Personal webpage for Dr.
Hello, I'm Yunwen.
I'm a researcher in the field of computational chemistry.
I studied under Prof. Dieter Cremer (deceased) and Prof. Elfi Kraka, then received my doctoral degree in theoretical chemistry at Southern Methodist University in 2018.
My current research interests emphasize alchemical free energy calculation and machine learning in computational chemistry.
My prior research covers multiple areas including chemical bonding, vibrational spectroscopy, chemical similarity, reaction mechanism, curvilinear coordinates and materials chemistry.
I enjoy developing new theories and tools in the field of computational chemistry. I'm familiar with Fortran 77/90, Python and C++/CUDA languages.
I would be glad to review manuscripts related to my expertise for international journals and conferences.
[Google Scholar Profile] [GitHub]
[Email: 
]
Software
[1] PyVibMS
PyMOL plugin to visualize vibrations in molecules and solids modeled by quantum chemical calculations
[2] LModeA-nano
PyMOL plugin to measure chemical bond strength in molecules and solids modeled by quantum chemical calculations based on local vibrational mode theory
[3] UniMoVib
Powerful program to calculate molecular harmonic vibrations interfaced to more than 30 quantum chemistry packages
[4] Three-Arm Turnstile Assistant
PyMOL plugin to modify molecular structure via turnstile rotation
[5] torchANI2Gaussian
Interface script from TorchANI to Gaussian (to use ANI potential in Gaussian)
[6] RAG-IF
RNA inverse folding within RNA-As-Graph (RAG) framework based on genetic algorithm
[7] pURVA
Standalone python Unified Reaction Valley Approach program (in-house only)
[8] CURVI
Curvilinear coordinates system for coordination compounds (in-house code interfaced to Gaussian 16)
PhD Dissertation
[1] Y. Tao, Advances in Local Vibrational Mode Theory and Unified Reaction Valley Approach (URVA), Southern Methodist University (2018).
Review and Comment Articles
[1] G. Luo, H. Zhang, Y. Tao, Q. Wu, D. Tian, Q. Zhang, Recent Progress in Ligand-Centered Homogeneous Electrocatalysts for Hydrogen Evolution Reaction, Inorg. Chem. Front. 6, 343 (2019).
[2] E. Kraka, W. Zou, Y. Tao, Decoding Chemical Information From Vibrational Spectroscopy Data – Local Vibrational Mode Theory, WIREs: Comput. Mol. Sci. 10, e1480 (2020).
[3] E. Kraka, W. Zou, Y. Tao, M. Freindorf, Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review, Catalysts 10, 691 (2020).
[4] S. Nanayakkara1, Y. Tao1, E. Kraka, Comment on: Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of SAPT, J. Comput. Chem. 42, 516 (2021).
Selected Research Articles
i. Method development on local vibrational mode theory
[1] Y. Tao, C. Tian, N. Verma, W. Zou, C. Wang, D. Cremer, E. Kraka, Recovering Intrinsic Fragmental Vibrations Using the Generalized Subsystem Vibrational Analysis, J. Chem. Theory Comput. 14, 2558 (2018).
[2] Y. Tao, W. Zou, D. Sethio, N. Verma, Y. Qiu, C. Tian, D. Cremer, E. Kraka, In Situ Measure of Intrinsic Bond Strength in Crystalline Structures: Local Vibrational Mode Theory for Periodic Systems, J. Chem. Theory Comput. 15, 1761 (2019).
[3] Y. Tao, W. Zou, S. Nanayakkara, E. Kraka, PyVibMS: A PyMOL Plugin for Visualizing Vibrations in Molecules and Solids, J. Mol. Model. 26, 290 (2020).
[4] Y. Tao, W. Zou, S. Nanayakkara, M. Freindorf, E. Kraka, A Revised Formulation of the Generalized Subsystem Vibrational Analysis (GSVA), Theor. Chem. Acc. 140, 31 (2021).
