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戴世杰木蟲 (著名寫手)
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[交流]
用高斯09計(jì)算手冊(cè)中乙醛在乙醇溶液中的熒光光譜的問題
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參照手冊(cè)，把乙醛在乙醇溶液中的熒光光譜計(jì)算了一下，但有很多不清楚的地方，希望大家指點(diǎn)。 第一步：基態(tài)的結(jié)構(gòu)優(yōu)化和頻率（平衡溶劑化）。這是對(duì)基態(tài)包含PCM平衡溶劑化的標(biāo)準(zhǔn)Opt Freq計(jì)算。 第二步：包含線性響應(yīng)溶劑化的垂直激發(fā)。這是垂直激發(fā)的TD-DFT計(jì)算，因此在基態(tài)平衡結(jié)構(gòu)計(jì)算，使用默認(rèn)溶劑，線性響應(yīng)，非平衡溶劑化。我們進(jìn)行單點(diǎn)TD-DFT計(jì)算，這對(duì)非平衡溶劑化是默認(rèn)的。 該任務(wù)的結(jié)果將用于識(shí)別感興趣的態(tài)及其順序。 這些結(jié)果給出激發(fā)態(tài)溶劑化的合理描述，但不如特定態(tài)溶劑化計(jì)算的結(jié)果好。在本例中，我們看到n→π*態(tài)是第一激發(fā)態(tài)。下一步，我們將使用特定態(tài)方法，對(duì)垂直激發(fā)步驟產(chǎn)生更好的描述。 我的問題：1.什么是線性響應(yīng)溶劑化的垂直激發(fā)？2.什么是平衡和非平衡溶劑化 第三步：垂直激發(fā)的特定態(tài)溶劑化。這需要兩個(gè)任務(wù)步驟：首先做基態(tài)計(jì)算，為了存儲(chǔ)基態(tài)的非平衡溶劑化信息，需要在PCM輸入部分指定NonEq=write。接下來做實(shí)際的特定態(tài)的計(jì)算，需要用NonEq=read讀取非平衡溶劑化的必要信息。 我的問題：什么是特定態(tài)溶劑化？ 第四步：放松激發(fā)態(tài)結(jié)構(gòu)。接下來，我們用平衡的線性響應(yīng)溶劑化進(jìn)行TD-DFT幾何優(yōu)化，以找到激發(fā)態(tài)勢(shì)能面上的最小能量點(diǎn)。由于這是TD-DFT優(yōu)化，程序默認(rèn)為平衡溶劑化。作為這類體系的典型情況，基態(tài)具有平面對(duì)稱性，而在激發(fā)態(tài)對(duì)稱性被破壞，因此在優(yōu)化的開始對(duì)基態(tài)結(jié)構(gòu)作了略微的擾動(dòng)以打破對(duì)稱性。 第五步：激發(fā)態(tài)結(jié)構(gòu)的振動(dòng)頻率�，F(xiàn)在我們通過運(yùn)行頻率計(jì)算來確認(rèn)第四步找到的結(jié)構(gòu)是能量極小點(diǎn)。 第六步：溶液中特定態(tài)的發(fā)射（第一部分）。這一步在激發(fā)態(tài)平衡構(gòu)型計(jì)算特定態(tài)的平衡溶劑化，并通過輸入中的PCM選項(xiàng)NonEq=write，把溶劑化數(shù)據(jù)的輸出寫到文件，用于下一步計(jì)算。 第七步：到最終基態(tài)的發(fā)射（第二部分）。最后，我們用非平衡溶劑化和來自激發(fā)態(tài)的靜態(tài)溶劑化，在激發(fā)態(tài)結(jié)構(gòu)計(jì)算基態(tài)能量。 因此我總結(jié)了一下，溶液中熒光光譜的計(jì)算步驟：首先做基態(tài)結(jié)構(gòu)的平衡溶劑化;然后做基態(tài)的垂直激發(fā)，這一步是非平衡溶劑化的，用于識(shí)別感興趣的態(tài)及其順序;并接著做特定態(tài)溶劑化計(jì)算以更好地描述，首先要存儲(chǔ)基態(tài)的非平衡溶劑化信息，因?yàn)檫@個(gè)信息用來做特定態(tài)溶劑化計(jì)算;緊接著做激發(fā)態(tài)的平衡溶劑化;最后做發(fā)射就行了。之所以比氣相中復(fù)雜，主要是由于基態(tài)的垂直激發(fā)和激發(fā)態(tài)的發(fā)射都受到溶劑化作用。 附件是我計(jì)算的輸入，輸出和點(diǎn)文件 ，有什么不對(duì)的地方請(qǐng)大家指正。 |
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2014-08-17 17:32:39, 13.57 M
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hairan
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gmy1990: 金幣+5 2014-08-18 02:26:33
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我以前回復(fù)過兩次類似的問題，但找不到相關(guān)的帖子了。 下面的英文是我問Gaussian官方技術(shù)支持關(guān)于熒光計(jì)算的問題，也是基于說明書的算例的問題。 樓主耐心點(diǎn)看看下面的英文。 應(yīng)該能解決你大部分的問題。 *************************************************************************** 1. A common TD job will give the enough information of verticle excitation and emission in gas phase, but a statespecific job need to be run for that in solvation. I want to the function of the statespecific job. （這一句是我問的問題） 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".These are a few relevant references that deal with different aspects of PCM, equilibrium vs. non-equilibrium solvation, solvation effects in electronic transition calculations: - A review that covers many of the aspects of continuum solvation models (including a section in non-equilibrium): J. Tomasi, B. Mennucci and R. Cammi, "Quantum Mechanical Continuum Solvation Models," Chem. Rev., 105 (2005) 2999-3093. - A couple of early references dealing with solvation in electronic transitions: M. Cossi and V. Barone, “Solvent effect on vertical electronic transitions by the polarizable continuum model,” J. Chem. Phys., 112 (2000) 2427-35. M. Cossi and V. Barone, “Time-dependent density functional theory for