Publications
Selected Publications
167 publications, 2010–2026.
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2026
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Machine learning driven ReaxFF optimization for combustion.
Chinese Journal of Chemical Physics 39 (2) , 233–244
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A graph neural network for the era of large atomistic models.
npj Computational Materials
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AutoLoop is an autoregressive deep learning method for protein loop prediction with high accuracy.
Cell Reports Physical Science 7 (1)
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Mechanistic Insights into Nitrogenase-Catalyzed Nitrogen Fixation: A QM/MM Study.
ACS Catalysis 16 (2) , 1224–1238
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Enhancing the Simulation Accuracy of Small Organic Molecules with an Optimized Lennard-Jones Coarse-Grained Model.
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SOT-RM: An equivariant shortcut and optimal transportation-based flow model for exploring chemical reaction mechanisms.
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A practical framework for rapid calculation of protein polarization energies with anisotropic atomic polarizabilities.
The Journal of Chemical Physics 164 (5)
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Understanding the Adsorption and Desorption Dynamics for On-surface Systems.
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Comparative binding mechanisms of SND1 with MTDH and small-molecule inhibitors: insights from molecular dynamics simulations and free energy calculations.
Physical Chemistry Chemical Physics 28 (16) , 10216–10229
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Automating computational chemistry workflows via OpenClaw and domain-specific skills.
Journal of Chemical Theory and Computation
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SOT-RM: An equivariant shortcut and optimal transport-based flow model for exploring chemical reaction mechanisms.
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GMFCC-UMA: A Fragment-Based Machine Learning Framework for Scalable Ab Initio-Quality Protein Energies.
Journal of Chemical Theory and Computation 22 (9) , 4822–4834
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LamNet: an alchemical-path-aware graph neural network to accelerate binding free energy calculations for drug discovery and beyond.
National Science Review 13 (3) , nwaf559
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From artificial intelligence for science to autonomous chemical innovation: closing the loop in energy and chemical engineering.
Clean Energy 10 (4) , 1–8
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Experimental astrochemistry and machine learning unravel the formation of oxygen-bearing organic molecules in extraterrestrial ices.
Communications Chemistry
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Automated Reaction Path Discovery for Coal Pyrolysis: Scalable Dataset Construction and Mechanistic Insights for Clean Energy Applications.
Clean Energy , zkag036
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RNARL: reinforcement learning-driven unified generative framework for multi-objective RNA codon design.
Genome Biology
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Coverage-Dependent Free-Energy Bottlenecks in CO Adsorption and Desorption on Ru (0001).
JACS Au
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Improvements in chemical reaction pathway exploration algorithms and dataset generation.
Scientific Data 13 (1101)
doi:10.1038/s41597-026-07771-6
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2025
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Ab Initio Accuracy Neural Network Potential for Drug-Like Molecules.
Research 8 , 0837
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On the design space between molecular mechanics and machine learning force fields.
Applied Physics Reviews 12 (2)
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The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H--Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States.
Journal of Chemical Theory and Computation 21 (7) , 3410–3425
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A Deep Learning-Augmented Density Functional Framework for Reaction Modeling with Chemical Accuracy.
JACS Au 5 (8) , 3892
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Transition state searching accelerated by neural network potential.
Journal of Chemical Information and Modeling 65 (5) , 2297–2303
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Vib2Mol: from vibrational spectra to molecular structures-a unified deep learning framework.
arXiv preprint arXiv:2503.07014
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ECTS: An ultra-fast diffusion model for exploring chemical reactions with equivariant consistency.
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Interaction of magnesium ion and acetate anion in bulk water: Toward high-level machine learning potential.
Chinese Journal of Chemical Physics 38 (1) , 95–101
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Invariant-Potential-Driven Molecular Dynamics Unravels Formose Reaction Kinetics.
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Atmospheric sulfate aerosol formation enhanced by interfacial anions.
PNAS nexus 4 (3) , pgaf058
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Real-fluid transport property computations based on the Boltzmann-weighted full-dimensional potential model.
Applications in Energy and Combustion Science 23 , 100342
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General reactive machine learning potentials for CHON elements.
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Pretrained E (3)-equivariant message-passing neural networks with multi-level representations for organic molecule spectra prediction.
npj Computational Materials 11 (1) , 203
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Insights into Binding Mechanisms of Potential Inhibitors Targeting PCSK9 Protein via Molecular Dynamics Simulation and Free Energy Calculation.
