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      A review of methods for the calculation of solution free energies and the modelling of systems in solution

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          Abstract

          We discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.

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          Current status of the AMOEBA polarizable force field.

          Jay Ponder, Chuanjie Wu, Pengyu Ren … (2010)
          Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
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            Refinement and Parametrization of COSMO-RS

            John C. W. Lohrenz, Thorsten Burger, Volker Jonas … (1998)
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              InChI - the worldwide chemical structure identifier standard

              Stephen Heller, Alan McNaught, Stephen Stein … (2013)
              Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the extensive use and dissemination of the InChI and InChIKey structure representations by and for the world-wide chemistry community, the chemical information community, and major publishers and disseminators of chemical and related scientific offerings in manuscripts and databases.
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                Author and article information

                Journal
                Journal ID (publisher-id): PPCPFQ
                Title: Phys. Chem. Chem. Phys.
                Abbreviated Title: Phys. Chem. Chem. Phys.
                Publisher: Royal Society of Chemistry (RSC)
                ISSN (Print): 1463-9076
                ISSN (Electronic): 1463-9084
                Publication date Created: 2015
                Publication date (Print): 2015
                Volume: 17
                Issue: 9
                Pages: 6174-6191
                Article
                DOI: 10.1039/C5CP00288E
                PubMed ID: 25660403
                SO-VID: 2ddd0509-9404-4487-a6ff-9678ee9218ba
                Copyright © © 2015
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