Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science

Distinct Electron Conductance Regimes in Bacterial Decaheme Cytochromes

(2018) Alexandre Barrozo et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Impact of long-range electrostatic and dispersive interactions on theoretical predictions of adsorption and catalysis in zeolites

(2018) Erum Mansoor et al.   CATALYSIS TODAY

New developments in force fields for biomolecular simulations

(2018) Paul S Nerenberg et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Pore diameter dependence of catalytic activity: p-nitrobenzaldehyde conversion to an aldol product in amine-functionalized mesoporous silica

(2018) Andres García et al.   JOURNAL OF CHEMICAL PHYSICS

Exact Fluctuations of Nonequilibrium Steady States from Approximate Auxiliary Dynamics

(2018) Ushnish Ray et al.   PHYSICAL REVIEW LETTERS

Constructing Bridges between Computational Tools in Heterogeneous and Homogeneous Catalysis

(2018) Laura Falivene et al.   ACS Catalysis

Understanding Surface-Mediated Electrochemical Reactions: CO2 Reduction and Beyond

(2018) Marco Dunwell et al.   ACS Catalysis

The many-body expansion combined with neural networks

(2017) Kun Yao et al.   JOURNAL OF CHEMICAL PHYSICS

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability

(2017) Robert M. Parrish et al.   Journal of Chemical Theory and Computation

Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases

(2017) Saurabh Belsare et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase

(2017) Asmit Bhowmick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

First-Principles Models for Biological Light-Harvesting: Phycobiliprotein Complexes from Cryptophyte Algae

(2017) Mi Kyung Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals

(2017) Narbe Mardirossian et al.   MOLECULAR PHYSICS

Catalysis by Design: Well-Defined Single-Site Heterogeneous Catalysts

(2016) Jérémie D. A. Pelletier et al.   ACCOUNTS OF CHEMICAL RESEARCH

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

(2016) M. Madan Babu   BIOCHEMICAL SOCIETY TRANSACTIONS

Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy

(2016) Alessandro Piai et al.   BIOPHYSICAL JOURNAL

Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

(2016) Atanu Acharya et al.   CHEMICAL REVIEWS

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

(2016) James Lincoff et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Machine learning potentials for atomistic simulations

(2016) Jörg Behler   JOURNAL OF CHEMICAL PHYSICS

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology

(2016) Federico Melaccio et al.   Journal of Chemical Theory and Computation

Advanced Potential Energy Surfaces for Molecular Simulation

(2016) Alex Albaugh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Finding Our Way in the Dark Proteome

(2016) Asmit Bhowmick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins

(2016) David H. Brookes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS

(2016) Mikayel Aznauryan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phenomena Affecting Catalytic Reactions at Solid–Liquid Interfaces

(2016) Carsten Sievers et al.   ACS Catalysis

Catalyst: Synthetic Organic Chemistry as a Force for Good

(2016) K.C. Nicolaou   Chem

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions

(2015) Jochen Blumberger   CHEMICAL REVIEWS

FireWorks: a dynamic workflow system designed for high-throughput applications

(2015) Anubhav Jain et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Appraisal of Surface Hopping as a Tool for Modeling Condensed Phase Linear Absorption Spectra

(2015) Andrew S. Petit et al.   Journal of Chemical Theory and Computation

Silanol-Assisted Carbinolamine Formation in an Amine-Functionalized Mesoporous Silica Surface: Theoretical Investigation by Fragmentation Methods

(2015) Ana P. de Lima Batista et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effects of electrolyte, catalyst, and membrane composition and operating conditions on the performance of solar-driven electrochemical reduction of carbon dioxide

(2015) Meenesh R. Singh et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Embedded Correlated Wavefunction Schemes: Theory and Applications

(2014) Florian Libisch et al.   ACCOUNTS OF CHEMICAL RESEARCH

Zeolites as catalysts in oil refining

(2014) Ana Primo et al.   CHEMICAL SOCIETY REVIEWS

Catalytic efficiency of designed catalytic proteins

(2014) Ivan V Korendovych et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

(2014) M. Breuer et al.   Journal of the Royal Society Interface

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

(2014) Yihan Shao et al.   MOLECULAR PHYSICS

Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials

(2014) M. Breuer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Journals unite for reproducibility

(2014) M. McNutt   SCIENCE

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

A review on the electrochemical reduction of CO2 in fuel cells, metal electrodes and molecular catalysts

(2013) Rern Jern Lim et al.   CATALYSIS TODAY

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

(2013) Andrea Cavalli et al.   JOURNAL OF CHEMICAL PHYSICS

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

(2013) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Solvent-Induced Reversal of Activities between Two Closely Related Heterogeneous Catalysts in the Aldol Reaction

(2013) Kapil Kandel et al.   ACS Catalysis

Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF

(2012) Marian Breuer et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Intrinsically disordered proteins: a 10-year recap

(2012) Peter Tompa   TRENDS IN BIOCHEMICAL SCIENCES

The Growing Impact of Catalysis in the Pharmaceutical Industry

(2011) Carl A. Busacca et al.   ADVANCED SYNTHESIS & CATALYSIS

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

Simulating Chemistry Using Quantum Computers

(2011) Ivan Kassal et al.   Annual Review of Physical Chemistry

Physical constraints on charge transport through bacterial nanowires

(2011) Nicholas F. Polizzi et al.   FARADAY DISCUSSIONS

SHIFTX2: significantly improved protein chemical shift prediction

(2011) Beomsoo Han et al.   JOURNAL OF BIOMOLECULAR NMR

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering

(2011) Pau Bernadó et al.   Molecular BioSystems

A review of solar photovoltaic technologies

(2011) Bhubaneswari Parida et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Reproducible Research in Computational Science

(2011) R. D. Peng   SCIENCE

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Modeling Intrinsically Disordered Proteins with Bayesian Statistics

(2010) Charles K. Fisher et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nanoscale Advances in Catalysis and Energy Applications

(2010) Yimin Li et al.   NANO LETTERS

Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1

(2010) M. Y. El-Naggar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

Accessible Reproducible Research

(2010) J. P. Mesirov   SCIENCE

Polymer synthesis by enzymatic catalysis

(2009) Jun-ichi Kadokawa et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Towards the computational design of solid catalysts

(2009) J. K. Nørskov et al.   Nature Chemistry

Function and structure of inherently disordered proteins

(2008) A Keith Dunker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure and Dynamics of the Aβ21–30Peptide from the Interplay of NMR Experiments and Molecular Simulations

(2008) Nicolas L. Fawzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantitative quantum chemistry

(2008) Trygve Helgaker et al.   MOLECULAR PHYSICS

Towards environmental systems biology of Shewanella

(2008) James K. Fredrickson et al.   NATURE REVIEWS MICROBIOLOGY

Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment

(2008) Jochen Blumberger   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Catalytic Conversion of Biomass to Monofunctional Hydrocarbons and Targeted Liquid-Fuel Classes

(2008) E. L. Kunkes et al.   SCIENCE