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daidai~

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[求助] Gaussian 09 中溶剂化的荧光发射

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在Gaussian 09 的计算荧光发射考虑了溶剂化效应的算例中（如下所示），在7步计算中，各自读取的chk文件分别是哪个啊？还有就是具体的“平衡溶解”和“非平衡溶解”是什么意思？

谢谢指导，苦恼了好几天的一个问题了，拿出来大家讨论一下
Fluoresence example: Emission (Fluorescence) from First Excited State (n→π*) of Acetaldehyde

Here we study the cycle:


Acetaldehyde Excitation and Emission Cycle

The primary process of interest is the emission, but this example shows how to study the complete cycle including the solvent effects.
Step 1: Ground state geometry optimization and frequencies (equilibrium solvation). This is a standard Opt Freq calculation on the ground state including PCM equilibrium solvation.

%chk=01-ac
# B3LYP/6-31+G(d,p) Opt Freq SCRF=(Solvent=Ethanol)

Acetaldehyde ground state

0 1
C
C,1,RA
X,2,1.,1,A
O,2,RB,3,A,1,180.,0
X,1,1.,2,90.,3,0.,0
H,1,R1,2,A1,5,0.,0
H,1,R23,2,A23,5,B23,0
H,1,R23,2,A23,5,-B23,0
H,2,R4,1,A4,3,180.,0

RA=1.53643
RB=1.21718
R1=1.08516
R23=1.08688
R4=1.10433
A=62.1511
A1=110.51212
A23=109.88119
A4=114.26114
B23=120.56468

Step 2: Vertical excitation with linear response solvation. This is a TD-DFT calculation of the vertical excitation, therefore at the ground state equilibrium geometry, with the default solvation: linear response, non-equilibrium. We perform a single-point TD-DFT calculation, which defaults to non-equilibrium solvation. The results of this job will be used to identify which state or states are of interest and their ordering. These results give a reasonable description of the solvation of the excited state, but not quite as good as that from a state-specific solvation calculation. In this case, we see that the n->π* state is the first excited state. Next, we will use the state-specific method to produce a better description of the vertical excitation step.

%chk=02-ac
# B3LYP/6-31+G(d,p) TD=NStates=6 SCRF=(Solvent=Ethanol)
  Geom=Check Guess=Read

Acetaldehyde: linear response vertical excited states

0 1

Step 3: State-specific solvation of the vertical excitation. This will require two job steps: first the ground state calculation is done, specifying NonEq=write in the PCM input section, in order to store the information about non-equilibrium solvation based on the ground state. Second, the actual state-specific calculation is done, reading in the necessary information for non-equilibrium solvation using NonEq=read.

%chk=03-ac
# B3LYP/6-31+G(d,p) SCRF=(Solvent=Ethanol,Read)
  Geom=Check Guess=Read

Acetaldehyde: prepare for state-specific non-eq solvation
by saving the solvent reaction field from the ground state

0 1

NonEq=write

--link1--
%chk=03-ac
# B3LYP/6-31+G(d,p) TD(NStates=6,Root=1)
  SCRF=(Solvent=Ethanol,StateSpecific,Read)
  Geom=Check Guess=Read

Acetaldehyde: read non-eq solvation from ground state and
compute energy of the first excited with the state-specific method

0 1

NonEq=read

Step 4: Relaxation of the excited state geometry. Next, we perform a TD-DFT geometry optimization, with equilibrium, linear response solvation, in order to find the minimum energy point on the excited state potential energy surface. Since this is a TD-DFT optimization, the program defaults to equilibrium solvation. As is typical of such cases, the molecule has a plane of symmetry in the ground state but the symmetry is broken in the excited state, so the ground state geometry is perturbed slightly to break symmetry at the start of the optimization.

%chk=04-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) SCRF=(Solvent=Ethanol)
  Geom=Modify Guess=Read Opt=RCFC

Acetaldehyde: excited state opt
Modify geometry to break Cs symmetry
since first excited state is A"

0 1

4 1 2 3 10.0
5 1 2 7 -50.0

Step 5: Vibrational frequencies of the excited state structure. Now we run a frequency calculation to verify that the geometry located in step 4 is a minimum. The results could also be used as part of a Franck-Condon calculation if desired (see below). This is a numerical frequency calculation.

%chk=05-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) Freq
  SCRF=(Solvent=Ethanol) Geom=Check Guess=Read

Acetaldehyde excited state freq

0 1

Step 6: Emission state-specific solvation (part 1). This step does state-specific equilibrium solvation of the excited state at its equilibrium geometry, writing out the solvation data for the next step via the PCM NonEq=write input.

%chk=06-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1)
  SCRF=(Solvent=Ethanol,StateSpecific,Read)
  Geom=Check Guess=Read

Acetaldehyde emission state-specific solvation
at first excited state optimized geometry

0 1

NonEq=write

Step 7: Emission to final ground state (part 2). Finally, we compute the ground state energy with non-equibrium solvation, at the excited state geometry and with the static solvation from the excited state.

%chk=07-ac
# B3LYP/6-31+G(d,p) SCRF=(Solvent=Ethanol,Read) Geom=Check Guess=Read

Acetaldehyde: ground state non-equilibrium
at excited state geometry.

0 1

NonEq=read
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1楼2011-08-23 15:22:51
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hairan

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youzhizhe(金币+3, 1ST强帖+1): 谢谢交流。 2011-08-25 23:38:45
我分析了一下那几步的计算，的确第6步需要第4步的chk
第3步使用第1或第2步的都行
第6步和第7步计算是和第3步的两个计算相对应，只不过第6/7步是发射，第3步是激发，第6/7两步得到的能量之差就是经过指定态的溶剂化效应校正之后的荧光发射能量，经过转换可以得到荧光的发射波长。

关于平衡和非平衡的问题是和statespecific计算有着不可分的关系的，你可以看一下下面的英文部分，这是我前一段时间从Gaussian官方技术顾问那里得到的详细解释，几句话精练不出来，翻译也要耗费一段时间，你耐心读一读。

另外，如果你是用的是Gaussian 09 A.01或者A.02，请使用ExternalIteration或者SelfConsistent代替Statespecific选项，因为后者有点问题，如果是G09 B.01，用这三个选项之一都行，意义相同。

===========================================
The "StateSpecific" approach in this context applies to the excited state, and yes it involves solving self-consistently the "fast" component of the solvent polarization for the target state and non-equilibrium solvation for the "slow" component of the solvent polarization (i.e. the "slow" component of the solvent polarization comes from the origin state).

The total polarization is always partitioned into two components, "slow" and "fast". The "slow" part can be regarded as the reorganization of the solvent molecules as a response to a change in the electronic density of the solute. The "fast" part can be regarded as the response of the electrons in the solvent to a change in the electronic density of the solute. For a change in the electronic density of the solute such as a vertical electronic transition, the "slow" component of the polarization is much slower than the timescale of the electronic transition, so the solvent does not have time to respond in this way to the vertical electronic transition. The "fast" component of the polarization, on the other hand, is closer in timescale to the vertical electronic transition on the solute.

In an equilibrium solvation calculation, both components are in equilibrium with the solute's density. By default, all ground state calculations assume equilibrium solvation, as well as geometry optimizations of excited states (and also any calculation that involves the computation of the relaxed density of the excited state). Again, in equilibrium solvation processes, both the "slow" and "fast" component of the solvent polarization are in equilibrium with the excited state density.

In the case of a TD energy calculation (no excited state density or geometry optimization) for the computation of a vertical electronic excitation, the default is to do a non-equilibrium process. For this case then, the "fast" component of the polarization "responds" to the change in the solute density from ground to excited state, but the "slow" component did not have time to "respond" so it still comes from the one that was in equilibrium with the solute's ground state density. This is the case of both "Step 2" and "Step 3" in the example shown in the manual.

In "Step 2", an energy calculation using TD is performed, thus it defaults to non-equilibrium solvation. The solvation effects on the excited states energies are computed by means of a linear response approach. The absorption energies via the linear response approach only are those reported directly in the output of this "Step 2" job.

In "Step 3", a step further is taken and a correction of the linear response excitation energy is performed by solving the "fast" component of the solvent polarization self-consistently with the selected excited state density (the "State-Specific" approach). This is generally an improvement over the excitation energies obtained by linear response alone. Note that since this "State-Specific" approach involves the calculation of the excited state density, the program would default to doing an equilibrium solvation calculation on the excited state. However, the goal of "Step 3" is to compute the vertical excitation energy, so as mentioned above, we would like to use the "slow" component of the solvent polarization from the ground state calculation (in "Step 3", the first part does an equilibrium calculation on the ground state saving the solvent reaction field to the checkpoint file) and solving self-consistently the "fast" component with the excited state density (the second part of "Step 3" reads the reaction field from the checkpoint file, the one from the ground state calculation, keeps the "slow" component as is, and solves the "fast" component self-consistently with the excited state density). The absorption energy via the "State-Specific" approach is the energy difference between the excited state energy after all PCM corrections from the non-equilibrium calculation in "Step 3" and the ground state energy resulting from the equilibrium process (either first part of "Step 3" or final, optimized geometry, energy from "Step 1", the two ground state energies should be the same).

In a TD geometry optimization of an excited state, since one is looking for the equilibrium geometry, the default is to do equilibrium solvation, so the two components, "slow" and "fast", of the polarization are in equilibrium with the solute's excited state density. All "Step 4", "Step 5" and "Step 6" use equilibrium solvation for the selected excited state.

The emission energy (vertical energy of the excited to ground state transition) by means of a linear response approach can be found in the output of "Step 4". For the final (optimized) geometry in "Step 4", the "excitation energy" shown in this output would be equal to the emission energy since it is the result of an equilibrium calculation on the selected excited state.

"Step 6" and "Step 7" are analogous to the two parts of "Step 3" but this time for the opposite transition (excited to ground states). Thus, "Step 6" is analogous to the first part of "Step 3", it is an equilibrium calculation on the origin state (now the excited state) in which both "slow" and "fast" components of solvent polarization are solved self-consistently with the excited state density (this calculation can be regarded as a correction of the excited state energy beyond the linear response approach, which was done in "Step 4". Now, this "Step 6" saves the solvent reaction field to the checkpoint file. "Step 7" reads this information from the file (just like the second part of "Step 3" and performs a non-equilibrium calculation of the ground state energy, using the "slow" component of the solvent polarization from the excited state calculation ("Step 6" and only doing the "fast" component of the solvent polarization self-consistent with the ground state density. The emission energy via the "State-Specific" approach would be the energy difference between the excited state energy after all PCM corrections from "Step 6" and the ground state energy resulting from the non-equilibrium process in "Step 7".
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据权威报纸调查，84%的青少年犯罪者有玩电子游戏的经历，故应该禁止经营电子游戏。据我们所知，100%的青少年犯罪者有穿鞋的经历，故制鞋厂应该停业。
5楼2011-08-25 11:25:18
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hairan

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瞌睡木虫

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★ ★ ★
daidai~(金币+5): 很感谢您的解答，使我明白了很多，我把算例再做一遍，呵呵 2011-08-24 09:12:31
youzhizhe(金币+3, 1ST强帖+1): 谢谢交流。 2011-08-24 10:30:03
每一步计算分别使用前一步计算保存的chk文件，所以从第二个计算开始时，你需要手动将前一个计算chk文件复制一下，名字为新的计算的chk文件名。

关于平衡性和费平衡性计算主要是涉及使用溶剂模型的激发态计算，具体区分如下。
SCRF计算中，溶质被激发时，溶剂会由于溶质的状态变化而被极化，其电子分布被改变，这是一个很快的过程，同时溶质分子需要适应这种改变(比如进行转动、平动等)，但这是一个很慢的过程。此时计算就分为两种：
平衡性计算：溶剂和溶质有足够的时间响应变化，调整到比较平衡的状态；激发态的几何优化及使用了ExternalIteration技术的计算默认使用平衡性计算。
非平衡性计算：近似描述因过程太快（比如电子的垂直激发）使溶剂没时间进行响应。激发态的单点计算默认使用非平衡性计算。
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据权威报纸调查，84%的青少年犯罪者有玩电子游戏的经历，故应该禁止经营电子游戏。据我们所知，100%的青少年犯罪者有穿鞋的经历，故制鞋厂应该停业。
2楼2011-08-23 18:07:34
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普通回帖

xzxueren

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学习了
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3楼2011-08-24 10:13:11
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daidai~

铁虫 (小有名气)
引用回帖:
2楼: Originally posted by hairan at 2011-08-23 18:07:34:
每一步计算分别使用前一步计算保存的chk文件，所以从第二个计算开始时，你需要手动将前一个计算chk文件复制一下，名字为新的计算的chk文件名。

关于平衡性和费平衡性计算主要是涉及使用溶剂模型的激发态计算， ...

还行向您咨询一下，就是第5部只是激发态的频率分析计算，起辅助作用，所以，第6步是不是应该读取的是第4步的chk文件？
相应的，第3步是不是应该先读第1步的chk文件，因为它前半部分进行的是基态的非平衡单点计算，说是保存了非平衡的溶剂反应场，这一点也不是很明白，求解答。
第6步和7步具体是什么关系？第6步已经做了激发态的发射，第7步做的是激发态结构的单点吗？6和7合起来好像和步骤3的两部分是相照应的，真的是晕了

谢谢，苦恼了好多天，解决后不胜感激
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4楼2011-08-24 10:18:13
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hairan

木虫 (著名写手)

瞌睡木虫
那几个脸型处没有遗漏信息，对应了括回的括号）
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据权威报纸调查，84%的青少年犯罪者有玩电子游戏的经历，故应该禁止经营电子游戏。据我们所知，100%的青少年犯罪者有穿鞋的经历，故制鞋厂应该停业。
6楼2011-08-25 11:28:27
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daidai~

铁虫 (小有名气)
引用回帖:
6楼: Originally posted by hairan at 2011-08-25 11:28:27:
那几个脸型处没有遗漏信息，对应了括回的括号）

太谢谢您了！！
我要仔细读读，把这个问题彻底解决了
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7楼2011-08-26 09:30:24
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xzxueren

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受用呀，学习
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8楼2011-08-31 09:13:52
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Illusionist

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送鲜花一朵
新手，有一个问题不明白，就是第四步进行结构优化，里面说到要打破对称性，
是不是就是最后
“4 1 2 3 10.0
5 1 2 7 -50.0”
但是这个怎么确定呢？
先在此谢过·

%chk=04-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) SCRF=(Solvent=Ethanol)
  Geom=Modify Guess=Read Opt=RCFC

Acetaldehyde: excited state opt
Modify geometry to break Cs symmetry
since first excited state is A"

0 1

4 1 2 3 10.0
5 1 2 7 -50.0
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9楼2011-11-28 23:55:37
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Illusionist

银虫 (正式写手)
引用回帖:
2楼: Originally posted by hairan at 2011-08-23 18:07:34:
每一步计算分别使用前一步计算保存的chk文件，所以从第二个计算开始时，你需要手动将前一个计算chk文件复制一下，名字为新的计算的chk文件名。

关于平衡性和费平衡性计算主要是涉及使用溶剂模型的激发态计算， ...

新手，有一个问题不明白，就是第四步进行结构优化，里面说到要打破对称性，
是不是就是最后
“4 1 2 3 10.0
5 1 2 7 -50.0”
但是这个怎么确定呢？
先在此谢过·

%chk=04-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) SCRF=(Solvent=Ethanol)
  Geom=Modify Guess=Read Opt=RCFC

Acetaldehyde: excited state opt
Modify geometry to break Cs symmetry
since first excited state is A"

0 1

4 1 2 3 10.0
5 1 2 7 -50.0
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10楼2011-11-29 12:42:52
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