A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

Bayly, Christopher I.; Cieplak, Piotr; Cornell, Wendy D.; Kollman, Peter A.

doi:10.1021/j100142a004

Cited by 7,015 publications

(6,553 citation statements)

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“…[29][30][31] Classical point charges were derived using the RESP procedure except for the 7 carboxylic anchoring groups, whose charges were chosen in such a way as to reproduce the experimental adsorption energy. 32,33 For this purpose we used the Gaussian 09 Package. 34 The force field was validated via full ab initio simulations of a single dye in vacuum.…”

Section: Methodsmentioning

confidence: 99%

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells

Voïtchovsky

Astani

Tavernelli

et al. 2015

ACS Appl. Mater. Interfaces

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Citation for published item:o¤ %t hovskyD uF nd esh ri est niD xF nd vernelliD sF nd etre ultD xF nd othlis ergerD F nd tell iD pF nd qr¤ tzelD wF nd erne r rmsD rF @PHISA 9snEsitu m pping of the mole ul r rr ngement of mphiphili dye mole ules t the iyP surf e of dye sensitized sol r ellsF9D eg pplied m teri ls interf esFD U @PHAF ppF IHVQREIHVRPF Further information on publisher's website: httpXGGdxFdoiForgGIHFIHPIG s miFS HITQV Publisher's copyright statement: This document is the Accepted Manuscript version of a Published Work that appeared in nal form in ACS applied materials interfaces, copyright c 2015 American Chemical Society after peer review and technical editing by the publisher. To access the nal edited and published work see http://dx.doi.org/10.1021/acsami.5b01638. Additional information:Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. Just Accepted "Just Accepted" manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides "Just Accepted" as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. "Just Accepted" manuscripts appear in full in PDF format accompanied by an HTML abstract. "Just Accepted" manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). "Just Accepted" is an optional service offered to authors. Therefore, the "Just Accepted" Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the "Just Accepted" Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these "Just Accepted" manuscripts. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59

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Section: Methodsmentioning

confidence: 99%

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells

Voïtchovsky

Astani

Tavernelli

et al. 2015

ACS Appl. Mater. Interfaces

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“…45,46 RESP atomic partial charges were fitted to the electrostatic potential from in Vacuo single-point calculations at the 6-31G* level (3-21G level for iodine-containing compounds) using GAMESS. 47 Molecular dynamics simulations were carried out using AMBER 9 software 48 with the general AMBER force field (GAFF) parameters 41 assigned to the solutes with PARMCHK and ANTECHAMBER, 49 and using the TIP3P water parameters 50,51 for the solvent.…”

Section: Rfmentioning

confidence: 99%

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Sulea

Corbeil

Purisima

2010

J. Chem. Theory Comput.

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Abstract:The present study provides a comprehensive systematic analysis on the applicability of the linear interaction energy (LIE) approximation to the prediction of gas-to-water transfer (hydration) free energy. The study is based on molecular dynamics simulations in explicit solvent for an extensive and diverse hydration data set comprising 564 neutral compounds with measured hydration free energies, including a "traditional" data set and the more challenging drug-like SAMPL1 data set. A highly correlative LIE model was achieved without empirical scaling of the solute-solvent interaction energy terms along with a cavity term calibrated to the experiment. This model was particularly accurate for the "traditional" data set and of acceptable accuracy for the SAMPL1 data set, with mean-unsigned-errors below 1 kcal/mol and slightly above 2 kcal/mol, respectively. We have analyzed the sensitivity of the LIE model to several parameters such as continuum correction terms applied outside the explicit water shell, the impact of various charging methods, the applicability of single-conformer representation of the solute, and the inclusion of internal energy terms. The parameters with the greatest sensitivity are the charging methods used, with AM1BCC-SP (without AM1 geometry optimization) charges favored over AM1BCC-OPT and RESP charges. The inclusion of the change in intramolecular van der Waals and electrostatic energies between the solution and gas phases can also lead to improved prediction accuracies. Functional group based error analysis identified several chemical classes as minor outliers with systematic errors. A direct comparison of the LIE and free energy perturbation (FEP) approaches using the same force field and charging method shows that the LIE approximation is at least as accurate as the FEP approach with a reduction of computing time by at least 1 order of magnitude.

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“…Geometry optimization and vibrational analyses were performed on TMP-P ϩ H 3 (Figure 1a), tTMP-P ϩ -CH 3 (Figure 1b), tTMP-Si-CH 3 ( Figure 1c), and CH 3 CO-(Asp)-NHCH 3 ( Figure 1d). Partial atomic charge distributions using the restrained ESP [64,65] method were applied to tTMP-P ϩ -CH 3 and tTMP-Si-CH 3 to ascertain the location of the positive charge. Vibrational frequencies were calculated to confirm that the geometries were minima on the potential energy surface.…”

Section: Molecular Modelingmentioning

confidence: 99%

Computational investigation and hydrogen/deuterium exchange of the fixed charge derivative tris(2,4,6-Trimethoxyphenyl) phosphonium: Implications for the aspartic acid cleavage mechanism

Herrmann

Wysocki

Vorpagel

2005

J. Am. Soc. Mass Spectrom.

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Aspartic acid (Asp)-containing peptides with the fixed charge derivative tris(2,4,6-trimethoxyphenyl) phosphonium (tTMP-P ϩ ) were explored computationally and experimentally by hydrogen/deuterium (H/D) exchange and by fragmentation studies to probe the phenomenon of selective cleavage C-terminal to Asp in the absence of a "mobile" proton. Ab initio modeling of the tTMP-P ϩ electrostatic potential shows that the positive charge is distributed on the phosphonium group and therefore is not initiating or directing fragmentation as would a "mobile" proton. Geometry optimizations and vibrational analyses of different Asp conformations show that the Asp structure with a hydrogen bond between the side-chain hydroxy and backbone carbonyl lies 2.8 kcal/mol above the lowest energy conformer. In reactions with D 2 O, the phosphonium-derived doubly charged peptide (H ϩ )P ϩ LDIFSDF rapidly exchanges all 12 of its exchangeable hydrogens for deuterium and also displays a nonexchanging population. With no added proton, P ϩ LDIFSDF exchanges a maximum of 4 of 11 exchangeable hydrogens for deuterium. No exchange is observed when all acidic groups are converted to the corresponding methyl esters. Together, these H/D exchange results indicate that the acidic hydrogens are "mobile locally" because they are able to participate in exchange even in the absence of an added proton. Fragmentation of two distinct (H ϩ )P ϩ LDIFSDF ion populations shows that the nonexchanging population displays selective cleavage, whereas the exchanging population fragments more evenly across the peptide backbone. This result indicates that H/D exchange can sometimes distinguish between and provide a means of separation of different protonation motifs and that these protonation motifs can have an effect on the fragmentation. (J Am Soc Mass Spectrom 2005, 16, 1067-1080

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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

Cited by 7,015 publications

References 6 publications

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Computational investigation and hydrogen/deuterium exchange of the fixed charge derivative tris(2,4,6-Trimethoxyphenyl) phosphonium: Implications for the aspartic acid cleavage mechanism

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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

Cited by 7,015 publications

References 6 publications

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO2 Surface of Dye-Sensitized Solar Cells

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO2 Surface of Dye-Sensitized Solar Cells

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Computational investigation and hydrogen/deuterium exchange of the fixed charge derivative tris(2,4,6-Trimethoxyphenyl) phosphonium: Implications for the aspartic acid cleavage mechanism

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In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells