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An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

Edward O. Pyzer-Knapp, Hugh P. G. Thompson, Graeme M. Day
2016 Acta Crystallographica. Section B: Structural Science, Crystal Engineering and Materials  
The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared  ...  Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics.  ...  When using the polarized charge densities (calculated within a PCM model of the crystal environment), the calculated lattice energy is corrected for the relaxation energy of the molecular charge density  ... 
doi:10.1107/s2052520616007708 pmid:27484370 pmcid:PMC4971546 fatcat:62xlmccmsjhfpaptqlsizozuvm

Accurate force fields and methods for modelling organic molecular crystals at finite temperatures

Jonas Nyman, Orla Sheehan Pundyke, Graeme M. Day
2016 Physical Chemistry, Chemical Physics - PCCP  
We assess a series of atom–atom force fields for lattice energy and free energy modelling of molecular organic crystals.  ...  Acknowledgements We thank Professor Neil Allan at the University of Bristol for pointing us to the work of Karo, Hardy and Gilat. 71  ...  The electrostatic model is generated from a quantum chemical calculation through either fitting to the molecular electrostatic potential or partitioning of distributed multipoles.  ... 
doi:10.1039/c6cp02261h pmid:27230942 fatcat:343h7weobne5jhanaoad54xzii

The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of theXDprogramming package to several solids including a pentapeptide

Yu. A. Abramov, A. Volkov, G. Wu, P. Coppens
2000 Acta Crystallographica Section A Foundations of Crystallography  
The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM ( H -restricted multipole model) re®nements, using the Buckingham expression for non-overlapping charge  ...  A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, l-asparagine monohydrate and  ...  The Center for Computational Research at SUNY/Buffalo is supported by grant DBI9871132 from the National Science Foundation.  ... 
doi:10.1107/s0108767300011405 pmid:11058845 fatcat:opztw6jlrreq7hbjbljhw33xm4

Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals

Gy�rgy G. Ferenczy, G�bor I. Csonka, G�bor N�ray-Szab�, J�nos G. �ngy�n
1998 Journal of Computational Chemistry  
We wish to thank the French and Hungarian governments for financial support in the framework of the program Ž .  ...  Acknowledgments The authors are grateful to Prof. N. Rivail for the continuous interest in this work.  ...  Coombes et al. 7 also use an ab initio distributed multipole model for representing electrostatic effects.  ... 
doi:10.1002/(sici)1096-987x(19980115)19:1<38::aid-jcc3>;2-# fatcat:kqssthdsbbfkfilylyuautwy74

Electrostatic properties of nine fluoroquinoloneantibiotics derived directly from their crystal structure refinements

Julian Jacob Holstein, Christian Bertram Hübschle, Birger Dittrich
2012 CrysteEngComm  
This article discusses the relevance of the similarity of the molecular electrostatic potential for rational drug design and optimization of lead structures on the basis of a comparison of nine fluoroquinolone  ...  Molecular electrostatic potentials and dipole moments were calculated directly from the electron-density distribution after crystal structure refinement with invarioms, theoretical nonspherical scattering  ...  Becker (MPI) for supporting the structure determination of lomefloxacin hydrochloride tetrahydrate. We would like to express our gratitude to G. M. Sheldrick and D. Stalke for diffractometer access.  ... 
doi:10.1039/c1ce05966a fatcat:xiouukwmczbdviz6hszxq6nzaa

Prediction of Charge-Induced Molecular Alignment of Biomolecules Dissolved in Dilute Liquid-Crystalline Phases

Markus Zweckstetter, Gerhard Hummer, Ad Bax
2004 Biophysical Journal  
Inclusion of electrostatic interactions in addition to steric effects makes the extended model applicable to all liquid crystals used in biological NMR to date.  ...  The extended model approximates the electrostatic interaction between a solute and an ordered phage particle as that between the solute's surface charges and the electric field of the phage.  ...  We thank Ben Ramirez for preparing DinI and GB3 samples and John Louis for the GB1 sample.  ... 
doi:10.1529/biophysj.103.035790 pmid:15189846 pmcid:PMC1304251 fatcat:olohxh54yjfw3bod7gfmmle2ta

Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions [article]

Moritz Thürlemann, Lennard Böselt, Sereina Riniker
2022 arXiv   pre-print
To showcase the potential of the proposed method, both a fixed-charge model and a polarizable model are parametrized for intermolecular interactions and applied to a wide range of systems including dimer  ...  As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems.  ...  These five potentials were obtained from the relaxed crystal structure and through the expansion/contraction of the lattice of the relaxed structure.  ... 
arXiv:2206.00355v1 fatcat:jlfc5poh4vhsdiuw4xhag37n5a

