Quantum Chemical Microsolvation by Automated Water Placement

Towards a converged strategy for including microsolvation in reaction mechanism calculations

(2021) Rebecca Sure et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom‐up investigation

(2020) Giuseppe Lanza et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

STACKED – Solvation Theory of Aromatic Complexes as Key for Estimating Drug binding

(2020) Johannes Reinhard Loeffler et al.   Journal of Chemical Information and Modeling

Self-Parametrizing System-Focused Atomistic Models

(2020) Christoph Brunken et al.   Journal of Chemical Theory and Computation

Systematic microsolvation approach with a cluster‐continuum scheme and conformational sampling

(2020) Gregor N. Simm et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Microhydration of a Carbonyl Group: How does the Molecular Electrostatic Potential (MESP) Impact the Formation of (H2O)n:(R2C═O)Complexes?

(2020) Emilie-Laure Zins   JOURNAL OF PHYSICAL CHEMISTRY A

ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design

(2020) Marko Jukič et al.   ACS Medicinal Chemistry Letters

Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes

(2020) Alex Elmi et al.   ACCOUNTS OF CHEMICAL RESEARCH

Water Docking Bias in [4]Helicene

(2019) Sérgio Rosa Domingos et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

DRoP: Automated detection of conserved solvent‐binding sites on proteins

(2019) Bradley M. Kearney et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DFT investigation on the intramolecular and intermolecular proton transfer processes in 2-aminobenzothiazole (ABT) in the gas phase and in different solvents

(2019) Nuha Wazzan et al.   STRUCTURAL CHEMISTRY

Hydration of Aromatic Heterocycles as Adversary of π-Stacking

(2019) Johannes Reinhard Loeffler et al.   Journal of Chemical Information and Modeling

Hybrid discrete‐continuum solvation methods

(2019) Josefredo R. Pliego et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces

(2019) Johannes Kraml et al.   Journal of Chemical Theory and Computation

Advances and challenges in modeling solvated reaction mechanisms for renewable fuels and chemicals

(2019) Yasemin Basdogan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Machine Learning-Guided Approach for Studying Solvation Environments

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

Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods

(2018) Denis Bucher et al.   Journal of Chemical Information and Modeling

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

(2018) Axel Rudling et al.   Journal of Chemical Information and Modeling

The molecular electrostatic potential analysis of solutes and water clusters: a straightforward tool to predict the geometry of the most stable micro-hydrated complexes of β-propiolactone and formamide

(2018) Cairedine Kalai et al.   THEORETICAL CHEMISTRY ACCOUNTS

Binding Pose Flip Explained via Enthalpic and Entropic Contributions

(2017) Michael Schauperl et al.   Journal of Chemical Information and Modeling

Averaged Condensed Phase Model for Simulating Molecules in Complex Environments

(2017) Dominique Nocito et al.   Journal of Chemical Theory and Computation

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery

(2017) Francesca Spyrakis et al.   JOURNAL OF MEDICINAL CHEMISTRY

Microhydration of a benzoic acid molecule and its dissociation

(2017) Parvathi Krishnakumar et al.   NEW JOURNAL OF CHEMISTRY

Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins

(2017) Michael Schauperl et al.   Scientific Reports

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

(2016) Steven Ramsey et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Urea hydration from dielectric relaxation spectroscopy: old findings confirmed, new insights gained

(2016) Vira Agieienko et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Strategies to Calculate Water Binding Free Energies in Protein–Ligand Complexes

(2014) Michael S. Bodnarchuk et al.   Journal of Chemical Information and Modeling

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa

(2014) Crystal N. Nguyen et al.   Journal of Chemical Theory and Computation

Second generation Car-Parrinello molecular dynamics

(2014) Thomas D. Kühne   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structural studies of aromatic carboxylic acids via computational chemistry and microwave spectroscopy

(2013) Peter D. Godfrey et al.   JOURNAL OF CHEMICAL PHYSICS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Urea in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)

(2013) Alexander K. H. Weiss et al.   Molecular BioSystems

The benzoic acid–water complex: a potential atmospheric nucleation precursor studied using microwave spectroscopy and ab initio calculations

(2013) Elijah G. Schnitzler et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Turbomole

(2013) Filipp Furche et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

(2012) Crystal N. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

Resolution of a Challenge for Solvation Modeling: Calculation of Dicarboxylic Acid Dissociation Constants Using Mixed Discrete–Continuum Solvation Models

(2012) Aleksandr V. Marenich et al.   Journal of Physical Chemistry Letters

(+)-syn-Benzotriborneol an enantiopure C3-symmetric receptor for water

(2012) Fabrizio Fabris et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms

(2012) Raghavan B. Sunoj et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A challenging system: Free energy prediction for factor Xa

(2011) Hannes G. Wallnoefer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Car-Parrinello molecular dynamics

(2011) Jürg Hutter   Wiley Interdisciplinary Reviews-Computational Molecular Science

The COSMO and COSMO-RS solvation models

(2011) Andreas Klamt   Wiley Interdisciplinary Reviews-Computational Molecular Science

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Solvent effects on the electronic absorption spectrum of camphor using continuum, discrete or explicit approaches

(2009) Jacob Kongsted et al.   CHEMICAL PHYSICS LETTERS

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

(2009) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

(2009) Eirik F. da Silva et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

(2009) Aleksandr V. Marenich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Universal Approach to Solvation Modeling

(2008) Christopher J. Cramer et al.   ACCOUNTS OF CHEMICAL RESEARCH

When Is a Molecule Properly Solvated by a Continuum Model or in a Cluster Ansatz? A First-Principles Simulation of Alanine Hydration

(2008) Jens Thar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculation of Solvation Free Energies of Charged Solutes Using Mixed Cluster/Continuum Models

(2008) Vyacheslav S. Bryantsev et al.   JOURNAL OF PHYSICAL CHEMISTRY B