Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

Theoretical study of the adsorption and dissociation mechanism for methylamine on Pd(111)

(2013) Jian-Hong Liu et al.   APPLIED SURFACE SCIENCE

Surface self-diffusion of Re adatom on the Re cluster with hexahedral structure

(2013) Xiongying Dai et al.   PHYSICA B-CONDENSED MATTER

Energetic landscape and diffusion of He inα-Fe grain boundaries from first principles

(2013) Lei Zhang et al.   PHYSICAL REVIEW B

A theoretical study of CH4 dissociation on NiPd(111) surface

(2013) Kai Li et al.   SURFACE SCIENCE

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

(2012) Conchín Meliá et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ab initio quantum chemical and ReaxFF-based study of the intramolecular iminium–enamine conversion in a proline-catalyzed reaction

(2012) Pierre O. Hubin et al.   THEORETICAL CHEMISTRY ACCOUNTS

Reactive Molecular Dynamics Simulation of Fullerene Combustion Synthesis: ReaxFF vs DFTB Potentials

(2011) Hu-Jun Qian et al.   Journal of Chemical Theory and Computation

Development of Interatomic ReaxFF Potentials for Au–S–C–H Systems

(2011) Tommi T. Järvi et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Reactive Molecular Dynamics Study on the First Steps of DNA Damage by Free Hydroxyl Radicals

(2011) Ramin M. Abolfath et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics

(2011) Si-ping Han et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hyperthermal Oxygen Interacting with Silicon Surfaces: Adsorption, Implantation, and Damage Creation

(2011) E. C. Neyts et al.   Journal of Physical Chemistry C

Hydroxylation Structure and Proton Transfer Reactivity at the Zinc Oxide−Water Interface

(2011) David Raymand et al.   Journal of Physical Chemistry C

Changing Chirality during Single-Walled Carbon Nanotube Growth: A Reactive Molecular Dynamics/Monte Carlo Study

(2011) Erik C. Neyts et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tunable nanomechanics of protein disulfide bonds in redox microenvironments

(2011) Sinan Keten et al.   Journal of the Mechanical Behavior of Biomedical Materials

Comprehensive computational study of gas-phase conformations of neutral, protonated and deprotonated glutamic acids

(2011) Lingbiao Meng et al.   Computational and Theoretical Chemistry

Catalyzed Growth of Carbon Nanotube with Definable Chirality by Hybrid Molecular Dynamics−Force Biased Monte Carlo Simulations

(2010) Erik C. Neyts et al.   ACS Nano

Computational enzymology

(2010) Richard Lonsdale et al.   CHEMICAL COMMUNICATIONS

Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential

(2010) Tobias Benighaus et al.   Journal of Chemical Theory and Computation

Evolving Carbapenemases: Can Medicinal Chemists Advance One Step Ahead of the Coming Storm?

(2010) Peter Oelschlaeger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Comprehensive ab initio study on the conformations of L-Threonine and L-allo-Threonine and related species in gas phase

(2010) Xuee Xu et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Development of a Reactive Force Field for Iron−Oxyhydroxide Systems

(2010) Masoud Aryanpour et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Modeling the Structure and Absorption Spectra of Stilbazolium Merocyanine in Polar and Nonpolar Solvents Using Hybrid QM/MM Techniques

(2010) N. Arul Murugan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization

(2010) Obaidur Rahaman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the origin of the chemical barrier and tunneling in enzymes

(2010) Sara Quaytman Machleder et al.   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

Embrittlement of Metal by Solute Segregation-Induced Amorphization

(2010) Hsiu-Pin Chen et al.   PHYSICAL REVIEW LETTERS

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic−Aromatic Side Chain Interactions in Proteins

(2009) H. Valdes et al.   Journal of Chemical Theory and Computation

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A β-Lactamase†

(2009) Johannes C. Hermann et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Assignment of the Vibrational Spectra of Enzyme-Bound Tryptophan Tryptophyl Quinones Using a Combined QM/MM Approach

(2009) Jiayun Pang et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-α-carboxamide

(2009) Duhee Bang et al.   Molecular BioSystems

Enzymatic transition states and dynamic motion in barrier crossing

(2009) Steven D Schwartz et al.   Nature Chemical Biology

A 21st century revisionist's view at a turning point in enzymology

(2009) Zachary D Nagel et al.   Nature Chemical Biology

An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods

(2009) Amareshwar Kumar Rai et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Optimization methods for finding minimum energy paths

(2008) Daniel Sheppard et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids

(2008) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Outsmarting metallo-β-lactamases by mimicking their natural evolution

(2008) Peter Oelschlaeger   JOURNAL OF INORGANIC BIOCHEMISTRY

A semi-empirical and ab initio combined approach for the full conformational searches of gaseous lysine and lysine–H2O complex

(2008) Yumin Leng et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

ReaxFF Reactive Force Field for Solid Oxide Fuel Cell Systems with Application to Oxygen Ion Transport in Yttria-Stabilized Zirconia

(2008) Adri C. T. van Duin et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Molecular Dynamics Simulations of the Interactions between Platinum Clusters and Carbon Platelets

(2008) Carlos F. Sanz-Navarro et al.   JOURNAL OF PHYSICAL CHEMISTRY A

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation

(2008) Kimberly Chenoweth et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Incorporation of a QM/MM Buffer Zone in the Variational Double Self-Consistent Field Method

(2008) Wangshen Xie et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation

(2008) M. Scott Shell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Role of the Zn1and Zn2sites in Metallo-β-lactamase L1

(2008) Zhenxin Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

(2008) Haydee Valdes et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS