Molecular simulation approaches to study crystal nucleation from solutions: Theoretical considerations and computational challenges

Collective Variables for Conformational Polymorphism in Molecular Crystals

(2023) Oren Elishav et al.   Journal of Physical Chemistry Letters

Non-Equilibrium Modeling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations

(2023) Tarak Karmakar et al.   Accounts of Chemical Research

A variational approach to assess reaction coordinates for two-step crystallization

(2023) A. R. Finney et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation of Biomolecular Condensates from Finite-Sized Simulations

(2023) Lunna Li et al.   Journal of Physical Chemistry Letters

Driving and characterizing nucleation of urea and glycine polymorphs in water

(2023) Ziyue Zou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classical and Nonclassical Nucleation and Growth Mechanisms for Nanoparticle Formation

(2022) Young-Shin Jun et al.   Annual Review of Physical Chemistry

A complete description of thermodynamic stabilities of molecular crystals

(2022) Venkat Kapil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Practical guide to replica exchange transition interface sampling and forward flux sampling

(2022) Steven W. Hall et al.   JOURNAL OF CHEMICAL PHYSICS

Understanding Metal–Organic Framework Nucleation from a Solution with Evolving Graphs

(2022) Loukas Kollias et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computer simulation of the early stages of self-assembly and thermal decomposition of ZIF-8

(2022) S. R. G. Balestra et al.   JOURNAL OF CHEMICAL PHYSICS

Collective Variables for Crystallization Simulations─from Early Developments to Recent Advances

(2022) Neha et al.   ACS Omega

Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering

(2021) Veselina Marinova et al.   Journal of Chemical Information and Modeling

Machine Learning for Chemical Reactions

(2021) Markus Meuwly   CHEMICAL REVIEWS

Speciation of Substituted Benzoic Acids in Solution: Evaluation of Spectroscopic and Computational Methods for the Identification of Associates and Their Role in Crystallization

(2021) Agris Be̅rziņš et al.   CRYSTAL GROWTH & DESIGN

The seven deadly sins: When computing crystal nucleation rates, the devil is in the details

(2021) Katarina E. Blow et al.   JOURNAL OF CHEMICAL PHYSICS

Reaction coordinates in complex systems-a perspective

(2021) Jutta Rogal   EUROPEAN PHYSICAL JOURNAL B

Pre-Nucleation Clusters Predict Crystal Structures in Models of Chiral Molecules

(2021) John E. Carpenter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Deep learning the slow modes for rare events sampling

(2021) Luigi Bonati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stable Prenucleation Calcium Carbonate Clusters Define Liquid-Liquid Phase Separation

(2020) Jonathan T. Avaro et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Amino Acid and Oligopeptide Effects on Calcium Carbonate Solutions

(2020) Aaron R. Finney et al.   CRYSTAL GROWTH & DESIGN

Molecular Force Field Development for Aqueous Electrolytes: 2. Polarizable Models Incorporating Crystalline Chemical Potential and Their Accurate Simulations of Halite, Hydrohalite, Aqueous Solutions of NaCl, and Solubility

(2020) Jan Dočkal et al.   Journal of Chemical Theory and Computation

Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics

(2020) Paolo Raiteri et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin

(2020) Mingjun Yang et al.   CRYSTAL GROWTH & DESIGN

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

(2020) Nicholas F. Francia et al.   CRYSTAL GROWTH & DESIGN

Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules

(2020) Nathan S. Abraham et al.   Journal of Chemical Theory and Computation

Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling

(2020) A. Arjun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multivalent Surface Cations Enhance Heterogeneous Freezing of Water on Muscovite Mica

(2020) Nurun Nahar Lata et al.   Journal of Physical Chemistry Letters

Polymorph-Selective Role of Hydrogen Bonding and π–π Stacking in p-Aminobenzoic Acid Solutions

(2020) Raitis Bobrovs et al.   CRYSTAL GROWTH & DESIGN

Reliable and practical computational description of molecular crystal polymorphs

(2019) Johannes Hoja et al.   Science Advances

Molecular Level Understanding of the Free Energy Landscape in Early Stages of Metal–Organic Framework Nucleation

(2019) Loukas Kollias et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nucleation in aqueous NaCl solutions shifts from 1-step to 2-step mechanism on crossing the spinodal

(2019) Hao Jiang et al.   JOURNAL OF CHEMICAL PHYSICS

Can clathrates heterogeneously nucleate ice?

