C4H6 的全球反应路线图

目的
选项和功能
默认输入
输出 1
EQOnly & KeepSCPath 输入
输出 2
EQOnly & KeepLUPPath 输入
输出 3

目的

使用不同近似精度的反应路径进行综合搜索

通过对 C₄H₆的应用示例，我们将学习 SC-AFIR 选项，以根据目标和计算资源高效地执行综合搜索。

选项和功能

表。SC-AFIR 选项和反应路径待优化^a

^aAFIR 路径是 IRC 路径的粗略反应路径，LUP 路径是更好的近似路径，因为它优化了 AFIR 路径。
^bAFIR 路径已计算，但结果未在主输出文件中描述。
计算时间的顺序变为“仅 EQ & 保持 SC 路径” < “仅 EQ & 保持 LUP 路径” < “默认”。

默认输入

# SC-AFIR2/RHF/6-31G 指定 SC-AFIR2

0 1 C -1.838404287973 0.119533694878 0.000000000001 C -0.615405923118 -0.396826557079 -0.000000000000 C 0.615405107688 0.396823317776 -0.000000000001 C 1.838404890511 -0.119531342069 0.000000000001 H -2.005621685770 1.181210920926 0.000000000000 H -2.713544917822 -0.500533906903 -0.000000000001 H -0.490768775742 -1.466281153046 -0.000000000001 H 0.490765045187 1.466277913926 0.000000000000 H 2.005632939247 -1.181205538618 -0.000000000001 H 2.713539929768 0.500542319041 0.000000000000 Options Add interaction Gamma=1000 指定伽马=1000 kJ mol^-1作为示例
END Gauproc=1 GauMem=800

输出 1：日志文件

c4h6_default.log
c4h6_default_EQ_list.log
c4h6_default_TS_list.log
c4h6_default_PT_list.log

如何读取日志文件：c4h6_default_EQ_list.log

# Geometry of EQ 0, SYMMETRY = C2h C -1.838404287973 0.119533694878 0.000000000001 …snip… H 2.713539929768 0.500542319041 0.000000000000 Energy = -154.864576395653 (-154.864576395653 : 0.000000000000) Spin(**2) = 0.000000000000 ZPVE = 0.092165672706 Normal mode eigenvalues : nmode = 24 0.001065322 0.004058282 0.012196272 0.013257292 0.028264197 …snip… # Geometry of EQ 1, SYMMETRY = Cs C -1.909612052040 0.139044446470 0.001805406420 C -0.728397038359 -0.466342686233 -0.000501104977 …snip…

平衡结构被列举。
通常，EQ0 对应于初始结构，而 EQ1 及以下是搜索过程中获得的优化结构。

如何读取日志文件：c4h6_default_TS_list.log

# Geometry of TS 0, SYMMETRY = C2 C -1.694319087901 0.141191397200 0.368424736715 …snip… H 2.660142999010 0.467778288804 -0.021229531391 Energy = -154.854740301486 (-154.854740301486 : 0.000000000000) Spin(**2) = 0.000000000000 ZPVE = 0.091496701099 Normal mode eigenvalues : nmode = 24 -0.001175441 0.005366340 0.006100352 0.020122685 0.023635562 …snip… CONNECTION : 9 - 0

过渡态结构被列举。
“连接：9 – 0”对应于与 TS0 相关的 EQ_list 中的平衡结构。

EQOnly & KeepSCPath 输入

输出 2：日志文件

c4h6_keepSCPath.log
c4h6_ keepSCPath_EQ_list.log
c4h6_ keepSCPath_TS_list.log
c4h6_ keepSCPath_PT_list.log
c4h6_keepSCPath_PTQQQ.log

如何读取日志文件：c4h6_keepSCPath_EQ_list.log

平衡结构被列举。
通常，EQ0 对应于初始结构，而 EQ1 及以下是搜索过程中获得的优化结构。

如何读取日志文件：c4h6_keepSCPath_PT_list.log

# Geometry of TS 1, SYMMETRY = C1 C -1.579727651738 0.122636265985 0.134064446290 …snip… H 0.447695602798 0.057746266941 0.691930263608 Energy = -154.598944498044 (-154.598944498044 : 0.000000000000) Spin(**2) = 0.000000000000 ZPVE = 0.000000000000 Normal mode eigenvalues : nmode = 24 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 …snip… 0.000000000 0.000000000 0.000000000 0.000000000 CONNECTION : 0 - ??

在 SC-AFIR 计算过程中获得的 AFIR 路径上的近似过渡态结构被列举出来。
“连接”描述了在 AFIR 路径上获得的结构之间的联系。
准确的过渡态结构可以通过对所描述结构的鞍点计算获得。

如何读取日志文件：c4h6_keepSCPath_10571.log

AFIR 路径的能量在日志文件末尾的“AFIR 路径概况”中描述。
在 AFIR 路径上，近似的过渡态结构和平衡结构被列举出来。
准确的过渡态和 IRC 路径可以通过鞍点计算或重路径或重构计算获得，这些计算针对 AFIR 路径上的过渡态结构候选者。

---Profile of AFIR path Itr. Length (ang) Energy (real) Energy (fit) 0 0.000000000000 -154.189471987828 -154.189412734629 -0.78 1 0.064942795410 -154.185530648728 -154.185758323410 -0.80 2 0.127386360596 -154.180850705819 -154.180669139313 -0.81 …snip… ---Approximate TS geometry (between 18 and 19)ITR on AFIR path, indicating there are transition
C -2.601112286807 -0.246259060101 -0.548607140235state structure candidates between 18 and 19.
…snip… H 1.456081420364 0.507653193974 0.648385058763 ENERGY = -154.046963051192 (-154.046963051192 : 0.000000000000)

EQOnly & KeepLUPPath Input

# SC-AFIR2/RHF/6-31GSpecify SC-AFIR2

0 1 C -1.838404287973 0.119533694878 0.000000000001 C -0.615405923118 -0.396826557079 -0.000000000000 C 0.615405107688 0.396823317776 -0.000000000001 C 1.838404890511 -0.119531342069 0.000000000001 H -2.005621685770 1.181210920926 0.000000000000 H -2.713544917822 -0.500533906903 -0.000000000001 H -0.490768775742 -1.466281153046 -0.000000000001 H 0.490765045187 1.466277913926 0.000000000000 H 2.005632939247 -1.181205538618 -0.000000000001 H 2.713539929768 0.500542319041 0.000000000000 Options Add interaction Gamma=1000Specify Gamma=1000 kJ mol^-1 as an example
END Gauproc=1 GauMem=800 EQOnlyPerform geometry optimization on equilibrium structures only
KeepLUPpathOptimize LUP path and keep the file

Output3: Log-files

c4h6_keepLUPPath.log
c4h6_ keepLUPPath_EQ_list.log
c4h6_ keepLUPPath_TS_list.log
c4h6_ keepLUPPath_PT_list.log
c4h6_keepLUPPath_PTQQQ.log

How to read the log file: c4h6_keepLUPPath_EQ_list.log

Equilibrium structures are enumerated.
Normally EQ0 corresponds to the initial structure and EQ1 and below are optimized structures obtained during the search.

How to read the log file: c4h6_keepLUPPath_PT_list.log

# Geometry of TS 0, SYMMETRY = C1 C -1.760372035348 0.182009395364 0.333038946577 …snip… H 2.699847402416 0.522235606356 -0.256604623120 Energy = -154.821102955644 (-154.821102955644 : 0.000000000000) Spin(**2) = 0.000000000000 ZPVE = 0.091575464972 Normal mode eigenvalues : nmode = 24 -0.004340298 0.003312917 0.005257720 0.017740421 0.021577244 …snip… 0.425724393 0.435883869 0.443434980 0.464815676 CONNECTION : 0 - 9

Approximate transition state structures on LUP path obtained during SC-AFIR calculation are enumerated.
“CONNECTION” describes the connections between structures obtained on LUP path.
The accurate transition state structure can be obtained by the Saddle calculation for the described structure.

How to read the log file: c4h6_keepSCPath_10571.log

The structure and energy after LUP path optimization are described.

# NODE 0 C -0.310296209821 1.606084214583 -0.104967332975 …snip… H 2.053903493510 1.126503518216 0.706909432861 Item Value Threshold ENERGY -154.619286214507 …snip… NORMAL MODE EIGENVALUE : N_MODE = 24 -0.002985623 0.005875821 0.010769888 0.014870272 0.023773466 …snip… # NODE 1 C -0.053615163401 1.551120101148 -0.382902048339 …snip… H 2.073142003557 1.054133995670 0.894672472301

The accurate transition state and IRC path can be obtained by Saddle calculation or Restruct calculation of transition state structure candidates on LUP path.