DL_MULTI—A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals

M. Leslie
2008 Molecular Physics  
DL_MULTI -A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals. Molecular Physics, Taylor Francis, 2008, 106 (12-13), pp.  ...  The use of distributed multipole electrostatic models [31, 2] , where the charge distribution of each molecule is represented by sets of atomic multipoles derived from the ab initio charge density of  ...  the relaxed structure of 5-azauracil as a starting point.  ... 
doi:10.1080/00268970802175308 fatcat:m5imje7u3jgijjkrd2gj2alvva

Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

Prashant Kumar, Małgorzata Katarzyna Cabaj, Paulina Maria Dominiak
2019 Crystals  
molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees.  ...  Understanding intermolecular interactions in crystals of molecular ions continues to be difficult.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/cryst9120668 fatcat:m3g6cyz7ezesviuegpd2uj4ghq

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

Thomas Heinemann, Karol Palczynski, Joachim Dzubiella, Sabine H. L. Klapp
2015 Journal of Chemical Physics  
To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc.  ...  The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion.  ...  To assess the quality of modeling, unit cell parameters and structural quantities of the coronene bulk crystal were calculated with constant pressure and temperature Molecular Dynamics.  ... 
doi:10.1063/1.4935063 pmid:26547161 fatcat:kzpsatnw4bb5fiwpwhvxbxh4ky

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, Pengyu Ren
2013 Journal of Chemical Theory and Computation  
In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation.  ...  Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities.  ...  The authors are grateful to the support by the National Institute of General Medical Sciences (R01GM079686 and R01GM106137) and Robert A. Welch Foundation (F-1691).  ... 
doi:10.1021/ct4003702 pmid:24163642 pmcid:PMC3806652 fatcat:bm6ocvog2rd55my4llyubrcjgu

Intermolecular interaction energies by topologically partitioned electric properties II. Dispersion energies in one-centre and multicentre multipole expansions

1997 Molecular Physics  
., 88, 69) it was shown that this indeed is the case for ® rst-order electrostatic and secondorder induction energies when employing distributed multipole moments and static polarizabilities generated  ...  from the topological partitioning of the molecular volume as provided by Bader's'atoms-in-molecules' theory.  ...  crystal: (Ð Ð ), distributed expansion; (± ± ± ), monocentred expansion. and that instead a di erent damping function will have to be used for each rank L .  ... 
doi:10.1080/002689797171841 fatcat:ubdybjzthzgltdcctsjtyk36ne

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

Zhifeng Jing, Chengwen Liu, Sara Y. Cheng, Rui Qi, Brandon D. Walker, Jean-Philip Piquemal, Pengyu Ren
2019 Annual Review of Biophysics  
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization.  ...  This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.  ...  Acknowledgement We are grateful for support by the National Institutes of Health (Nos. R01GM106137 and R01GM114237), the Robert A. Welch Founda-tion (No. F-1691) and CPRIT(RP160657). Literature Cited  ... 
doi:10.1146/annurev-biophys-070317-033349 pmid:30916997 pmcid:PMC6520134 fatcat:jtne5cggercddd7o3pgg4o7pfy

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

Riccardo Destro, Pietro Roversi, Mario Barzaghi, Leonardo Lo Presti
2021 Molecules  
Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD.  ...  Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)max = 1.143 Å−1 are compared.  ...  Meindl are warmly acknowledged for providing us with a copy of their jnk2RDA program. The crystal (here studied) was a gift of the late B. Craven.  ... 
doi:10.3390/molecules26113075 pmid:34063908 fatcat:aaltmcrdnrfebn4xiqw7eng7ia

Evaluation of weak intermolecular interactions in molecular crystalsviaexperimental and theoretical charge densities

Parthapratim Munshi, Tayur N. Guru Row
2005 Crystallography Reviews  
Analysis of charge density distributions in molecular crystals has received considerable attention in the last decade both from high-resolution X-ray diffraction studies and from high-level theoretical  ...  An overview of the progress made in deriving one-electron properties, intermolecular interactions in  ...  Vijayan for his constant encouragement and for being instrumental in getting us to write the review article. P.M. thanks the CSIR, India for a senior research fellowship.  ... 
doi:10.1080/08893110500245899 fatcat:u5r4uqyovzewlpfxtj2lbrnndm
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