615.S5S2.W31.4S11.SS52.4S22.7562.S243.02432593 41115.W22.6721.4761.SS12.452.7542.S233.02443092.S-3315.9522.6711.4721S792.45S2.7542.9233.0245359205115 8782.8581.41S772

16、.45S2.7532.9223.02有势能面图可得最低能量作用点为:当乙烯与丁二烯以如图所示方式相互作用时能量最低。Equationy=p1*(昭瘠 12-2*(p2)Adj. R-Sq0.97052ValueStandardC-203495.1.6248870626E8Cp2f 0.44601 J 314.0951由势能面图以及势能曲线图可得平衡距离为0.446A ,势能垒高度203495.2+(-48965.600362 - 97209.526939)=57320kcal/mol这个结果显然是不合理的，这与计算软件的精确度有极大关系，与Lennard Joness函数匹配度低，使得拟合数

17、据出现严重偏差，解决问题的最好办法是提高软件的模拟精度。断面的存在也使得拟合难度增大。三、反应途径计算：为了研究反应途径我采取了多种计算能量的方法，主要有GAMESS中 的HF/6-31G(d)和Mopac中的PM3，同时还研究了溶剂对反映的影响。(1)反应热计算乙烯：ZPF= 34.369513 KCAL/MOL H= 36.829 KCAL/MOL S= 54.843 cal/(mol K) E= -48965.600362 Kcal/MolH298K-H0k=36.829 KCAL/MOL - 34.369513 KCAL/MOL = 2.46 KCAL/MOLE(C)= -23645.

18、077286 Kcal/MolE (H) = -312.645612 Kcal/MolH f0k(C2H4)=2x169.98+4x51.63-2x(-23645.077286 Kcal/Mol)-4x(-312.645612 Kcal/Mol)+(-48965.600362 Kcal/Mol)+34.369513 KCAL/MOL =155.97KCAL/MOLHf298 k(C2H4)=155.97KCAL/MOL + 2.46 KCAL/MOL-(2x0.25+4x1.01) KCAL/MOL=153.92KCAL/MOLGf298 k(C2H4)=153.92KCAL/MOL-298.

19、15x(54.829-2x1.36-4x15.6)/100Kcal/mol=156.89kcal/mol1,3-丁 二烯ZPF= 57.272926 KCAL/MOL H= 60.264 Kcal/Mol S= 64.626 cal/(mol K) E= -97209.526939 Kcal/MolH298K-H0k=60.264 Kcal/Mol - 57.272926 KCAL/MOL =2.99 KCAL/MOLE(C)= -23645.077286 Kcal/MolE (H) = -312.645612 Kcal/MolH f0k(C4H6)=4x169.98+6x51.63-4x(-

20、23645.077286 Kcal/Mol)-6x(-312.645612 Kcal/Mol)+(-97209.526939 Kcal/Mol )+57.272926 KCAL/MOL =293.56KCAL/MOLHf298 k(C4H6)=293.56KCAL/MOL + 2.99 KCAL/MOL- (4x0.25+6x1.01) KCAL/MOL=289.49KCAL/MOLGf298 k(C4H6)=289.49KCAL/MOL-298.15x (64.626 -4x1.36-6x15.6)/100Kcal/mol=299.75kcal/mol环己烯ZPF= 98.595069 KC

21、AL/MOL H=102.418 KCAL/MOL S= 72.608 cal/(mol K) E= -146221.885759 Kcal/MolH298K-H0k=102.418 KCAL/MOL -98.595069KCAL/MOL = 3.823 KCAL/MOLE(C)= -23645.077286 Kcal/MolE (H) = -312.645612 Kcal/MolHf0k(C6H10)=6x169.98+10 x51.63-6x(-23645.077286Kcal/Mol)-10 x(-312.645612Kcal/Mol)+(-146221.88575 Kcal/Mol)+

22、 98.595069 KCAL/MOL =409.77KCAL/MOLHf298 k(C6H10)=409.77KCAL/MOL + 3.823 KCAL/MOL- (6x0.25+10 x1.01) KCAL/MOL=402.003KCAL/MOLGf298 k(C6H10)=402.003KCAL/MOL-298.15x ( 72.608 -6x1.36-10 x15.6)/100Kcal/mol=429.299kcal/mol反应的焓变为： H r,298 k=402.003KCAL/MOL-289.49KCAL/MOL-153.92KCAL/MOL= -41.4Kcal/mol焓变是负

23、值，与实验测量值(-39.61) kcal/mol相比十分相近，说明模拟计算的能量精度比较高。反应的吉布斯自由能为 G r,298 k=429.299kcal/mol-299.75kcal/mol-156.89kcal/mol= -27.34Kcal/mol说明反应是可以自发进行的。(2)反应途经计算：1、HF方法近)J过渡态(HF/6-31G(d)虚频 901.46 IGAMESS Job: Optimize to Transition State RHF6-31G (d)Finish energy = -146134.028877 Kcal/Mol (-232.879591 Hartree

24、s)2、Mopac-PM3 方法丁二烯Mopac Job: PM3 CHARGE=0 EF GNORM=0.100 SHIFT=80Finished RMS Gradient = 0.07554 ( 0.10000) Heat of Formation = 31.71404 Kcal/MolCOSMO溶剂化Mopac Job: EPS=78.39 PM3 CHARGE=0 SHIFT=80Mopac Interface: Heat of Formation = 31.05474 Kcal/Mol乙烯Mopac Job: PM3 CHARGE=0 EF GNORM=0.100 SHIFT=80F

25、inished RMS Gradient = 0.08875 ( 0.10000) Heat of Formation = 16.60853 Kcal/Mol溶剂化Mopac Job: EPS=78.39 PM3 CHARGE=0 SHIFT=80畔）53)-C(5) I1.4A顷4广 双成侦11)C(3) 2.1 AMopac Interface: Heat of Formation = 16.36709 Kcal/Mol虚频 Frequency = -911.03Mopac过渡态优化Mopac Job: PM3 CHARGE=0 GNORM=0.100 SHIFT=80 TSFinishe

26、d RMS Gradient = 0.06084 ( 0.10000) Heat of Formation = 74.63470 Kcal/Mol溶剂化Mopac Job: EPS=78.39 PM3 CHARGE=0 SHIFT=80Mopac Interface: Heat of Formation = 47.69557 Kcal/Mol环己烯Mopac Job: PM3 CHARGE=0 EF GNORM=0.100 SHIFT=80Finished RMS Gradient = 0.08605 (!a.a?-a.as -a.as -a.04 -a.as -a.02 -a.oi -i0 00 -i J-J J 1I I I I I I I I I I I I