分子模擬綜合實驗打印版

1、 綜合實驗報告 2011301040057 化基三班 楊麗引言：為了復(fù)習(xí)本學(xué)期所學(xué)過的一些分子模擬實驗的基本操作，我運用在分子模擬實驗課堂上學(xué)習(xí)到的理論原理和計算方法試著對Diels-Alder反應(yīng)進(jìn)行了理論上的研究。選取的是最常規(guī)的乙烯與丁二烯的D-A反應(yīng)。通過對D-A反應(yīng)的從頭算模擬，我更加系統(tǒng)的理解和掌握了分子模擬的基本原理及方法；初步學(xué)會了如何應(yīng)用化學(xué)計算軟件處理實際化學(xué)問題。實驗內(nèi)容：1、 反應(yīng)物和產(chǎn)物的電子結(jié)構(gòu)為了探究乙烯與丁二烯電子結(jié)構(gòu)對反應(yīng)的影響，我采用了Chem3D中的“surface”模塊對反應(yīng)物及產(chǎn)物作了分子軌道模擬、靜電勢模擬以及總電子密度模擬。結(jié)果與分析如下。乙烯GA

2、MESS Job: Minimize (Energy/Geometry) RHF/6-31G(d)Finish energy = -48965.597501 Kcal/Mol (-78.031711 Hartrees)Wire-frame ball-stick cylindrical bonds space filling 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)HOMO= -17.645 ev LUMO= -0.282 ev total charge densi

3、ty molecular electrostatic potential1,3-丁二烯GAMESS Job: Minimize (Energy/Geometry) RHF/6-31G(d)Finish energy = -97209.583899 Kcal/Mol (-154.913461 Hartrees) Wire-frame ball-stick cylindrical bonds space filling ChargesC -0.114 C(1) C 0.004 C(2) H 0.039 H(3)H 0.038 H(4) H 0.004 H(5) C 0.033 C(6)H -0.1

4、15 H(7) C 0.033 C(8) H 0.039 H(9) H 0.039 H(10)HOMO= -15.068 ev LUMO= -3.719ev total charge density molecular electrostatic potential環(huán)己烯GAMESS Job: Minimize (Energy/Geometry) RHF/6-31G(d)Finish energy = -146221.8807 Kcal/Mol (-233.019592 Hartrees) Wire-frame ball-stick cylindrical bonds space fillin

5、g ChargesC -0.059 C(1) C -0.059 C(2) H -0.073 H(3) C -0.073 C(4)C -0.082 C(5) H 0.030 H(6) H -0.082 H(7) C 0.030 C(8)H 0.052 H(9) H 0.052 H(10) H 0.052 H(11) H 0.052 H(12)H 0.040 H(13) C 0.040 C(14) H 0.040 H(15) H 0.040 H(16)HOMO= -14.895 ev LUMO= 1.618 ev total charge density molecular electrostat

6、ic potential從分子軌道的對稱性來看，乙烯的HOMO軌道關(guān)于鏡面呈對稱，LUMO反對稱，丁二烯的HOMO反對稱，LUMO對稱，環(huán)己烯HOMO對稱，LUMO反對稱。如果乙烯提供LUMO，丁二烯提供HOMO分子軌道對稱性是匹配若乙烯提供HOMO丁二烯提供LUMO對稱性也是匹配的。因此將他們的軌道能量按能級次序排列為：LUMOHOMO1.618 ev -14.895 ev-3.719ev -0.282 ev -17.645 ev -15.068 ev ethylenebutadienecyclohexene從能級圖可以看出乙烯提供LUMO，丁二烯提供HOMO是能極差更小，所以更有利于加成反