Molecules 30 (14) , 2962
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Identification of Nogo-B as a potential therapeutic target of osteosarcoma via stereochemically selective covalent probes.
Cell Death \& Disease 16 (1) , 537
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DeePaTB: A deep learning powerd semi-empirical quantum mechanical method.
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Deep learning for bidirectional translation between molecular structures and vibrational spectra.
Journal of the American Chemical Society 147 (31) , 27525–27536
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Identification of EEF1A2 as a potential therapy target of osteosarcoma using novel compound 8e.
European Journal of Medicinal Chemistry , 118355
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Coarse-Grained Simulation of Persistence Length and Twisting Dynamics of Micrometer-Scale Microtubules.
The Journal of Physical Chemistry Letters 16 (29) , 7300–7306
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Thiazolidinones as Potential PGK1 Inhibitors for Treatment of Osteosarcoma Growth and Metastasis.
Journal of Medicinal Chemistry 68 (21) , 22216–22245
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QM/MM study of cytochrome P450 TxtE catalysis: Substrate reorganization enables selective aromatic nitration.
The Journal of Chemical Physics 163 (16)
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Application of Modern Intelligent Algorithms in Retrosynthesis Prediction.
Communications in Computational Chemistry 7 (4) , 289–310
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Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains.
Cell 188 (24) , 6987–7005
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2024
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A machine learning-based high-precision density functional method for drug-like molecules.
Artificial Intelligence Chemistry 2 (1) , 100037
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Designer cellular spheroids with DNA origami for drug screening.
Science advances 10 (29) , eado9880
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Predicting Two-Photon Absorption Spectra of Octupolar Molecules: A Deep-Learning Approach Based Exclusively on Molecular Structures.
The Journal of Physical Chemistry A 128 (2) , 431–438
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Visible-light-promoted $\alpha$-C (sp3)--H amination of ethers with azoles and amides.
Organic Letters 26 (4) , 933–938
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Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model.
Advanced Science 11 (42) , 2409880
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Application of modern intelligent algorithms in retrosynthesis prediction.
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Transition State Searching Accelerated by Deep Learning Potential.
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A one-pot photocatalytic triazole-based linkerology for PROTACs.
Cell Reports Physical Science 5 (8)
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Iodide ion-enabled highly regioselective $\alpha$-C (sp3)--H triazolization of ethers with N-sulfonyl-1, 2, 3-triazoles.
New Journal of Chemistry 48 (34) , 15002–15007
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Rapid identification of drug mechanisms with deep learning-based multichannel surface-enhanced Raman spectroscopy.
ACS sensors 9 (8) , 4227–4235
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EnviroDetaNet: Pretrained E (3)-equivariant Message-Passing Neural Networks with Multi-Level Molecular Representations for Organic Molecule Spectra Prediction.
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Novel Alkynylamide-Based Nonpeptidic Allosteric Inhibitors for SARS-CoV-2 3-Chymotrypsin-like Protease.
ACS Pharmacology \& Translational Science 7 (10) , 3170–3191
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Discovery of chalcone derivatives as bifunctional molecules with anti-SARS-CoV-2 and anti-inflammatory activities.
Journal of Natural Products 87 (12) , 2680–2694
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Discovery of new synthetic routes of amino acids in prebiotic chemistry.
JACS Au 4 (12) , 4757
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DPA-2: Towards a universal large atomic model for molecular and materials simulation.
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DPA-2: a large atomic model as a multi-task learner.
npj computational materials 10 (1) , 293
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Enzymatic ring contraction for the biosynthesis of sulfur-containing cyclopentachromone.
Journal of the American Chemical Society 147 (1) , 548–556
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Correction to “Rapid Identification of Drug Mechanisms with Deep Learning-Based Multichannel Surface-Enhanced Raman Spectroscopy”.
ACS sensors 10 (1) , 574–574
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Ab initio accuracy neural network potential for drug-like molecules.
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2023
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Neural network potentials.
Quantum Chemistry in the Age of Machine Learning , 279–294
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Function-oriented synthesis of Imidazo [1, 2-a] pyrazine and Imidazo [1, 2-b] pyridazine derivatives as potent PI3K/mTOR dual inhibitors.
European Journal of Medicinal Chemistry 247 , 115030
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Theoretical study of the absorption and emission spectrum and non-adiabatic excited state dynamics of gas-phase xanthone.
Journal of the Chinese Chemical Society 70 (3) , 372–385
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Ensemble-based virtual screening of human PI4KIII$\alpha$ inhibitors toward the Hepatitis C virus.
Chemical Physics Letters 815 , 140354
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Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection.
ChemPlusChem 88 (9) , e202300083
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Interaction of divalent cations and amino acids in bulk water: Molecular simulations with neural network potentials.
Chinese Journal of Chemical Physics 36 (2) , 162–168
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Regioselectively Electrochemical Synthesis of N 2-Selective C--H Amination of Ethers with N-Tosyl 1, 2, 3-Triazole via Triazole Radical Cation.
Organic Letters 25 (28) , 5383–5388
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DPA-2: Towards a universal large atomic model for molecular and material simulation.
arXiv e-prints , arXiv–2312
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A new inhibitor of human peptide deformylase suppresses cell proliferation and induces cell apoptosis and autophagy in cancers.
Anti-Cancer Drugs 34 (4) , 483–494
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Theoretical investigation of the lack of chiral self-sorting behaviour of a molecular cinquefoil knot.
Supramolecular Chemistry 34 (5-6) , 247–256
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A Machine Learning Protocol to Directly Translate Molecular Infrared or Raman Spectra into Molecular Formula.
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Front Cover: Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection (ChemPlusChem 9/2023)..
ChemPlusChem 88 (9) , 1
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2022
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Exploring the selective mechanism of inhibitors towards different subtypes of class I PI3K.
Chemical Physics Letters 786 , 139174
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Theoretical investigations on photodissociation dynamics of deuterated alkyl halides CD3CH2F.
Chinese Journal of Chemical Physics 35 (3) , 431–442
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Growth of polycyclic aromatic hydrocarbon and soot inception by in silico simulation.
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Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT.
Physical Chemistry Chemical Physics 24 (19) , 11801–11811
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Molecular convolutional neural networks with DNA regulatory circuits.
Nature Machine Intelligence 4 (7) , 625–635
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An efficient method to predict protein thermostability in alanine mutation.
Physical Chemistry Chemical Physics 24 (48) , 29629–29639
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Novel 2-phenyl-3-(Pyridin-2-yl) thiazolidin-4-one derivatives as potent inhibitors for proliferation of osteosarcoma cells in vitro and in vivo.
European Journal of Medicinal Chemistry 228 , 114010
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Multiplex base-editing enables combinatorial epigenetic regulation for genome mining of fungal natural products.
Journal of the American Chemical Society 145 (1) , 413
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2021
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Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement.
RSC advances 11 (20) , 12036–12042
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Automated construction of neural network potential energy surface: The enhanced self-organizing incremental neural network deep potential method.
Journal of Chemical Information and Modeling 61 (11) , 5425–5437
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Extensive Evaluation of Force Fields for G-Quadruplexes.
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Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations.
Physical Chemistry Chemical Physics 23 (17) , 10636–10649
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Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: a theoretical study.
Physical Chemistry Chemical Physics 23 (21) , 12408–12420
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Automatically constructed neural network potentials for molecular dynamics simulation of zinc proteins.
Frontiers in Chemistry 9 , 692200
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Fragment-based ab initio molecular dynamics simulation for combustion.
Molecules 26 (11) , 3120
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Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins.
Nature communications 12 (1) , 4158
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Benchmark force fields for the molecular dynamic simulation of G-quadruplexes.
Molecules 26 (17) , 5379
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Molecular convolutional neural networks with DNA regulatory circuits.
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2020
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ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations.
Physical chemistry chemical physics 22 (2) , 683–691
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Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations.
Journal of Biomolecular Structure and Dynamics
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Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies.
Journal of Biomolecular Structure and Dynamics
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Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling.
Chemical Physics Letters 741 , 137126
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An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH3OH+ and CH3OH++ dissociation.
Journal of Molecular Structure 1217 , 128410
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Reaction mechanism and product branching ratios of OH+ C2H3F reaction: A theoretical study.