molecules in liquid solutions,” J. Chem. Phys., 115 (2001) 4708-17. - A couple of references related to the State-Specific (or external iteration) treatment of solvation in electronic transitions: R. Improta, V. Barone, G. Scalmani, and M. J. Frisch, “A state-specific polarizable continuum model time dependent density functional method for excited state calculations in solution,” J. Chem. Phys., 125 (2006) 054103. R. Improta, G. Scalmani, M. J. Frisch, and V. Barone, “Toward effective and reliable fluorescence energies in solution by a new State Specific Polarizable Continuum Model Time Dependent Density Functional Theory Approach,” J. Chem. Phys., 127 (2007) 074504. 2. For seven example steps in the guide of scrf keywords, each step need read the data from chk file from the second step on. But the guide of those steps does not specify which step's chk should be used in current step. For example, the third step read the chk of first step or second step? Each step use the chk of former step? （這一段也是我問的問題） - Step 2: requires a copy of the checkpoint file from Step 1. - Step 3: will work with either a copy of checkpoint file from Step 1 or from Step 2. - Step 4: requires a copy of the checkpoint file from Step 2. - Step 5: requires a copy of the checkpoint file from Step 4. - Step 6: requires a copy of the checkpoint file from Step 4. - Step 7: requires a copy of the checkpoint file from Step 6. Please, note that there was a problem with G09 rev. A.02 because the "StateSpecific" option was connected incorrectly, but this has been fixed in our latest release, G09 rev. B.01. So, if you are using G09 rev. A.02, you would need to use "ExternalIteration" or "SelfConsistent" instead of the "StateSpecific" (shown in the example in the manual). If you are using G09 rev. B.01, then you can use "ExternalIteration", "SelfConsistent" or "StateSpecific", as the three are synonyms. If you follow the whole example given in the manual with G09 rev. A.02 but using "ExternalIteration", you should obtain the following results on each one of the 7 proposed jobs in the example: 1) Energy of ground state optimized geometry in solution: SCF Done: E(RB3LYP) = -153.851761719 A.U. after 1 cycles 2) Vertical excitation (absorption) to first excited state from Linear Response calculation in solution (using ground state optimized geometry from job 1): Excited State 1: Singlet-A" 4.3767 eV 283.28 nm f=0.0000 =0.000 3) Vertical excitation (absorption) to first excited state from a non-equilibrium state-specific calculation (using "ExternalIteration" in solution (using ground state optimized geometry from job 1):SC-PCM: The total energy including the PCM contribution is -153.687679830 a.u. Taking the difference of this energy minus the ground state energy (job 1), the excitation energy is 277.69 nm. 4) Geometry optimization of first excited state in solution (Final energy): Excited State 1: Singlet-A 3.2076 eV 386.53 nm f=0.0014 =0.000 5) Frequency calculation to confirm that the geometry optimized in job 4 is a stationary point, and a minimum in the potential energy surface of the excited state. 6) Energy of first excited state from a equilibrium state-specific calculation (using "ExternalIteration" in solution (using optimized geometry from job 4):SC-PCM: The total energy including the PCM contribution is -153.707151097 a.u. 7) Energy of ground state from a non-equilibrium calculation in solution (using first excited state optimized geometry from job 4 and its reaction field from job 6): SCF Done: E(RB3LYP) = -153.822029934 A.U. after 10 cycles The difference between these last two energies gives the vertical emission energy, which, in this case, is 396.62 nm. |
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2樓2014-08-17 22:15:20
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4樓2014-09-22 23:33:01
小范范1989
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這么好的帖子為什么沒人頂？我也是計(jì)算熒光的時(shí)候，收到hairan的指點(diǎn)，到了這個(gè)帖子上，我感覺我能理解這些步驟了。比原來好多了。 再就是，我感覺要定下心來閱讀以下這個(gè)英文的說明，還有后面的解釋，非常非常的好。只要是你想學(xué)，一定會(huì)學(xué)會(huì)的。 我們實(shí)驗(yàn)室的師姐，我問他高斯計(jì)算熒光，他說就是守則上的沒看明白，我感覺就是沒用心，只要用心，什么事都能學(xué)會(huì)。 最后，謝謝hairan，希望小木蟲成為我們科研的交流平臺(tái)。 |
5樓2014-09-30 21:48:59
zhuyunfy
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6樓2015-06-21 23:22:02
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7樓2015-06-21 23:41:39
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8樓2015-06-22 01:40:52
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小木蟲: 金幣+0.5, 給個(gè)紅包，謝謝回帖
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第四步優(yōu)化激發(fā)態(tài)結(jié)構(gòu)的時(shí)候沒有加SCRF=externaliteration，若加上，結(jié)果應(yīng)該不一樣？是不是無論快過程還是慢過程，若加上SCRF=externaliteration則自動(dòng)依據(jù)溶質(zhì)電子狀態(tài)調(diào)整溶劑電子狀態(tài)，若不加SCRF=externaliteration,則無論快過程還是慢過程，都不會(huì)依據(jù)溶質(zhì)電子狀態(tài)調(diào)整溶劑電子狀態(tài)。比如step4就沒加，實(shí)際step4是個(gè)慢過程。step1也沒加，實(shí)際也是慢過程。在step1和step4過程中，都不會(huì)依據(jù)溶質(zhì)電子狀態(tài)調(diào)整溶劑電子狀態(tài)？step1和step4過程中溶劑是否都進(jìn)行了reorganization of the solvent molecules as a response to a change in the electronic density of the solute？是不是都沒有，或者只有step4有(因step1電子結(jié)構(gòu)未變)？ step1為基態(tài)結(jié)構(gòu)優(yōu)化不做詳細(xì)介紹。以下是step4的輸入文件： %chk=C:\Users\DaiShijie\Desktop\04-ac.chk # b3lyp/6-31+g(d,p) td=(read,nstates=6,root=1) scrf=(solvent=ethanol) geom=modify guess=read opt=rcfc Title Card Required 0 1 4 1 2 3 10.0 5 1 2 7 -50.0 |
9樓2015-06-22 01:50:58
zhuyunfy
新蟲 (小有名氣)
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小木蟲: 金幣+0.5, 給個(gè)紅包，謝謝回帖
小木蟲: 金幣+0.5, 給個(gè)紅包，謝謝回帖
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樓主戴世杰提出了三個(gè)問題： 1.什么是線性響應(yīng)溶劑化的垂直激發(fā)？2.什么是平衡和非平衡溶劑化？3.我的問題：什么是特定態(tài)溶劑化？ 我沒做過熒光，理論底子也不好，也很想學(xué)習(xí)熒光。讀了樓上帖子，試著回答這三個(gè)問題，希望同時(shí)提高自己 1.線性響應(yīng)linear response approach的意思是，把溶劑對(duì)溶質(zhì)的影響作為一個(gè)微擾項(xiàng)放到哈密頓算符中去，然后重新計(jì)算溶質(zhì)的性質(zhì)；一般程序都是做線性響應(yīng)計(jì)算的，但PCM方法不是。垂直激發(fā)就是基態(tài)和激發(fā)態(tài)結(jié)構(gòu)全同。但問題1還是不能回答。 2.非平衡溶劑化意思是盡管溶質(zhì)電子結(jié)構(gòu)發(fā)生了改變，但溶劑不能翻轉(zhuǎn)扭轉(zhuǎn)以適應(yīng)新的溶質(zhì)狀態(tài)，相當(dāng)于幾何凍結(jié)，但此時(shí)溶劑的electron density可以改變而不凍結(jié)；一般躍遷前后都是這種情況；其實(shí)此時(shí)溶質(zhì)也是幾何凍結(jié)的。平衡溶劑化意思是溶劑既可以改變electron density又可以同時(shí)調(diào)整幾構(gòu)型，其實(shí)此時(shí)溶質(zhì)也是可以調(diào)整幾何結(jié)構(gòu)和改變electron density的。一般(基態(tài)激發(fā)態(tài))結(jié)構(gòu)優(yōu)化都是平衡溶劑化。 3.針對(duì)溶質(zhì)，不同的(激發(fā))態(tài)有不同的electron density，溶劑會(huì)依據(jù)溶質(zhì)的electron density調(diào)整溶劑的electron density。所以不同的溶質(zhì)態(tài)應(yīng)對(duì)應(yīng)不同的溶劑electron density。不能采用同一種溶劑electron density應(yīng)付所有的溶質(zhì)態(tài)。這里的溶質(zhì)態(tài)指的是溶質(zhì)的激發(fā)態(tài)，需要用ROOT=N指定。當(dāng)指定溶質(zhì)的激發(fā)態(tài)后，若采用關(guān)鍵詞scrf=externaliteration, 則程序會(huì)依據(jù)指定溶質(zhì)態(tài)調(diào)整溶劑electron density，但此時(shí)由于是NonEq過程，所以溶質(zhì)幾何凍結(jié)依然保持為基態(tài)時(shí)候的結(jié)合狀況。 |
10樓2015-06-22 20:03:18
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