本文的例子是我们在研究鬼箭羽时发现的一个新化合物，当时其绝对构型采用经验规则与已知绝对构型的进行比较来确定的，发表在Natural Product Research上。后来，我们采用量化计算的方式，同样的确定了该化合物的绝对构型，下面详细的笔记，与诸位分享。Gaussian模拟溶剂下的ECD光谱
该化合物的英文名我们定为catechin lactone A (CLA)，其化学结构和甲醇中实测CD光谱如下：
CLA的2，3位为手性中心，通过它们在氢谱中的耦合常数，可知2,3位的两个氢处于对位，因此CLA可能为(2R,3S)和(2S,3R)两种绝对构型。下面详细说明具体的步骤：
1. 首先在gaussview中将构建CLA的3D分子模型，并对其结构进行优化。
这个化合物有两个手性中心，分别为图中箭头所指的位置。事先已经得知OH和Ar的朝向相反，所以若连接Ar的手性碳为S构型，则连接OH的手性碳为R，称为情况1.若连接Ar的手性碳为R构型，则连接OH的手性碳为S构型，称为情况2.
在情况1下，构建的输入文件如下：
%nprocshared=16
%mem=32GB
%chk=/home/xs/yjh/cdtry2-1C.chk
# opt freq b3lyp/6-31g(d) scrf=(solvent=methanol)[No Title]
0 1
C -5.55628238 -1.31201768 0.41502838
C -5.49337448 -2.68989041 0.66771390
C -4.26766705 -3.36415459 0.60073789
C -3.09945710 -2.66258202 0.28120647
C -3.13176688 -1.26596279 0.14496384
C -4.36150486 -0.59503739 0.20799081
C -1.78779957 -3.42132119 0.06524691
C -0.60584820 -2.48940164 0.34186691
C -0.79125907 -1.23039583 -0.51813155
O -1.92754854 -0.49268059 -0.03099656
C -4.39446030 0.92949183 0.07457510
C -3.23488067 1.65664195 -0.22206940
C -3.28962707 3.05618841 -0.28271823
C -4.50192220 3.71953238 -0.04168854
C -5.65965114 2.98056177 0.24103719
C -5.59961760 1.58146545 0.27783860
O -6.85529518 -0.68189906 0.36430910
O -4.21166207 -4.77166494 0.84711722
O 0.60690589 -3.16358866 -0.00397741
C 0.45578307 -0.33296230 -0.41278679
C 0.82247778 0.48633577 -1.48902081
C 1.95726104 1.30305033 -1.39304324
C 2.72538924 1.30037579 -0.22093011
C 2.35872770 0.48108566 0.85525942
C 1.22393132 -0.33559747 0.75935590
O 3.88338530 2.13368389 -0.12309114
O 2.33143775 2.13918630 -2.49114241
C -6.85745230 0.74511248 0.55131655
O -2.11109688 3.80653057 -0.58766669
O -4.55731531 5.14779257 -0.08560301
O -7.91114496 1.31777015 0.93254772
H -6.38644560 -3.22981737 0.90394351
H -1.74041869 -4.27570438 0.70763311
H -1.74454076 -3.73940199 -0.95547319
H -0.57132605 -2.20966978 1.37407495
H -0.93686365 -1.51839788 -1.53829856
H -2.31102127 1.14659716 -0.39885433
H -6.58600125 3.48335631 0.42524492
H -3.49551023 -5.15753079 0.33735143
H 1.35305317 -2.57983490 0.15130380
H 0.23604138 0.48831139 -2.38399703
H 2.94521767 0.47909963 1.75018541
H 0.94400497 -0.96116465 1.58107971
H 4.52697928 1.72039032 0.45711910
H 3.28440708 2.25496928 -2.49499921
H -2.15682246 4.66330899 -0.15696865
H -5.23756687 5.46029692 0.51540498
优化结果如下：
显示没有虚频。对于情况2，构建的输入文件如下：
%nprocshared=16
%mem=32GB
%chk=/home/xs/yjh/cdtry2-2C.chk
# opt freq b3lyp/6-31g(d) scrf=(solvent=methanol) geom=connectivity[No Title]
0 1
C 1.96153200 2.04911400 -0.68088800
C 1.24956400 3.22899400 -0.85887800
C -0.03616800 3.31847700 -0.34459600
C -0.62178700 2.23979000 0.34306100
C 0.11800100 1.06107900 0.48424000
C 1.44490700 0.91943500 -0.01243900
C -2.00876700 2.36236400 0.93457000
C -2.24597300 1.30728000 2.00915700
C -1.79295800 -0.06621900 1.48367000
O -0.40900700 -0.03228300 1.12024800
C 2.30851000 -0.26399000 0.10246000
C 1.95830100 -1.46718700 0.75073800
C 2.84228100 -2.53479000 0.81155200
C 4.12082200 -2.44372200 0.22250000
C 4.49024500 -1.28035100 -0.41525200
C 3.59939000 -0.19452800 -0.47909400
O 3.21971000 2.06973900 -1.22680600
O -0.69722600 4.49555100 -0.54221000
O -1.49404300 1.70223200 3.14697400
C -2.67552100 -0.60522000 0.36571100
C -4.01762100 -0.90358700 0.65298100
C -4.86311200 -1.39840400 -0.33269000
C -4.36515400 -1.60648600 -1.63168900
C -3.03652500 -1.32570500 -1.92005700
C -2.18946400 -0.82814800 -0.92331300
O -5.28297900 -2.09887400 -2.53182700
O -6.16214600 -1.68364700 -0.03663600
C 4.08404100 1.00064000 -1.17177200
O 2.46983900 -3.67721100 1.44653800
O 4.90268600 -3.56880200 0.34999300
O 5.17093300 1.12642600 -1.69394900
H 1.69757500 4.06044900 -1.38856800
H -2.14357100 3.34041500 1.41701700
H -2.78560500 2.26258600 0.16395800
H -3.31847500 1.25624200 2.24630200
H -1.81798800 -0.77818700 2.32023600
H 0.99523000 -1.58752200 1.21898500
H 5.46626100 -1.16770400 -0.87910500
H -1.58275100 4.44227100 -0.15286500
H -1.51644400 0.98227700 3.79708000
H -4.42794600 -0.76997800 1.65024700
H -2.65268300 -1.49813900 -2.92376100
H -1.15098900 -0.63053000 -1.15851700
H -4.85524000 -2.24543700 -3.38885000
H -6.57687400 -2.03039500 -0.84536900
H 3.21555000 -4.30002200 1.39055800
H 5.76455000 -3.41436700 -0.06578900结果显示：
显示没有虚频
2. 然后，我们会对优化完的化合物进行ECD的模拟，我们采用的是TD-SCF的方法来模拟ECD光谱。
对于情况1：
输入文件如下，其中Nstates=M代表计算M个电子态，Root=N，指定感兴趣的态计算广义密度（通俗点，就是优化第N个激发态）。默认是第一激发态（N=1）。而Symm=Loose代表对对称性要求很宽松，大分子经常有多个低频振动模式，因此用 DFT 对其进行优化时，使用精密的 DFT 积分网格（Int=UltraFine）往往会更可靠。
%nprocshared=16
%mem=32GB
%chk=/home/xs/yjh/cdtry2-1C-sTD311r19.chk
#p TD=(Nstates=19,Root=19) B3LYP/6-311g(d,p) scrf=(solvent=methanol) SCF=Tight Symm=Loose Int=UltraFine[No Title]
0 1
C -3.09104200 1.53663300 0.02701200
C -3.04328600 2.92488500 0.03403500
C -1.80361300 3.55167300 0.00485500
C -0.61165600 2.80330200 -0.04205100
C -0.70232400 1.40589600 -0.01937000
C -1.94811600 0.71367200 0.01002600
C 0.72561700 3.50792100 -0.13955400
C 1.85317000 2.54659000 -0.49594300
C 1.68103300 1.24913900 0.31477000
O 0.42658900 0.63611600 -0.04853800
C -2.14898700 -0.74075200 0.03176400
C -1.11586000 -1.70095700 0.03070500
C -1.39798800 -3.05958700 0.05449100
C -2.73294900 -3.52324900 0.07809400
C -3.76155100 -2.60620300 0.07919900
C -3.48279400 -1.22583600 0.05718600
O -4.36533600 1.01909100 0.05137100
O -1.80721200 4.91387300 0.00910000
O 3.07633100 3.19614000 -0.18624400
C 2.78191300 0.24602100 0.06414800
C 3.86185500 0.17234100 0.95713000
C 4.92141000 -0.69700000 0.71442600
C 4.90732600 -1.51132600 -0.43288500
C 3.83811000 -1.44361300 -1.32147900
C 2.78122100 -0.56179400 -1.07878800
O 5.99482800 -2.33449900 -0.57136000
O 5.96411000 -0.76128000 1.59288000
C -4.63134800 -0.32701900 0.06310400
O -0.37482900 -3.95203000 0.05392500
O -2.87027400 -4.88440800 0.09797900
O -5.80413300 -0.65816300 0.07916200
H -3.95896000 3.50314700 0.06209700
H 0.69135500 4.30232900 -0.89719700
H 0.98911600 3.98727800 0.81450700
H 1.80336000 2.28428600 -1.56317600
H 1.64719200 1.51118500 1.38074100
H -0.07988800 -1.40223100 0.01321400
H -4.79819600 -2.92713000 0.09748800
H -0.89989700 5.25573500 0.04608000
H 3.79922600 2.60973500 -0.46578700
H 3.88677000 0.78245400 1.85554500
H 3.83190400 -2.07847900 -2.20412000
H 1.95067700 -0.51741300 -1.77527000
H 5.91087300 -2.86962400 -1.37681700
H 6.59210300 -1.42562600 1.25737300
H -0.75771600 -4.84803200 0.07281700
H -3.80935600 -5.13074600 0.11104700
运行的结果用gausssum读取，选择波长210~400nm，sigm=0.34
对比上面的实测CD图谱，显然不是此构型。
对于情况2：
输入文件如下：
%nprocshared=16
%mem=32GB
%chk=/home/xs/yjh/cdtry2-2C-s311TDr19.chk
#p TD=(Nstates=19,Root=19) B3LYP/6-311g(d,p) scrf=(solvent=methanol) SCF=Tight Symm=Loose Int=UltraFine[No Title]
0 1
C 2.02941600 2.03592800 -0.66065800
C 1.34821400 3.23218800 -0.84363100
C 0.05040800 3.34216200 -0.35832100
C -0.57011000 2.26987800 0.30864100
C 0.14105700 1.07269500 0.45222300
C 1.47762000 0.90958500 -0.01937500
C -1.96533200 2.41055400 0.87658100
C -2.22330000 1.37200700 1.96197500
C -1.80052500 -0.01762300 1.45473100
O -0.41510400 -0.01184800 1.06670900
C 2.31339600 -0.29226200 0.09561300
C 1.91905200 -1.49758600 0.71334000
C 2.77579900 -2.58729500 0.77715800
C 4.07395800 -2.52271000 0.22247100
C 4.48654100 -1.35631100 -0.38457300
C 3.62241500 -0.24608100 -0.45210600
O 3.30600900 2.03322000 -1.17459300
O -0.57706400 4.53508400 -0.55928700
O -1.45862500 1.75386200 3.10058300
C -2.70031900 -0.56160500 0.35449400
C -4.02859800 -0.88545600 0.67964100
C -4.89452700 -1.38198900 -0.28731000
C -4.43733800 -1.56887000 -1.60588600
C -3.12173900 -1.26201200 -1.93111500
C -2.25355200 -0.76144100 -0.95294300
O -5.37342600 -2.06513200 -2.47770100
O -6.18166700 -1.69381400 0.04553200
C 4.14242500 0.94794900 -1.10851700
O 2.35696100 -3.72860100 1.38175400
O 4.81389900 -3.66646300 0.35215100
O 5.24958200 1.07242200 -1.60287200
H 1.82342400 4.05954000 -1.35669400
H -2.10438600 3.39830200 1.33411600
H -2.72779900 2.30365200 0.09420600
H -3.29373900 1.34691800 2.20205700
H -1.82145100 -0.71246900 2.30229300
H 0.93996100 -1.60085700 1.15234200
H 5.47812700 -1.27122100 -0.81792500
H -1.49200700 4.49211000 -0.23919900
H -1.65216600 1.12706400 3.81686600
H -4.40572700 -0.76698600 1.69194700
H -2.76786400 -1.41656900 -2.94753000
H -1.22706800 -0.54302500 -1.22232100
H -4.98014600 -2.19294000 -3.35585500
H -6.61763800 -2.03661700 -0.75488500
H 3.08333500 -4.37671100 1.33573300
H 5.69084000 -3.55025000 -0.04795300结果用gausssum查看，选择波长210~400nm，sigm=0.34结果如下：
对比实测图谱，发现所有峰形轮廓基本吻合，在260nm左右都具有最突出的峰。证明化合物连接Ar的手性碳为R构型，则连接OH的手性碳为S构型（即我们文章中报道的(2R, 3S)构型）
在做ECD模拟的时候，要采用多种基组6-31G（d），6-311（d,p）等，要摸索Nstate和Root的具体数值，还要在gausssum中查看时，改变sigma等参数，直到找到与实验结果最吻合的图谱。
张老师：
认真的读了，有所了解，只是高斯的计算过程还是不清楚，感觉很难，不过得到的结果还是可靠的
一开始就照猫画虎，多尝试，多了自然有所悟。