Chinese Journal of Chemical Physics 33 (2) , 203–209
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OH+ C_2H_3F 的反应机理及产物支化比反应的理论研究 (英文).
Chinese Journal of Chemical Physics
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Explore the Chemical.
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Explore the Chemical Space of Linear Alkanes Pyrolysis via Deep Potential Generator.
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An Approach to Computing Solvent Reorganization Energy.
Journal of Chemical Theory and Computation 16 (10) , 6513–6519
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Design, synthesis, and structure activity relationship (SAR) studies of novel imidazo [1, 2-a] pyridine derivatives as Nek2 inhibitors.
Bioorganic \& Medicinal Chemistry 28 (23) , 115775
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Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation.
Nature communications 11 (1) , 5713
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Ab Initio Molecular Dynamics Simulation of Zinc metalloproteins with Enhanced Self-Organizing Incremental High Dimensional Neural Network.
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Pharmacological activation of the p53 pathway by a new compound CYZ2017 exerts anti-tumor effects.
Biochemical and biophysical research communications 533 (4) , 1069–1075
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Exploring the chemical space of linear alkane pyrolysis via deep potential generator.
Energy \& fuels 35 (1) , 762–769
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Design, synthesis, and biological evaluation of imidazo [1, 2-a] pyridine derivatives as novel PI3K/mTOR dual inhibitors.
Journal of Medicinal Chemistry 63 (6) , 3028–3046
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2019
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A fragment quantum mechanical method for metalloproteins.
Journal of chemical theory and computation 15 (2) , 1430–1439
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L-4, a well-tolerated and orally active inhibitor of hedgehog pathway, exhibited potent anti-tumor effects against medulloblastoma in vitro and in vivo.
Frontiers in Pharmacology 10 , 89
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Theoretical investigations of photoionization efficiency of naphthalene.
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Formation Mechanism of a Nonterrestrial C6H Radical: An Ab Initio/RRKM Study on the Reaction of Tetracarbon with Acetylene.
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Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations.
Chemical Physics Letters 728 , 94–101
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Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.
Journal of Molecular Graphics and Modelling 91 , 10–21
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Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.
Nucleic Acids Research 47 (13) , 6618–6631
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Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential.
The Journal of Physical Chemistry A 123 (30) , 6587–6595
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Comparison of RP-3 pyrolysis reactions between surrogates and 45-component model by ReaxFF molecular dynamics simulations.
Energy \& Fuels 33 (8) , 7176–7187
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Understanding the selectivity of inhibitors toward PI4KIII$\alpha$ and PI4KIII$\beta$ based molecular modeling.
Physical Chemistry Chemical Physics 21 (39) , 22103–22112
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Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study.
Physical Chemistry Chemical Physics 21 (41) , 23044–23055
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Neural network based in silico simulation of combustion reactions.
arXiv preprint arXiv:1911.12252
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Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation.
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Self-assembly of metallo-nucleoside hydrogels for injectable materials that promote wound closure.
ACS applied materials \& interfaces 11 (22) , 19743–19750
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2018
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A quantum mechanical computational method for modeling electrostatic and solvation effects of protein.
Scientific reports 8 (1) , 5475
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Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes.
Frontiers in Chemistry 6 , 150
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A force balanced fragmentation method for ab initio molecular dynamic simulation of protein.
Frontiers in Chemistry 6 , 189
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Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method.
Chemical Physics Letters 706 , 400–408
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Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations.
Chemical Physics Letters 706 , 594–600
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Effect of substituents in different positions of aminothiazole hinge-binding scaffolds on inhibitor--CDK2 association probed by interaction entropy method.
ACS Omega 3 (12) , 18052–18064
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Multi-point wireless temperature sensing system for monitoring pharmaceutical lyophilization.
Frontiers in chemistry 6 , 288
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ReacNetGen: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations.
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Zhang JZH and He X (2018) Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems--Recent Developments and Advanced Applications , 15057
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2017
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Discovery of bisindole as a novel scaffold for protein tyrosine phosphatase 1B inhibitors.
Archiv der Pharmazie 350 (1) , e1600173
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Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.
Scientific Reports 7 (1) , 42223
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Structure-based design and synthesis of imidazo [1, 2-a] pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities.
European Journal of Medicinal Chemistry 126 , 1083–1106
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Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction.