[5] Y. Tao*, W. Zou, S. Nanayakkara, E. Kraka*, LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis, J. Chem. Theory Comput. 18, 1821 (2022).
ii. Biochemistry, Biophysics, RNA design
[1] C. Guo, Y. Chen, Y. Zheng, W. Zhang, Y. Tao, J. Feng, L. Tang, Exploring the Enatioselective Mechanism of Halohydrin Dehalogenase from Agrobacterium radiobacter AD1 by Iterative Saturation Mutagenesis, Appl. Environ. Microbiol. 81, 2919 (2015).
[2] Z. Tang, D. Li, Y. Luan, L. Zhu, H. Du, Y. Tao, Y. Wang, D. M. Haddleton, H. Chen, Conjugation of Polymers to Proteins Through an Inhibitor-Derived Peptide: Taking up the Inhibitor Berth, Chem. Commun. 51, 10099 (2015).
[3] S. Jain1, Y. Tao1, T. Schlick, Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies, J. Struct. Biol. 209, 107438 (2020).
[4] K. Nam, Y. Tao, V. Ovchinnikov, Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway, J. Phys. Chem. B 127, 5789 (2023).
iii. Hydrogen bonding, Water, Ice
[1] Y. Tao, W. Zou, J. Jia, W. Li, D. Cremer, Different Ways of Hydrogen Bonding in Water – Why Does Warm Water Freeze Faster than Cold Water?, J. Chem. Theory Comput. 13, 55 (2017).
[2] Y. Tao, W. Zou, E. Kraka, Strengthening of Hydrogen Bonding with the Push-Pull Effect, Chem. Phys. Lett. 685, 251 (2017).
[4] N. Verma, Y. Tao, E. Kraka, Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes, J. Phys. Chem. B 125, 2551 (2021).
[5] S. Nanayakkara1, Y. Tao1, E. Kraka, Capturing Individual Hydrogen Bond Strengths in Ices via Periodic Local Vibrational Mode Theory: Beyond the Lattice Energy Picture, J. Chem. Theory Comput. 18, 562 (2022).
iv. Machine learning, Chemical similarity
[1] Y. Tao, W. Zou, D. Cremer, E. Kraka, Characterizing Chemical Similarity with Vibrational Spectroscopy: New Insights into the Substituent Effects in Monosubstituted Benzenes, J. Phys. Chem. A 121, 8086 (2017).
[2] Y. Tao, W. Zou, D. Cremer, E. Kraka, Correlating the Vibrational Spectra of Structurally Related Molecules: A Spectroscopic Measure of Similarity, J. Comput. Chem. 39, 293 (2018).
[3] N. Verma1, Y. Tao1, B. L. Marcial, E. Kraka, Correlation Between Molecular Acidity (pKa) and Vibrational Spectroscopy, J. Mol. Model. 25, 48 (2019).
[4] L. Huang, L. Wang, X. Hu, S. Chen, Y. Tao, H. Su, J. Yang, W. Xu, V. Vedarethinam, S. Wu, B. Liu, X. Wan, J. Lou, Q. Wang, K. Qian, Machine Learning of Serum Metabolic Patterns Encodes Early-Stage Lung Adenocarcinoma, Nat. Commun. 11, 3556 (2020).
[5] N. Verma, X. Qu, F. Trozzi, M. Elsaied, N. Karki, Y. Tao, B. Zoltowski, E. Larson, E. Kraka, SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction, Int. J. Mol. Sci. 22, 1392 (2021).
v. Homogeneous catalysis for hydrogen evolution reaction
[1] Z. Pan1, Y. Tao1, Q. He1, Q. Wu, L. Chen, Z. Wei, J. Wu, J. Lin, D. Sun, Q. Zhang, D. Tian, G. Luo, The Difference Se Makes: A Bio-Inspired Dppf-Supported Nickel Selenolate Complex Boosts Dihydrogen Evolution with High Oxygen Tolerance, Chem. Eur. J. 24, 8275 (2018).
[3] A. Xie, Y. Tao*, C. Peng, G. Luo*, A Nickel Pyridine-Selenolate Complex for the Photocatalytic Evolution of Hydrogen from Aqueous Solutions, Inorg. Chem. Commun. 110, 107598 (2019).
[4] W. Xiao, Y. Tao*, G. Luo*, Hydrogen Formation Using A Synthetic Heavier Main-Group Bismuth-Based Electrocatalyst, Int. J. Hydrog. Energy 45, 8177 (2020).
[5] W. Xiao, Y. Tao, Y. Zhao, J. Luo, W. Lai, Synthesis, Crystal Structure and Photochemical H2 Generation of A Co-Based Supramolecular Assembly Containing A Bisthienyl Bodipy Sensitizer, Inorg. Chem. Commun. 113, 107800 (2020).
vi. Molecular crystals, Non-covalent forces, MOF
[1] Y. Tao, Y. Qiu, W. Zou, S. Nanayakkara, S. Yannacone, E. Kraka, In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory, Molecules 25, 1589 (2020).
[2] Z. Zhang, Y. Tao, H. Tian, Q. Yue, S. Liu, Y. Liu, X. Li, Y. Lu, Z. Sun, E. Kraka, S. Liu, Chelation-Assisted Selective Etching Construction of Hierarchical Polyoxometalate-Based Metal-Organic Framework, Chem. Mater. 32, 5550 (2020).
[3] C. A. McConville, Y. Tao, H. A. Evans, B. A. Trump, J. B. Lefton, W. Xu, A. A. Yakovenko, E. Kraka, C. M. Brown, T. Runčevski, Peritectic Phase Transition of Benzene and Acetonitrile Into a Cocrystal Relevant to Titan, Saturn’s Moon, Chem. Commun. 56, 13520 (2020).
[4] M. Huang, R. Qiu, Z. Pan, D. Tian, Y. Tao*, J. Lin*, G. Luo*, Thermally Triggered Isomerization in a Naphthalene-Based Acylhydrazone with Solid-State Optical Nonlinearity Response, Eur. J. Inorg. Chem. 2020, 4313 (2020).
vii. Curvilinear coordinates (as extension to Cremer-Pople coordinates), Fluxionality of coordination compounds
[1] W. Zou1, Y. Tao1, E. Kraka, Describing Polytopal Rearrangements of Fluxional Molecules with Curvilinear Coordinates Derived from Normal Vibrational Modes: A Conceptual Extension of Cremer-Pople Puckering Coordinates, J. Chem. Theory Comput. 16, 3162 (2020).
[2] W. Zou, Y. Tao, E. Kraka, Systematic Description of Molecular Deformations with Cremer–Pople Puckering and Deformation Coordinates Utilizing Analytic Derivatives: Applied to Cycloheptane, Cyclooctane, and Cyclo[18]carbon, J. Chem. Phys. 152, 154107 (2020).
[3] Y. Tao, W. Zou, G. Luo, E. Kraka, Describing Polytopal Rearrangement Processes of Octacoordinate Structures. I. Renewed Insights into Fluxionality of the Rhenium Polyhydride Complex ReH5(PPh3)2(Pyridine), Inorg. Chem. 60, 2492 (2021).
[4] Y. Tao*, X. Wang*, W. Zou, G. Luo, E. Kraka*, Unusual Intramolecular Motion of ReH92- in K2ReH9 Crystal: Circle Dance and Three-Arm Turnstile Mechanisms Revealed by Computational Studies, Inorg. Chem. 61, 1041 (2022).
viii. Reaction mechanism, Unified reaction valley approach
[1] H. Cui, J. Zhang, Y. Tao, C. Cui, Controlled Oxidation of an NHC-Stabilized Phosphinoaminosilylene with Dioxygen, Inorg. Chem. 55, 46 (2016).
[2] M. Freindorf, Y. Tao, D. Sethio, D. Cremer, E. Kraka, New Mechanistic Insights into the Claisen Rearrangement of Chorismate — A Unified Reaction Valley Approach Study, Mol. Phys. 117, 1172 (2019).
[3] S. Nanayakkara, M. Freindorf, Y. Tao, E. Kraka, Modeling Hydrogen Release from Water with Borane and Alane Catalysts: A Unified Reaction Valley Approach, J. Phys. Chem. A 124, 8978 (2020).
[4] M. Z. Makoś, M. Freindorf, Y. Tao, E. Kraka, Theoretical Insights into [NHC]Au(I) Catalyzed Hydroalkoxylation of Allenes: A Unified Reaction Valley Approach Study, J. Org. Chem. 86, 5714 (2021).
[5] M. Freindorf, N. Beiranvand, A. Delgado, Y. Tao, E. Kraka, On the formation of CN bonds in Titan’s Atmosphere—A Unified Reaction Valley Approach Study, J. Mol. Model. 27, 320 (2021).
[6] X. Liang, F. Guan, Z. Ling, H. Wang, Y. Tao, E. Kraka, H. Huang, C. Yu, D. Li, J. He, H. Fang, Pivotal Role of Water Molecules in the Photodegradation of Pymetrozine: New Insights for Developing Green Pesticides, J. Hazard. Mater. 423, 127197 (2022).
[7] M. Freindorf, Y. Tao, E. Kraka, A Closer Look at the Isomerization of 5-Androstene-3,17-Dione to 4-Androstene-3,17-Dione in Ketosteroid Isomerase, J. Comput. Biophys. Chem. 21, 313 (2022).
ix. Coinage metal cluster
[1] W. Xiao, A. Xie, Y. Tao*, G. Luo*, Synthesis, Crystal Structure, DFT Analysis and Properties of A Sub-Nanometer Sized Hexanuclear Silver(I) Cluster, J. Mol. Struct. 1207, 127789 (2020).
[2] C. Deng, C. Sun, Z. Wang, Y. Tao, Y. Chen, J. Lin, G. Luo, B. Lin, D. Sun, L. Zheng, A Sodalite-Type Silver Orthophosphate Cluster in a Globular Silver Nanocluster, Angew. Chem. Int. Ed. 59, 12659 (2020).
[3] Q. Guo, B. Han, C. Sun, Z. Wang, Y. Tao*, J. Lin, G. Luo*, C. Tung, D. Sun*, Observation of a bcc-like Framework in Polyhydrido Copper Nanoclusters, Nanoscale 13, 19642 (2021).
[4] G. Dong, Z. Pan, B. Han, Y. Tao, X. Chen, G. Luo, P. Sun, C. Sun, D. Sun, Multi-layer 3D Chirality and Double-Helical Assembly in a Copper Nanocluster with a Triple-Helical Cu15 Core, Angew. Chem. Int. Ed. 62, e202302595 (2023).
[5] G. Luo, Z. Pan, B. Han, D. Dong, C. Deng, M. Azam, Y. Tao, J. He, C. Sun, D. Sun, Total Structure, Electronic Structure and Catalytic Hydrogenation Activity of Metal-Deficient Chiral Polyhydride Cu57 Nanoclusters, Angew. Chem. Int. Ed. 62, e202306849 (2023).
x. Quantum chemical method
[1] Y. Tao1, Z. Pei1, N. Bellonzi, Y. Mao, Z. Zou, W. Liang, Z. Yang, Y. Shao, Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions. I. A Shared-Orbital Implementation, Int. J. Quantum Chem. 120, e26123 (2020).
Media Coverage
[1] Carmen Drahl, Why Does Hot Water Sometimes Freeze Faster Than Cold Water?, Forbes (2017).
[2] Emily Conover, Debate heats up over claims that hot water sometimes freezes faster than cold, ScienceNews (2017).
[3] Bec Crew, The Claim Hot Water Freezes Faster Than Cold Water Is Even Weirder Than You Think, ScienceAlert (2017).
[4] Jennifer Ouellette, When cold warms faster than hot, Physics World (2017).
[5] Tim Sandle, Which freezes faster: Hot water or cold water?, Digital Journal (2017).
[6] David Bradley, Why Warm Water Freezes Faster Than Cold Water, ChemistryViews (2017).
[7] Sofia Olea, Nueva teoría podría explicar por qué el agua caliente se congela más rápido (A new theory could explain why hot water freezes faster), El Ciudadano (2017).
[8] Philipp Nagels, Darum gefriert heißes Wasser schneller als kaltes (This is why hot water freezes faster than cold water), WELT (2018).
[9] Tomasz Kromp, Dlaczego ciepła woda szybciej zamarza? Zagadkowy efekt Mpemby (Why does hot water freeze faster? The puzzling Mpemba effect), Interia Geekweek (2024).