Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory

Ion Permeation, Selectivity, and Electronic Polarization in Fluoride Channels

(2022) Zhi Yue et al.   BIOPHYSICAL JOURNAL

Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate

(2021) M.R. VanGordon et al.   BIOPHYSICAL JOURNAL

Toward a First-Principles Framework for Predicting Collective Properties of Electrolytes

(2021) Timothy T. Duignan et al.   ACCOUNTS OF CHEMICAL RESEARCH

Thermodynamics of Hydration from the Perspective of the Molecular Quasichemical Theory of Solutions

(2021) Dilipkumar N. Asthagiri et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energies of Hydrated Halide Anions: High Through-Put Computations on Clusters to Treat Rough Energy-Landscapes

(2021) Diego T. Gomez et al.   MOLECULES

Hydration Mimicry by Membrane Ion Channels

(2020) Mangesh I. Chaudhari et al.   Annual Review of Physical Chemistry

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

(2020) Thomas D. Kühne et al.   JOURNAL OF CHEMICAL PHYSICS

Machine Learning-Guided Approach for Studying Solvation Environments

(2019) Yasemin Basdogan et al.   Journal of Chemical Theory and Computation

Strontium and barium in aqueous solution and a potassium channel binding site

(2018) Mangesh I. Chaudhari et al.   JOURNAL OF CHEMICAL PHYSICS

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

(2018) Wojciech Kopec et al.   Nature Chemistry

Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F–) Anion Hydration

(2018) A. Muralidharan et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Quasi-chemical theory of F−(aq): The “no split occupancies rule” revisited

(2017) Mangesh I. Chaudhari et al.   JOURNAL OF CHEMICAL PHYSICS

Partial Molar Volumes of Aqua Ions from First Principles

(2017) Julia Wiktor et al.   Journal of Chemical Theory and Computation

Utility of chemical computations in predicting solution free energies of metal ions

(2017) Mangesh I. Chaudhari et al.   MOLECULAR SIMULATION

Real single ion solvation free energies with quantum mechanical simulation

(2017) Timothy T. Duignan et al.   Chemical Science

Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel

(2016) David Medovoy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Protons and Hydroxide Ions in Aqueous Systems

(2016) Noam Agmon et al.   CHEMICAL REVIEWS

Toward a quantitative theory of Hofmeister phenomena: From quantum effects to thermodynamics

(2016) Travis P. Pollard et al.   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Free Energies of Ion Binding in the Bacterial CLC-ec1 Chloride Transporter with Implications for the Transport Mechanism and Selectivity

(2016) Zhihong Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ion-Specific Effects in Carboxylate Binding Sites

(2016) Mark J. Stevens et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

(2016) Kuglae Kim et al.   Nature Communications

Organic Toxins as Tools to Understand Ion Channel Mechanisms and Structure

(2015) Sara Morales-Lazaro et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Octa-Coordination and the Aqueous Ba2+ Ion

(2015) Mangesh I. Chaudhari et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crystal structures of a double-barrelled fluoride ion channel

(2015) Randy B. Stockbridge et al.   NATURE

Mysteries of Metals in Metalloenzymes

(2014) Crystal E. Valdez et al.   ACCOUNTS OF CHEMICAL RESEARCH

Importance of Metal Hydration on the Selectivity of Mg2+ versus Ca2+ in Magnesium Ion Channels

(2013) Todor Dudev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Role of methyl-induced polarization in ion binding

(2013) M. Rossi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combined Density Functional Theory (DFT) and Continuum Calculations of pKa in Carbonic Anhydrase

(2012) Dian Jiao et al.   BIOCHEMISTRY

Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations

(2012) Valéry Weber et al.   Journal of Chemical Theory and Computation

Communication: Regularizing binding energy distributions and thermodynamics of hydration: Theory and application to water modeled with classical and ab initio simulations

(2011) Valéry Weber et al.   JOURNAL OF CHEMICAL PHYSICS

Ion-water clusters, bulk medium effects, and ion hydration

(2011) Safir Merchant et al.   JOURNAL OF CHEMICAL PHYSICS

Design principles for K+selectivity in membrane transport

(2011) Sameer Varma et al.   JOURNAL OF GENERAL PHYSIOLOGY

Selectivity and Permeation of Alkali Metal Ions in K+-channels

(2011) Simone Furini et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing the Thermodynamics of Competitive Ion Binding Using Minimum Energy Structures

(2011) David M. Rogers et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Chemistry of Hofmeister Anions and Osmolytes

(2010) Yanjie Zhang et al.   Annual Review of Physical Chemistry

Multibody Effects in Ion Binding and Selectivity

(2010) Sameer Varma et al.   BIOPHYSICAL JOURNAL

Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton

(2010) Dominik Marx et al.   CHEMICAL REVIEWS

Quasichemical and structural analysis of polarizable anion hydration

(2010) David M. Rogers et al.   JOURNAL OF CHEMICAL PHYSICS

First Principles Calculations of Atomic Nickel Redox Potentials and Dimerization Free Energies: A Study of Metal Nanoparticle Growth

(2010) Dian Jiao et al.   Journal of Chemical Theory and Computation

Probing the Hydration Structure of Polarizable Halides: A Multiedge XAFS and Molecular Dynamics Study of the Iodide Anion

(2010) John L. Fulton et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ion selectivity from local configurations of ligands in solutions and ion channels

(2009) D. Asthagiri et al.   CHEMICAL PHYSICS LETTERS

Specific ion effects in colloidal and biological systems

(2009) Werner Kunz   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Quasichemical theory with a soft cutoff

(2009) Shaji Chempath et al.   JOURNAL OF CHEMICAL PHYSICS

Chloride ion conduction without water coordination in the pore of ClC protein

(2009) Youn Jo Ko et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Selectivity of K+ Ion Channels: Testing the Hypotheses

(2008) Philip W. Fowler et al.   BIOPHYSICAL JOURNAL

K+Channel Modulators for the Treatment of Neurological Disorders and Autoimmune Diseases

(2008) Heike Wulff et al.   CHEMICAL REVIEWS

The structure of aqueous sodium hydroxide solutions: A combined solution x-ray diffraction and simulation study

(2008) Tünde Megyes et al.   JOURNAL OF CHEMICAL PHYSICS

Structural Transitions in Ion Coordination Driven by Changes in Competition for Ligand Binding

(2008) Sameer Varma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

K+/Na+ Selectivity in K Channels and Valinomycin: Over-coordination Versus Cavity-size constraints

(2007) Sameer Varma et al.   JOURNAL OF MOLECULAR BIOLOGY

Studies of the Thermodynamic Properties of Hydrogen Gas in Bulk Water

(2007) Dubravko Sabo et al.   JOURNAL OF PHYSICAL CHEMISTRY B