Bioorganic \& Medicinal Chemistry Letters 27 (4) , 1105–1108
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A test of AMBER force fields in predicting the secondary structure of $\alpha$-helical and $\beta$-hairpin peptides.
Chemical Physics Letters 679 , 112–118
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Direct folding simulation of helical proteins using an effective polarizable bond force field.
Physical Chemistry Chemical Physics 19 (23) , 15273–15284
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An electrochemical biosensor with dual signal outputs: toward simultaneous quantification of pH and O2 in the brain upon ischemia and in a tumor during cancer starvation therapy.
Angewandte Chemie 129 (35) , 10607–10611
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Single biosensor for simultaneous quantification of glucose and pH in a rat brain of diabetic model using both current and potential outputs.
Analytical Chemistry 89 (12) , 6656–6662
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Origins of Protons in C--H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.
The Journal of Physical Chemistry A 121 (34) , 6523–6529
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MFCC-Based Fragmentation Methods for Biomolecules.
Fragmentation: Toward Accurate Calculations on Complex Molecular Systems , 323–348
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Optimization of convergence criteria for fragmentation methods.
Chemical Physics Letters 687 , 163–170
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Genome-wide microRNA expression profiling in malignant pleural effusion to identify a ten-microRNA signature..
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A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids.
RSC advances 7 (81) , 51521–51527
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2016
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Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases.
Journal of Experimental \& Clinical Cancer Research 35 (1) , 183
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PBSA_E: A PBSA-Based Free Energy Estimator for Protein--Ligand Binding Affinity.
Journal of Chemical Information and Modeling 56 (5) , 854–861
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A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach.
RSC advances 6 (110) , 108590–108602
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Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity.
Oncotarget 7 (48) , 79327
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New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment.
Bioorganic \& Medicinal Chemistry Letters 26 (15) , 3714–3718
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2015
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AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
Journal of biomolecular NMR 63 (2) , 125–139
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Quantum fragment based ab initio molecular dynamics for proteins.
Journal of chemical theory and computation 11 (12) , 5897–5905
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A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods.
Journal of chemical information and modeling 55 (9) , 1903–1913
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Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.
Physical Chemistry Chemical Physics 17 (18) , 12367–12367
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2014
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Fragment quantum mechanical calculation of proteins and its applications.
Accounts of chemical research 47 (9) , 2748–2757
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Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Physical Chemistry Chemical Physics 16 (34) , 18163–18169
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Electronic polarization stabilizes tertiary structure prediction of HP-36.
Journal of Molecular Modeling 20 (4) , 2195
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Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Advance in Structural Bioinformatics , 49–70
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2013
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Automated fragmentation QM/MM calculation of amide proton chemical shifts in proteins with explicit solvent model.
Journal of chemical theory and computation 9 (4) , 2104–2114
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A new quantum calibrated force field for zinc--protein complex.
Journal of Chemical Theory and Computation 9 (3) , 1788–1798
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An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins.
Journal of molecular modeling 19 (6) , 2605–2612
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Development of an effective polarizable bond method for biomolecular simulation.
The Journal of Physical Chemistry B 117 (48) , 14885–14893
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2012
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Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.
Physical Chemistry Chemical Physics 14 (21) , 7837–7845
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2010
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Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations.
European journal of medicinal chemistry 45 (1) , 227–235
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Quasi-classical trajectory study of the reaction O (3P)+ HCl→ OH+ Cl and O (3P)+ DCl→ OD+ Cl: Vector and scalar properties.
Journal of Molecular Structure: THEOCHEM 948 (1-3) , 36–42
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Theoretical study of stereodynamics for reaction O (3P)+ HCl.
Chinese Physics B 19 (8) , 083402
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THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O (3 P)+ HCl→ OH+ Cl FOR THE 3 A ″ELECTRONIC STATES.
Journal of Theoretical and Computational Chemistry 9 (06) , 1033–1042
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Quasi-classical Trajectory Study of Reaction O (3 P)+ HCl (v= 2; j= 1, 6, 9)→ OH+ Cl.
Chinese Physics Letters 27 (3) , 033102
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Quasi-classical Trajectory Study of Reaction O (P-3) plus HCl (v= 2; j= 1, 6, 9)-> OH plus Cl.
CHINESE PHYSICS LETTERS 27 (3)
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