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Zhang C, Zhao DX, Feng Y, Wang J, Yang ZZ. Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution. Phys Chem Chem Phys 2022; 24:4232-4250. [DOI: 10.1039/d1cp05676j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...
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2
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Thaunay F, Calvo F, Nicol E, Ohanessian G, Clavaguéra C. Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence‐Bond Modeling. Chemphyschem 2019; 20:803-814. [PMID: 30695125 DOI: 10.1002/cphc.201800947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Indexed: 01/08/2023]
Abstract
Experimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO2 (CH2 )n CO 2 - (n=2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm-1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polarizable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems.
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Affiliation(s)
| | - Florent Calvo
- LIPhyUniversité Grenoble Alpes, CNRS, LiPhy 38000 Grenoble France
| | - Edith Nicol
- LCM, CNRSEcole Polytechnique 91128 Palaiseau Cedex France
| | | | - Carine Clavaguéra
- Laboratoire de Chimie PhysiqueCNRS – Université Paris Sud, Université Paris-Saclay 15 avenue Jean Perrin 91405 Orsay Cedex France
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3
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Riffet V, Bouchoux G, Frison G. Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach. J Phys Chem B 2015; 119:11527-39. [PMID: 26252717 DOI: 10.1021/acs.jpcb.5b05581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.
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Affiliation(s)
- Vanessa Riffet
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
| | - Guy Bouchoux
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
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4
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Thaunay F, Dognon JP, Ohanessian G, Clavaguéra C. Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp02270c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.
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Affiliation(s)
- Florian Thaunay
- Laboratoire de Chimie Moléculaire
- Ecole Polytechnique
- CNRS
- 91128 Palaiseau Cedex
- France
| | - Jean-Pierre Dognon
- CEA/Saclay
- DSM/IRAMIS/NIMBE
- CNRS
- UMR 3685
- Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie
| | - Gilles Ohanessian
- Laboratoire de Chimie Moléculaire
- Ecole Polytechnique
- CNRS
- 91128 Palaiseau Cedex
- France
| | - Carine Clavaguéra
- Laboratoire de Chimie Moléculaire
- Ecole Polytechnique
- CNRS
- 91128 Palaiseau Cedex
- France
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5
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Semrouni D, Sharma A, Dognon JP, Ohanessian G, Clavaguéra C. Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:3190-9. [DOI: 10.1021/ct5004065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- David Semrouni
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Ashwani Sharma
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Jean-Pierre Dognon
- CEA/Saclay, DSM/IRAMIS/NIMBE,
CNRS, Laboratoire de Chimie Moléculaire et de Catalyse pour
l’Energie, 91191 Gif-sur-Yvette, France
| | - Gilles Ohanessian
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Carine Clavaguéra
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
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Hoffgaard F, Heil J, Kast SM. Three-Dimensional RISM Integral Equation Theory for Polarizable Solute Models. J Chem Theory Comput 2013; 9:4718-26. [PMID: 26583390 DOI: 10.1021/ct400699q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Modeling solute polarizability is a key ingredient for improving the description of solvation phenomena. In recent years, polarizable molecular mechanics force fields have emerged that circumvent the limitations of classical fixed charge force fields by the ability to adapt their electrostatic potential distribution to a polarizing environment. Solvation phenomena are characterized by the solute's excess chemical potential, which can be computed by expensive fully atomistic free energy simulations. The alternative is to employ an implicit solvent model, which poses a challenge to the formulation of the solute-solvent interaction term within a polarizable framework. Here, we adapt the three-dimensional reference interaction site model (3D RISM) integral equation theory as a solvent model, which analytically yields the chemical potential, to the polarizable AMOEBA force field using an embedding cluster (EC-RISM) strategy. The methodology is analogous to our earlier approach to the coupling of a quantum-chemical solute description with a classical 3D RISM solvent. We describe the conceptual physical and algorithmic basis as well as the performance for several benchmark cases as a proof of principle. The results consistently show reasonable agreement between AMOEBA and quantum-chemical free energies in solution in general and allow for separate assessment of energetic and solvation-related contributions. We find that, depending on the parametrization, AMOEBA reproduces the chemical potential in better agreement with reference quantum-chemical calculations than the intramolecular energies, which suggests possible routes toward systematic improvement of polarizable force fields.
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Affiliation(s)
- Franziska Hoffgaard
- Physikalische Chemie III, TU Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Jochen Heil
- Physikalische Chemie III, TU Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Stefan M Kast
- Physikalische Chemie III, TU Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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Semrouni D, Clavaguéra C, Ohanessian G, Parks JH. Relationship between Conformational Dynamics and Electron Transfer in a Desolvated Peptide. Part I. Structures. J Phys Chem B 2013; 117:1746-55. [DOI: 10.1021/jp3078375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- David Semrouni
- Laboratoire des Mécanismes Réactionnels,
Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels,
Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels,
Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Joel H. Parks
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge,
Massachusetts 02142, United
States
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Balaj OP, Semrouni D, Steinmetz V, Nicol E, Clavaguéra C, Ohanessian G. Structure of Sodiated Polyglycines. Chemistry 2012; 18:4583-92. [DOI: 10.1002/chem.201102812] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 11/11/2022]
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van der Rest G, Hui R, Frison G, Chamot-Rooke J. Dissociation channel dependence on peptide size observed in electron capture dissociation of tryptic peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1631-1644. [PMID: 21953266 DOI: 10.1007/s13361-011-0166-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/02/2011] [Accepted: 05/06/2011] [Indexed: 05/31/2023]
Abstract
Electron capture dissociation (ECD) of a series of five residue peptides led to the observation that these small peptides did not lead to the formation of the usual c/z ECD fragments, but to a, b, y, and w fragments. In order to determine how general this behavior is for small sized peptides, the effect of peptide size on ECD fragments using a complete set of ECD spectra from the SwedECD spectra database was examined. Analysis of the database shows that b and w fragments are favored for small peptide sizes and that average fragment size shows a linear relationship to parent peptide size for most fragment types. From these data, it appears that most of the w fragments are not secondary fragments of the major z ions, in sharp contrast with the proposed mechanism leading to these ions. These data also show that c fragment distributions depend strongly on the nature of C-terminal residue basic site: arginine leads to loss of short neutral fragments, whereas lysine leads to loss of longer neutral fragments. It also appears that b ions might be produced by two different mechanisms depending on the parent peptide size. A model for the fragmentation pathways in competition is proposed. These relationships between average fragment size and parent peptide size could be further exploited also for CID fragment spectra and could be included in fragmentation prediction algorithms.
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Affiliation(s)
- Guillaume van der Rest
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique and CNRS, 91128, Palaiseau Cedex, France.
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Riffet V, Frison G, Bouchoux G. Acid–base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met). Phys Chem Chem Phys 2011; 13:18561-80. [DOI: 10.1039/c1cp22206f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Semrouni D, Balaj OP, Calvo F, Correia CF, Clavaguéra C, Ohanessian G. Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:728-38. [PMID: 20189824 DOI: 10.1016/j.jasms.2010.01.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 05/25/2023]
Abstract
The structure of the sodiated peptide GGGGGGGG-Na(+) or G(8)-Na(+) was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G(8)-Na(+) is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G(8)-Na(+) at room temperature.
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Affiliation(s)
- David Semrouni
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique and CNRS, Palaiseau, France
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