7、應(yīng)。理論上環(huán)己烯HOMO的能量應(yīng)該比1,3-丁二烯的HOMO低但系由于計算誤差的存在使得環(huán)己烯能級能量稍高，這是由于環(huán)己烯并不是共軛體系，因此在計算電子軌道時，并不完全準(zhǔn)確，誤差很大。從電性上分析，兩個反應(yīng)物分子在相互靠近時電性相同，互相排斥，因此不利于加成反應(yīng)。綜上，乙烯與丁二烯在軌道匹配性上是有利于反應(yīng)的，但在電學(xué)性質(zhì)上對反應(yīng)不利。兩者綜合起來造成了乙烯與丁二烯間的D-A反應(yīng)條件比較苛刻。2、 構(gòu)想搜索與分子間長程相互作用為了研究乙烯分子與丁二烯分子靠近時的能量變化我首先進(jìn)行了建模，再采用Chem3D中的Dihedral driver模塊探究了能量與接觸面以及接觸面間距離的關(guān)系。結(jié)果及分析

8、如下。(1)丁二烯分子繞CCCC二面角轉(zhuǎn)動的構(gòu)象穩(wěn)定構(gòu)型為能壘一：E(-180°) - 11.27 kcal/mol + 52.17 kcal/mol E(-90°) = 40.90 kcal/mol能壘二：E(0°) - 12.80 kcal/mol+52.17 kcal/mol E(90°) = 39.37 kcal/mol(2) 掃描3D勢能面初始模型勢能面圖及表格有勢能面圖可得最低能量作用點為：當(dāng)乙烯與丁二烯以如圖所示方式相互作用時能量最低。由勢能面圖以及勢能曲線圖可得平衡距離為0.446Å，勢能壘高度203495.2+(-48965.

9、600362 - 97209.526939)=57320kcal/mol這個結(jié)果顯然是不合理的，這與計算軟件的精確度有極大關(guān)系，與Lennard Joness 函數(shù)匹配度低，使得擬合數(shù)據(jù)出現(xiàn)嚴(yán)重偏差，解決問題的最好辦法是提高軟件的模擬精度。斷面的存在也使得擬合難度增大。3、 反應(yīng)途徑計算：為了研究反應(yīng)途徑我采取了多種計算能量的方法，主要有GAMESS中的HF/6-31G（d）和Mopac中的PM3，同時還研究了溶劑對反映的影響。（1）反應(yīng)熱計算乙烯：ZPF= 34.369513 KCAL/MOL H= 36.829 KCAL/MOL S= 54.843 cal/(mol K) E= -4896

10、5.600362 Kcal/MolH298K-H0K=36.829 KCAL/MOL - 34.369513 KCAL/MOL = 2.46 KCAL/MOLE(C)= -23645.077286 Kcal/MolE (H) = -312.645612 Kcal/MolHf,0k(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/MOL Hf,298 k(C2H4)=155.97KCA

11、L/MOL + 2.46 KCAL/MOL-（2x0.25+4x1.01) KCAL/MOL=153.92KCAL/MOLGf,298 k(C2H4)=153.92KCAL/MOL-298.15x（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 KCA

12、L/MOLE(C)= -23645.077286 Kcal/MolE (H) = -312.645612 Kcal/MolHf,0k(C4H6)=4x169.98+6x51.63-4x(-23645.077286 Kcal/Mol)-6x(-312.645612 Kcal/Mol)+(-97209.526939 Kcal/Mol)+57.272926 KCAL/MOL =293.56KCAL/MOLHf,298 k(C4H6)=293.56KCAL/MOL + 2.99 KCAL/MOL-（4x0.25+6x1.01) KCAL/MOL=289.49KCAL/MOLGf,298 k(C4H6)

13、=289.49KCAL/MOL-298.15x（64.626 -4x1.36-6x15.6)/100Kcal/mol=299.75kcal/mol環(huán)己烯ZPF= 98.595069 KCAL/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/MolHf,0k(C6H10)=6x

14、169.98+10x51.63-6x(-23645.077286Kcal/Mol)-10x(-312.645612Kcal/Mol)+(-146221.88575 Kcal/Mol) + 98.595069 KCAL/MOL =409.77KCAL/MOL Hf,298 k(C6H10)=409.77KCAL/MOL + 3.823 KCAL/MOL-（6x0.25+10x1.01) KCAL/MOL=402.003KCAL/MOLGf,298 k(C6H10)=402.003KCAL/MOL-298.15x（ 72.608 -6x1.36-10x15.6)/100Kcal/mol=429.2

15、99kcal/mol反應(yīng)的焓變?yōu)椋篐r,298 k=402.003KCAL/MOL-289.49KCAL/MOL-153.92KCAL/MOL= -41.4Kcal/mol焓變是負(fù)值，與實驗測量值 (-39.6±1) kcal/mol相比十分相近，說明模擬計算的能量精度比較高。反應(yīng)的吉布斯自由能為Gr,298 k=429.299kcal/mol-299.75kcal/mol-156.89kcal/mol= -27.34Kcal/mol說明反應(yīng)是可以自發(fā)進(jìn)行的。（2）反應(yīng)途經(jīng)計算：1、HF方法過渡態(tài)（HF/6-31G(d)）虛頻901.46 IGAMESS Job: Optimize

16、to Transition State RHF/6-31G（d）Finish energy = -146134.028877 Kcal/Mol (-232.879591 Hartrees)過渡態(tài) -146134.028877 Kcal/Mol 環(huán)己烯-146221.885759 Kcal/Mol乙烯(-48965.600362 Kcal/Mol)丁二烯(-97209.526939 Kcal/Mol）)勢壘高度41.1 kcal/mol比測量值高了接近8 kcal/mol差距相當(dāng)大，這說明我們的計算方法誤差很大。 2、Mopac-PM3方法丁二烯Mopac Job: PM3 CHARGE=0 E

17、F GNORM=0.100 SHIFT=80Finished RMS Gradient = 0.07554 (< 0.10000) Heat of Formation = 31.71404 Kcal/MolCOSMO溶劑化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=80Finished RMS Gradient = 0.08875 (< 0.1

18、0000) Heat of Formation = 16.60853 Kcal/Mol溶劑化Mopac Job: EPS=78.39 PM3 CHARGE=0 SHIFT=80Mopac Interface: Heat of Formation = 16.36709 Kcal/Mol虛頻 Frequency = -911.03Mopac過渡態(tài)優(yōu)化Mopac Job: PM3 CHARGE=0 GNORM=0.100 SHIFT=80 TSFinished RMS Gradient = 0.06084 (< 0.10000) Heat of Formation = 74.63470 Kca

19、l/Mol溶劑化Mopac Job: EPS=78.39 PM3 CHARGE=0 SHIFT=80Mopac Interface: Heat of Formation = 47.69557 Kcal/Mol環(huán)己烯Mopac Job: PM3 CHARGE=0 EF GNORM=0.100 SHIFT=80Finished RMS Gradient = 0.08605 (< 0.10000) Heat of Formation = -4.95460 Kcal/Mol溶劑化Mopac Job: EPS=78.39 PM3 COSMO CHARGE=0 SHIFT=80Mopac Inter

20、face: Heat of Formation = -5.47587 Kcal/Mol環(huán)己烯 -4.95460 Kcal/Mol乙烯31.05474 Kcal/Mol丁二烯16.36709 Kcal/Mol)過渡態(tài) 74.63470 Kcal/Mol勢壘高度：26.3kcal/mol與HF/6-31G(d)結(jié)果相比偏小。原因在于他們用的方法不同，PM3用的是半經(jīng)驗方法，HF/6-31G(d)用的是HF自洽場方法，按理論來說沒有一定誰的計算結(jié)果更準(zhǔn)確。但由于處理方法的不同使得給體系帶來的誤差存在差異。PM3方法偏低，而HF方法偏高。2.1 PM3加溶劑化加入溶劑化后，過渡態(tài)能量與反應(yīng)物能量十分相

21、近，所以反應(yīng)幾乎不經(jīng)過過渡態(tài)直接就生成了產(chǎn)物。所以引進(jìn)水作溶劑有利于反應(yīng)的進(jìn)行，這與水能提供質(zhì)子有關(guān)，質(zhì)子氫可以催化Diels-Alder反應(yīng)。乙烯31.71404 Kcal/Mol丁二烯 16.60853 Kcal/Mol)過渡態(tài) 74.63470 Kcal/Mol環(huán)己烯 -5.47587Kcal/Mol四、乙烯分子光譜模擬（1）為了研究乙烯的反應(yīng)活性，我用GAMESS程序中的【CIS HF/6-31G（d）】對乙烯作了紫外可見光普模擬。分析了光照對實驗的影響。C(1)C(2)C(1)1.3163H(3)C(2)1.1000C(1)120.4998H(5)C(2)1.1000C(1)120.

22、4986H(3)118.9992Pro-RH(4)C(1)1.1000C(2)120.4998H(3)179.9560DihedralH(6)C(1)1.1000C(2)120.4986H(4)118.9992Pro-RGAMESS Job: Minimize (Energy/Geometry) RHF/6-31G(d)Finish energy = -48965.601568 Kcal/Mol (-78.031718 Hartrees)單重激發(fā)態(tài)： - CI-SINGLES EXCITATION ENERGIES STATE HARTREE EV KCAL/MOL CM-1 - 1A 0.3

23、227493151 8.7825 202.5283 70835.29 1A 0.3578344452 9.7372 224.5445 78535.58 1A 0.3786428779 10.3034 237.6020 83102.51 1A 0.3802464419 10.3470 238.6083 83454.45 1A 0.3925945588 10.6830 246.3568 86164.55單重激發(fā)太態(tài)能GAMESS Job: Compute Properties CIS/6-31G(d)GAMESS Interface: Total Energy = -48763.0735 Kcal

24、/Mol單重激發(fā)太態(tài)能單重激發(fā)波長：E=-48763.0735 Kcal/Mol-（-48965.601568 Kcal/Mol）=202.5 kcal/mol=141 nm三重激發(fā)態(tài)： - CI-SINGLES EXCITATION ENERGIES STATE HARTREE EV KCAL/MOL CM-1 - 3A 0.1385838847 3.7711 86.9627 30415.65 3A 0.3344942853 9.1021 209.8984 73413.01 3A 0.3614885249 9.8366 226.8375 79337.56 3A 0.3635509739 9.

25、8927 228.1317 79790.22 3A 0.3661781521 9.9642 229.7803 80366.81三重激發(fā)態(tài)能GAMESS Job: Compute Properties CIS/6-31G(d)GAMESS Interface: Total Energy = -48878.6389 Kcal/Mol三重激發(fā)波長E= -48878.6389 Kcal/Mol -（-48965.601568 Kcal/Mol）=87 kcal/mol=328 nm C(1)C(2)C(1)1.3163H(3)C(2)1.1000C(1)120.4998H(5)C(2)1.1000C(

26、1)120.4986H(3)118.9992Pro-RH(4)C(1)1.1000C(2)120.4998H(3)179.9560DihedralH(6)C(1)1.1000C(2)120.4986H(4)118.9992Pro-RGAMESS Job: Minimize (Energy/Geometry) CIS/6-31G(d)Finish energy = 0 Kcal/Mol (0 Hartrees)由于三重態(tài)的乙烯分子能量優(yōu)化不出來，所以三重態(tài)的乙烯分子不能穩(wěn)定存在。因此確定不了絕熱激發(fā)波長。光照會使得乙烯的LUMO軌道變?yōu)橐蚁┑腍OMO光照后軌道，非光照時，乙烯與丁二烯的軌道對稱性

27、是匹配的，光照后軌道對稱性改變使得反應(yīng)更加困難，從而使得不利于反應(yīng)的進(jìn)行。（2）接著用GAMESS程序中的B3LYP/6-31G（d）對乙烯分子的紅外光譜以及拉曼光譜作了模擬GAMESS Job: Minimize (Energy/Geometry) B3LYP/6-31G(d)Finish energy = -49277.81857 Kcal/Mol (-78.529267 Hartrees) 6 7 8 9 10 FREQUENCY: 72.48 832.94 957.27 978.84 1069.70 REDUCED MASS: 1.00784 1.04365 1.52010 1.16076 1.00783IR INTENSITY: 0.00025 0.01749 0.00057 1.97372 0.00001 11 12 13 14 15 FREQUENCY: 1235.83 1406.28 1511.94 1