The missing term in effective pair potentials

Computer Simulation of Liquids

Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945

The Amber biomolecular simulation programs

Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535

Solvent Structure, Dynamics, and Ion Mobility in Aqueous Solutions at 25 °C

Koneshan, S., Rasaiah, J. C., Lynden-Bell, R. M., & Lee, S. H. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp980642x · Cited by 965

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Rühle, V., Junghans, C., Lukyanov, A., Kremer, K., & Andrienko, D. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct900369w · Cited by 485

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Mashl, R. J., Joseph, S., Aluru, N. R., & Jakobsson, E. (2003) · Nano Letters · doi:10.1021/nl0340226 · Cited by 447

An overview of current issues in the uptake of atmospheric trace gases by aerosols and clouds

Kolb, C. E., Cox, R. A., Abbatt, J. P. D., Ammann, M., Davis, E. J., Donaldson, D. J., Garrett, B. C., George, C., Griffiths, P. T., Hanson, D. R., et al. (2010) · Atmospheric Chemistry and Physics · doi:10.5194/acp-10-10561-2010 · Cited by 405

Critical Knowledge Gaps in Mass Transport through Single-Digit Nanopores: A Review and Perspective

Faucher, S., Aluru, N., Bazant, M. Z., Blankschtein, D., Brozena, A. H., Cumings, J., Pedro de Souza, J., Elimelech, M., Epsztein, R., Fourkas, J. T., et al. (2019) · The Journal of Physical Chemistry C · doi:10.1021/acs.jpcc.9b02178 · Cited by 365

Structured and viscous water in subnanometer gaps

Li, T.-D., Gao, J., Szoszkiewicz, R., Landman, U., & Riedo, E. (2007) · Physical Review B · doi:10.1103/physrevb.75.115415 · Cited by 359

Dielectric Constant of Water Confined in a Nanocavity

Senapati, S., & Chandra, A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp011058i · Cited by 302

Molecular Dynamics Simulations of Water Structure and Diffusion in Silica Nanopores

Bourg, I. C., & Steefel, C. I. (2012) · The Journal of Physical Chemistry C · doi:10.1021/jp301299a · Cited by 286

Tetrahedral structure or chains for liquid water

Head-Gordon, T., & Johnson, M. E. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510593103 · Cited by 265

The Properties of Water: Insights from Quantum Simulations

Paesani, F., & Voth, G. A. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp810590c · Cited by 256

Phase Transitions Induced by Nanoconfinement in Liquid Water

Giovambattista, N., Rossky, P. J., & Debenedetti, P. G. (2009) · Physical Review Letters · doi:10.1103/physrevlett.102.050603 · Cited by 253

The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data

Kollman, P., Dixon, R., Cornell, W., Fox, T., Chipot, C., & Pohorille, A. (1997) · Computer Simulation of Biomolecular Systems · doi:10.1007/978-94-017-1120-3_2 · Cited by 242

Using AMBER18 for Relative Free Energy Calculations

Song, L. F., Lee, T.-S., Zhu, C., York, D. M., & Merz, K. M. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00105 · Cited by 234

Molecular simulation of water confined in nanoporous silica

Bonnaud, P. A., Coasne, B., & Pellenq, R. J.-M. (2010) · Journal of Physics: Condensed Matter · doi:10.1088/0953-8984/22/28/284110 · Cited by 182

Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

Nguyen, T. T., Székely, E., Imbalzano, G., Behler, J., Csányi, G., Ceriotti, M., Götz, A. W., & Paesani, F. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5024577 · Cited by 171

Molecular Dynamics Studies of Interfacial Water at the Alumina Surface

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Hydration repulsion between biomembranes results from an interplay of dehydration and depolarization

Schneck, E., Sedlmeier, F., & Netz, R. R. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205811109 · Cited by 163

Osmolyte Trimethylamine-N-Oxide Does Not Affect the Strength of Hydrophobic Interactions: Origin of Osmolyte Compatibility

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Osmotic coefficients of atomistic NaCl (aq) force fields

Hess, B., Holm, C., & van der Vegt, N. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2185105 · Cited by 147

Probability distributions of molecular observables computed from Markov models

Noé, F. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2916718 · Cited by 135

Zinc complexation in chloride-rich hydrothermal fluids (25–600 °C): A thermodynamic model derived from ab initio molecular dynamics

Mei, Y., Sherman, D. M., Liu, W., Etschmann, B., Testemale, D., & Brugger, J. (2015) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2014.09.023 · Cited by 124

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Hess, B., Holm, C., & van der Vegt, N. (2006) · Physical Review Letters · doi:10.1103/physrevlett.96.147801 · Cited by 121

Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants

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Grünewald, F., Punt, M. H., Jefferys, E. E., Vainikka, P. A., König, M., Virtanen, V., Meyer, T. A., Pezeshkian, W., Gormley, A. J., Karonen, M., et al. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00757 · Cited by 116

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Influence of Hydrophilic Surface Specificity on the Structural Properties of Confined Water

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Ab initio molecular dynamics simulation and free energy exploration of copper(I) complexation by chloride and bisulfide in hydrothermal fluids

Mei, Y., Sherman, D. M., Liu, W., & Brugger, J. (2013) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2012.10.027 · Cited by 96

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Mendes de Oliveira, D., Zukowski, S. R., Palivec, V., Hénin, J., Martinez-Seara, H., Ben-Amotz, D., Jungwirth, P., & Duboué-Dijon, E. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp02987d · Cited by 73

Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration

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Lane, J. M. D., Chandross, M., Stevens, M. J., & Grest, G. S. (2008) · Langmuir · doi:10.1021/la704005v · Cited by 52

Origin of hydration lubrication of zwitterions on graphene

Li, J., Cao, W., Wang, Z., Ma, M., & Luo, J. (2018) · Nanoscale · doi:10.1039/c8nr05724a · Cited by 51

Thermodynamically dominant hydration structures of aqueous ions

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Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry

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Relaxation and jump dynamics of water at the mica interface

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Emerging investigator series: ion diffusivities in nanoconfined interfacial water films contribute to mineral carbonation thresholds

Miller, Q. R. S., Kaszuba, J. P., Kerisit, S. N., Schaef, H. T., Bowden, M. E., McGrail, B. P., & Rosso, K. M. (2020) · Environmental Science: Nano · doi:10.1039/c9en01382b · Cited by 41

A Diffusive Anomaly of Water in Aqueous Sodium Chloride Solutions at Low Temperatures

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Ion Association in Hydrothermal Sodium Sulfate Solutions Studied by Modulated FT-IR-Raman Spectroscopy and Molecular Dynamics

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Three Reasons Why Aspartic Acid and Glutamic Acid Sequences Have a Surprisingly Different Influence on Mineralization

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Fluorination to enhance superlubricity performance between self-assembled monolayer and graphite in water

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A computational study of Mg2+ dehydration in aqueous solution in the presence of HS− and other monovalent anions – Insights to dolomite formation

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Confinement Effects on Carbon Dioxide Methanation: A Novel Mechanism for Abiotic Methane Formation

Le, T., Striolo, A., Turner, C. H., & Cole, D. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-09445-1 · Cited by 33

Crucial Importance of Water Structure Modification on Trimethylamine N-Oxide Counteracting Effect at High Pressure

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Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics

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An Eco‐Friendly, Tunable and Scalable Method for Producing Porous Functional Nanomaterials Designed Using Molecular Interactions

Manning, J. R. H., Yip, T. W. S., Centi, A., Jorge, M., & Patwardhan, S. V. (2017) · ChemSusChem · doi:10.1002/cssc.201700027 · Cited by 29

Anisotropic Dielectric Relaxation of the Water Confined in Nanotubes for Terahertz Spectroscopy Studied by Molecular Dynamics Simulations

Qi, W., Chen, J., Yang, J., Lei, X., Song, B., & Fang, H. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp3120435 · Cited by 28

Solution additives promoting the onset of MgCO3 nucleation

Toroz, D., Song, F., Uddin, A., Chass, G. A., & Di Tommaso, D. (2021) · doi:10.26434/chemrxiv-2021-kl62l · Cited by 24

A Database of Solution Additives Promoting Mg 2+ Dehydration and the Onset of MgCO 3 Nucleation

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Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations

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Vibrational Behavior of Water Adsorbed on Forsterite (Mg2SiO4) Surfaces

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Refinement of protein-protein complexes in contact map space with metadynamics simulations

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FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning

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Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane

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Probing the Microscopic Behavior of PFOS Clustering and Adsorption at LNAPL Interfaces; a PFOS–Water–Cyclohexane System

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The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm?

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Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold

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Conformations of a highly expressed Z19 α-zein studied with AlphaFold2 and MD simulations

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Novel Calcium-Binding Ablating Mutations Induce Constitutive RET Activity and Drive Tumorigenesis

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