(2019) Matías H. Factorovich et al.   JOURNAL OF CHEMICAL PHYSICS

Unbiased atomistic insight in the competing nucleation mechanisms of methane hydrates

(2019) Arjun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adding Anisotropy to the Standard Quasi-Harmonic Approximation Still Fails in Several Ways to Capture Organic Crystal Thermodynamics

(2019) Nathan S. Abraham et al.   CRYSTAL GROWTH & DESIGN

Understanding Polymorph Selection of Sulfamerazine in Solution

(2019) Chengxiang Liu et al.   CRYSTAL GROWTH & DESIGN

Simulation of Calcium Phosphate Prenucleation Clusters in Aqueous Solution: Association beyond Ion Pairing

(2019) Natalya A. Garcia et al.   CRYSTAL GROWTH & DESIGN

Assessment of Approximate Methods for Anharmonic Free Energies

(2019) Venkat Kapil et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential

(2019) Tarak Karmakar et al.   Journal of Chemical Theory and Computation

Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution

(2019) Paramvir Ahlawat et al.   CHEMISTRY OF MATERIALS

Classical nucleation theory approach to two-step nucleation of crystals

(2019) Dimo Kashchiev   JOURNAL OF CRYSTAL GROWTH

Two-Step Nucleation Process of Calcium Silicate Hydrate, the Nanobrick of Cement

(2018) Nina Krautwurst et al.   CHEMISTRY OF MATERIALS

Crystal structure prediction is changing from basic science to applied technology

(2018) Jonas Nyman et al.   FARADAY DISCUSSIONS

Recent progress in the molecular simulation of thermodynamic properties of aqueous electrolyte solutions

(2018) William R. Smith et al.   FLUID PHASE EQUILIBRIA

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions

(2018) Hao Jiang et al.   JOURNAL OF CHEMICAL PHYSICS

NaCl nucleation from brine in seeded simulations: Sources of uncertainty in rate estimates

(2018) Nils. E. R. Zimmermann et al.   JOURNAL OF CHEMICAL PHYSICS

SSAGES: Software Suite for Advanced General Ensemble Simulations

(2018) Hythem Sidky et al.   JOURNAL OF CHEMICAL PHYSICS

Forward-flux sampling with jumpy order parameters

(2018) Amir Haji-Akbari   JOURNAL OF CHEMICAL PHYSICS

Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces

(2018) Philipp Pedevilla et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation of Molecular Crystals Driven by Relative Information Entropy

(2018) Gianpaolo Gobbo et al.   Journal of Chemical Theory and Computation

Modelling nucleation from solution with the string method in the osmotic ensemble

(2018) Chengxiang Liu et al.   MOLECULAR PHYSICS

Crystal structure prediction is changing from basic science to applied technology

(2018) Jonas Nyman et al.   FARADAY DISCUSSIONS

Computational methodology for solubility prediction: Application to sparingly soluble organic/inorganic materials

(2018) Lunna Li et al.   JOURNAL OF CHEMICAL PHYSICS

Predicting polymorphism in molecular crystals using orientational entropy

(2018) Pablo M. Piaggi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reactive molecular dynamics: From small molecules to proteins

(2018) Markus Meuwly   Wiley Interdisciplinary Reviews-Computational Molecular Science

Solvent-mediated morphology selection of the active pharmaceutical ingredient isoniazid: Experimental and simulation studies

(2018) Dandan Han et al.   CHEMICAL ENGINEERING SCIENCE

Harnessing Cloud Architecture for Crystal Structure Prediction Calculations

(2018) Peiyu Zhang et al.   CRYSTAL GROWTH & DESIGN

Nucleation of urea from aqueous solution: Structure, critical size, and rate

(2017) Taraknath Mandal et al.   JOURNAL OF CHEMICAL PHYSICS

Computational methodology for solubility prediction: Application to the sparingly soluble solutes

(2017) Lunna Li et al.   JOURNAL OF CHEMICAL PHYSICS

Analyzing and Driving Cluster Formation in Atomistic Simulations

(2017) Gareth A. Tribello et al.   Journal of Chemical Theory and Computation

Heterogeneous Ice Nucleation: Interplay of Surface Properties and Their Impact on Water Orientations

(2017) Brittany Glatz et al.   LANGMUIR

Estimating the solubility of 1:1 electrolyte aqueous solutions: the chemical potential difference rule

(2017) A.L. Benavides et al.   MOLECULAR PHYSICS

Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation

(2017) Aydin Ozcan et al.   Chemical Science

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Reaction Coordinates and Mechanistic Hypothesis Tests

(2016) Baron Peters   Annual Review of Physical Chemistry

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

(2016) Gabriele C. Sosso et al.   CHEMICAL REVIEWS

Entropy Drives Calcium Carbonate Ion Association

(2016) Matthias Kellermeier et al.   CHEMPHYSCHEM

A Review of Classical and Nonclassical Nucleation Theories

(2016) S. Karthika et al.   CRYSTAL GROWTH & DESIGN

Seeding approach to crystal nucleation

(2016) Jorge R. Espinosa et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation barrier reconstruction via the seeding method in a lattice model with competing nucleation pathways

(2016) Yuri Lifanov et al.   JOURNAL OF CHEMICAL PHYSICS

Ice formation on kaolinite: Insights from molecular dynamics simulations

(2016) Gabriele C. Sosso et al.   JOURNAL OF CHEMICAL PHYSICS

Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route

(2016) A. L. Benavides et al.   JOURNAL OF CHEMICAL PHYSICS

On the calculation of solubilities via direct coexistence simulations: Investigation of NaCl aqueous solutions and Lennard-Jones binary mixtures

(2016) J. R. Espinosa et al.   JOURNAL OF CHEMICAL PHYSICS

Recent progress in molecular simulation of aqueous electrolytes: force fields, chemical potentials and solubility

(2016) Ivo Nezbeda et al.   MOLECULAR PHYSICS

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

(2016) Mariana Rossi et al.   PHYSICAL REVIEW LETTERS

Report on the sixth blind test of organic crystal structure prediction methods

(2016) Anthony M. Reilly et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Nonclassical nucleation and growth of inorganic nanoparticles

(2016) Jisoo Lee et al.   Nature Reviews Materials

The ReaxFF reactive force-field: development, applications and future directions

(2016) Thomas P Senftle et al.   npj Computational Materials

Recent advances in molecular simulation: A chemical engineering perspective

(2015) Jeremy C. Palmer et al.   AICHE JOURNAL

Secondary Crystal Nucleation: Nuclei Breeding Factory Uncovered

(2015) Jamshed Anwar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Facts and fictions about polymorphism

(2015) Aurora J. Cruz-Cabeza et al.   CHEMICAL SOCIETY REVIEWS

Two-Step Nucleation Rather than Self-Poisoning: An Unexpected Mechanism of Asymmetrical Molecular Crystal Growth

(2015) Philipp Ectors et al.   CRYSTAL GROWTH & DESIGN

From oligomers towards a racemic crystal: molecular simulation ofdl-norleucine crystal nucleation from solution

(2015) Philipp Ectors et al.   CRYSTENGCOMM

Nucleation in complex multi-component and multi-phase systems: general discussion

(2015) Sarah Price et al.   FARADAY DISCUSSIONS

Solvent and additive interactions as determinants in the nucleation pathway: general discussion

(2015) Changquan Calvin Sun et al.   FARADAY DISCUSSIONS

Urea homogeneous nucleation mechanism is solvent dependent

(2015) Matteo Salvalaglio et al.   FARADAY DISCUSSIONS

A general method for molecular modeling of nucleation from the melt

(2015) Erik E. Santiso et al.   JOURNAL OF CHEMICAL PHYSICS

Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations

(2015) Zoltan Mester et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations of solutions at constant chemical potential

(2015) C. Perego et al.   JOURNAL OF CHEMICAL PHYSICS

Chemical Potentials, Activity Coefficients, and Solubility in Aqueous NaCl Solutions: Prediction by Polarizable Force Fields

(2015) Filip Moučka et al.   Journal of Chemical Theory and Computation

Thermodynamically Consistent Force Field for Molecular Dynamics Simulations of Alkaline-Earth Carbonates and Their Aqueous Speciation

(2015) Paolo Raiteri et al.   Journal of Physical Chemistry C

A two-parameter extension of classical nucleation theory

(2015) James F Lutsko et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates

(2015) Nils E. R. Zimmermann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mesoscopic nucleation theory for confined systems: A one-parameter model

(2015) Miguel A. Durán-Olivencia et al.   PHYSICAL REVIEW E

Direct calculation of ice homogeneous nucleation rate for a molecular model of water

(2015) Amir Haji-Akbari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleation in complex multi-component and multi-phase systems: general discussion

(2015) Sarah Price et al.   FARADAY DISCUSSIONS

Solvent and additive interactions as determinants in the nucleation pathway: general discussion

(2015) Changquan Calvin Sun et al.   FARADAY DISCUSSIONS

Urea homogeneous nucleation mechanism is solvent dependent

(2015) Matteo Salvalaglio et al.   FARADAY DISCUSSIONS

Metadynamics studies of crystal nucleation

(2015) Federico Giberti et al.   IUCrJ

Pre-nucleation clusters as solute precursors in crystallisation

(2014) Denis Gebauer et al.   CHEMICAL SOCIETY REVIEWS

Nucleation near the eutectic point in a Potts-lattice gas model

(2014) Vishal Agarwal et al.   JOURNAL OF CHEMICAL PHYSICS

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Methane Clathrate Hydrate Nucleation Mechanism by Advanced Molecular Simulations

(2014) Marco Lauricella et al.   Journal of Physical Chemistry C

Molecular-dynamics simulations of urea nucleation from aqueous solution

(2014) Matteo Salvalaglio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

1,3,5-Tris(4-bromophenyl)benzene prenucleation clusters from metadynamics

(2014) Matteo Salvalaglio et al.   Acta Crystallographica Section C-Structural Chemistry

