计算化学相关 | Plastocyanin

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程序安装与教程

WSL下做量子化学计算

Packmol (分子动力学初始结构构建程序Packmol的使用)

Gromacs Win (GROMACS的原生Windows版的编译和安装方法（支持GPU加速）)

Gromacs Tutorial (https://tutorials.gromacs.org, http://www.mdtutorials.com/gmx)

xTB (将Gaussian与Grimme的xtb程序联用搜索过渡态、产生IRC、做振动分析)

xTB Manual (https://xtb-docs.readthedocs.io/en/latest)

Crest Manual (https://crest-lab.github.io/crest-docs)

泛函与基组

BSE (https://www.basissetexchange.org)

几何优化相关

在Gaussian中做限制性优化的方法

将Gaussian与ORCA联用搜索过渡态、产生IRC、做振动分析

过渡态、反应路径的计算方法及相关问题

激发态相关

跃迁密度分析方法-自然跃迁轨道(NTO)简介

使用Multiwfn做自然跃迁轨道(NTO)分析

Multiwfn支持的电子激发分析方法一览

分叉反应（两可反应、Bifurcation）

Post-Transition State Bifurcations and Dynamic Effects（http://blueline.ucdavis.edu/2ndTier/3rdTier/Bifurcations.html）

The existence of post-transition state bifurcations (PTSBs) on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but only recently have theoretical chemists come to terms with the implications of this unusual feature of some potential energy surfaces. Beyond simply discovering bifurcations, computational chemists are developing techniques to understand what aspects of molecular structure and vibrations control the product selectivity in systems containing bifurcations. We have found a variety of reactions involving PTSBs and continue to look for more, all the while seeking deeper understanding of their origins and implications. Key papers:

Nouri, D. H.; Tantillo, D. J. J. Org. Chem. 2006, 71, 3686-3695: "Hiscotropic Rearrangements: Hybrids of Electrocyclic and Sigmatropic Reactions"
Hong, Y. J.; Tantillo, D. J. Nature Chem. 2009, 1, 384-389: "A Potential Energy Surface Bifurcation in Terpene Biosynthesis." This article was highlighted in Nature Chemical Biology (2009, 5, 614).
Hong, Y. J.; Tantillo, D. J. Nature Chem. 2014, 6, 104-111: "Biosynthetic Consequences of Multiple Sequential Post-Transition State Bifurcations," highlighted in a News & Views article (Hornsby, C. E.; Paton, R. S. Nature Chem. 2014, 6, 88-89).
Hare, S. R.; Tantillo, D. J. Chem. Sci. 2017, 8, 1442-1449: "Cryptic Post-Transition State Bifurcations Reduce the Efficiency of Lactone-Forming Rh-Carbenoid C-H Insertions"
Hare, S. R.; Tantillo, D. J. Pure Appl. Chem. 2017, 89, 679-698: "Post-Transition State Bifurcations Gain Momentum – Current State of the Field," invited as part of a special issue associated with the ICPOC23 meeting.
Hare, S. R.; Pemberton, R. P.; Tantillo, D. J. J. Am. Chem. Soc. 2017, 139, 7485-7493: "Navigating Past a Fork in the Road—Carbocation–π Interactions Can Manipulate Dynamic Behavior of Reactions Facing Post-Transition State Bifurcations"
Blumel, M.; Nagasawa, S.; Blackford, K.; Hare, S. R.; Tantillo, D. J.; Sarpong, R. J. Am. Chem. Soc. 2018, 140, 9291-9298: "Rearrangement of Hydroxylated Pinene Derivatives to Fenchone-Type Frameworks: Computational Evidence for Dynamically-Controlled Selectvity"
Hare, S. H.; Li, A.; Tantillo, D. J. Chem. Sci. 2018, 9, 8937-8945: "Post-Transition State Bifurcations Induce Dynamical Detours in Pummerer-Like Reactions"
Tantillo, D. J., American Scientist 2019, 107, 22-23: "Wiggling and Jiggling"
Laconsay, C. J.; Tsui, K. Y.; Tantillo, D. J. Chem. Sci. 2020, 11, 2231-2242: "Tipping the Balance: Theoretical Interrogation of Divergent Extended Heterolytic Fragmentations"
Chuang, H.-H.; Tantillo, D. J.; Hsu, C.-P. J. Chem. Theor. Comput. 2020, 16, 4050-4060: "The Construction of Two-Dimensional Potential Energy Surfaces of Reactions with Post-Transition State Bifurcations"
Bai, M.; Feng, Z.; Li, J.; Tantillo, D. J. Chem. Sci. 2020, 11, 9937-9944: "Bouncing Off Walls - Widths of Exit Channels from Shallow Minima Can Dominate Selectivity Control"
Xing, Y.-Y.; Chen, S.-S.; Chen, D.-Z.; Tantillo, D. J. Phys. Chem. Chem. Phys. 2020, 22, 26955-26960: "Effects of Electrostatic Drag on the Velocity of Hydrogen Migration - Pre- and Post-Transition State Enthalpy/Entropy Compensation"
Feng, Z.; Tantillo, D. J. J. Am. Chem. Soc. 2021143, 1088-1097: "Dynamic Effects on Migratory Aptitudes in Carbocation Reactions"
Sun, Q.; Lu, X.; Tantillo, D. J. ChemPhysChem 2021, 22, 649-656: "Dynamic Effects in Intramolecular Schmidt Reactions – Entropy, Electrostatic Drag, and Selectivity Prediction"
Tantillo, D. J. J. Phys. Org. Chem. 2021, 34, e4202: "Dynamic Effects on Organic Reactivity – Pathways to (and from) Discomfort," featured on the cover.
Tantillo, D. J. Adv. Phys. Org. Chem. 2021, 55, 1-16: "Beyond Transition State Theory – Non-statistical Dynamic Effects for Organic Reactions"
Tantillo, D. J. J. Am. Chem. Soc. 2022, 144, 13996-14004: "Portable Models for Entropy Effects on Kinetic Selectivity," invited.
Guo, W.; Hare, S. R.; Chen. S.-S.; Saunders, C.; Tantillo, D. J. J. Am. Chem. Soc. 2022, 144, 17219-17231: "C-H Insertion in Dirhodium Tetracarboxylate-Catalyzed Reactions Despite Dynamical Tendencies Toward Fragmentation – Implications for Reaction Efficiency and Catalyst Design"
Guo, W.; Tantillo, D. J. J. Am. Chem. Soc. 2024, 146, 7039-7051: "Running Wild through Dirhodium Tetracarboxylate-Catalyzed Combined CH(C)-Functionalization/Cope Rearrangement Landscapes. Does Post-Transition-State Dynamic Mismatching Influence Product Distributions?"
Feng, Z.; Guo, W.; Kong, W.-K.; Chen., D.; Wang, S.; Tantillo, D. J. Nature Chem. 2024, 16, 615-623: "Analogies between Photochemical Reactions and Ground State Post-Transition-State Bifurcations Shed Light on Dynamical Origins of Selectivity"

[4+2]/[4+3] Bifurcations（https://doi.org/10.1021/jacs.1c05293）