Controlling and Predicting Crystal Shapes: The Case of Urea

(2013) Matteo Salvalaglio et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Nucleation of Organic Crystals-A Molecular Perspective

(2013) Roger J. Davey et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Predicting crystal structures of organic compounds

(2013) Sarah L. Price   CHEMICAL SOCIETY REVIEWS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Classical nucleation theory from a dynamical approach to nucleation

(2013) James F. Lutsko et al.   JOURNAL OF CHEMICAL PHYSICS

Large scale molecular dynamics simulations of homogeneous nucleation

(2013) Jürg Diemand et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular simulation of aqueous electrolytes: Water chemical potential results and Gibbs-Duhem equation consistency tests

(2013) Filip Moučka et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Force Field Development for Aqueous Electrolytes: 1. Incorporating Appropriate Experimental Data and the Inadequacy of Simple Electrolyte Force Fields Based on Lennard-Jones and Point Charge Interactions with Lorentz–Berthelot Rules

(2013) Filip Moučka et al.   Journal of Chemical Theory and Computation

Transient Polymorphism in NaCl

(2013) Federico Giberti et al.   Journal of Chemical Theory and Computation

Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions

(2013) A. F. Wallace et al.   SCIENCE

Ion-association complexes unite classical and non-classical theories for the biomimetic nucleation of calcium phosphate

(2013) Wouter J. E. M. Habraken et al.   Nature Communications

Probing the structure and stability of calcium carbonate pre-nucleation clusters

(2012) Aaron R. Finney et al.   FARADAY DISCUSSIONS

The non-classical nucleation of crystals: microscopic mechanisms and applications to molecular crystals, ice and calcium carbonate

(2012) R P Sear   INTERNATIONAL MATERIALS REVIEWS

Solubility of NaCl in water by molecular simulation revisited

(2012) J. L. Aragones et al.   JOURNAL OF CHEMICAL PHYSICS

Homogeneous Nucleation of Methane Hydrates: Unrealistic under Realistic Conditions

(2012) Brandon C. Knott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic Improvement of Classical Nucleation Theory

(2012) Santi Prestipino et al.   PHYSICAL REVIEW LETTERS

Uncovering Molecular Processes in Crystal Nucleation and Growth by Using Molecular Simulation

(2011) Jamshed Anwar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Progress in Crystal Structure Prediction

(2011) John Kendrick et al.   CHEMISTRY-A EUROPEAN JOURNAL

Free-energy landscape of nucleation with an intermediate metastable phase studied using capillarity approximation

(2011) Masao Iwamatsu   JOURNAL OF CHEMICAL PHYSICS

A general set of order parameters for molecular crystals

(2011) Erik E. Santiso et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Simulation of Aqueous Electrolyte Solubility. 2. Osmotic Ensemble Monte Carlo Methodology for Free Energy and Solubility Calculations and Application to NaCl

(2011) Filip Moučka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current approaches to predicting molecular organic crystal structures

(2011) Graeme M. Day   Crystallography Reviews

Stable prenucleation mineral clusters are liquid-like ionic polymers

(2011) Raffaella Demichelis et al.   Nature Communications

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A Computational Study of the Mechanism of the Selective Crystallization of α- and β-Glycine from Water and Methanol−Water Mixture

(2010) Jie Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The two-step mechanism of nucleation of crystals in solution

(2010) Peter G. Vekilov   Nanoscale

Observation of two-step nucleation in methane hydrates

(2010) Jenel Vatamanu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Precursor-Mediated Crystallization Process in Suspensions of Hard Spheres

(2010) T. Schilling et al.   PHYSICAL REVIEW LETTERS

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

Nucleation of Crystals from Solution: Classical and Two-Step Models

(2009) Deniz Erdemir et al.   ACCOUNTS OF CHEMICAL RESEARCH

Evaluating nucleation rates in direct simulations

(2009) Guram Chkonia et al.   JOURNAL OF CHEMICAL PHYSICS

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Homogeneous nucleation under shear in a two-dimensional Ising model: Cluster growth, coalescence, and breakup

(2008) Rosalind J. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate determination of crystal structures based on averaged local bond order parameters

(2008) Wolfgang Lechner et al.   JOURNAL OF CHEMICAL PHYSICS

Crystal growth of α and γ glycine polymorphs and their polymorphic phase transformations

(2008) K. Srinivasan   JOURNAL OF CRYSTAL GROWTH

Computational Study of Solvent Effects on the Molecular Self-Assembly of Tetrolic Acid in Solution and Implications for the Polymorph Formed from Crystallization

(2008) Jie Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Stable Prenucleation Calcium Carbonate Clusters

(2008) Denis Gebauer et al.   SCIENCE

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry