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Kulichenko M, Barros K, Lubbers N, Fedik N, Zhou G, Tretiak S, Nebgen B, Niklasson AMN. Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation. J Chem Theory Comput 2023. [PMID: 37163680 DOI: 10.1021/acs.jctc.3c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) in its most recent shadow potential energy version has been implemented in the semiempirical PyTorch-based software PySeQM. The implementation includes finite electronic temperatures, canonical density matrix perturbation theory, and an adaptive Krylov subspace approximation for the integration of the electronic equations of motion within the XL-BOMB approach (KSA-XL-BOMD). The PyTorch implementation leverages the use of GPU and machine learning hardware accelerators for the simulations. The new XL-BOMD formulation allows studying more challenging chemical systems with charge instabilities and low electronic energy gaps. The current public release of PySeQM continues our development of modular architecture for large-scale simulations employing semi-empirical quantum-mechanical treatment. Applied to molecular dynamics, simulation of 840 carbon atoms, one integration time step executes in 4 s on a single Nvidia RTX A6000 GPU.
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Affiliation(s)
- Maksim Kulichenko
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Kipton Barros
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicholas Lubbers
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nikita Fedik
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Guoqing Zhou
- NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, California 95051, United States
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Benjamin Nebgen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Anders M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Schultz M, Parker SL, Fernando MT, Wellalage MM, Thomas DA. Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:745-753. [PMID: 36975839 DOI: 10.1021/jasms.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transferring biomolecules from solution to vacuum facilitates a detailed analysis of molecular structure and dynamics by isolating molecules of interest from a complex environment. However, inherent in the ion desolvation process is the loss of solvent hydrogen bonding partners, which are critical for the stability of a condensed-phase structure. Thus, transfer of ions to vacuum can favor structural rearrangement, especially near solvent-accessible charge sites, which tend to adopt intramolecular hydrogen bonding motifs in the absence of solvent. Complexation of monoalkylammonium moieties (e.g., lysine side chains) with crown ethers such as 18-crown-6 can disfavor structural rearrangement of protonated sites, but no equivalent ligand has been investigated for deprotonated groups. Herein we describe diserinol isophthalamide (DIP), a novel reagent for the gas-phase complexation of anionic moieties within biomolecules. Complexation is observed to the C-terminus or side chains of the small model peptides GD, GE, GG, DF-OMe, VYV, YGGFL, and EYMPME in electrospray ionization mass spectrometry (ESI-MS) studies. In addition, complexation is observed with the phosphate and carboxylate moieities of phosphoserine and phosphotyrosine. DIP performs favorably in comparison to an existing anion recognition reagent, 1,1'-(1,2-phenylene)bis(3-phenylurea), that exhibits moderate carboxylate binding in organic solvent. This improved performance in ESI-MS experiments is attributed to reduced steric constraints to complexation with carboxylate groups of larger molecules. Overall, diserinol isophthalamide is an effective complexation reagent that can be applied in future work to study retention of solution-phase structure, investigate intrinsic molecular properties, and examine solvation effects.
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Affiliation(s)
- Madeline Schultz
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah L Parker
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Maleesha T Fernando
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Miyuru M Wellalage
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel A Thomas
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
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3
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Kotobi A, Schwob L, Vonbun-Feldbauer GB, Rossi M, Gasparotto P, Feiler C, Berden G, Oomens J, Oostenrijk B, Scuderi D, Bari S, Meißner RH. Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble. Commun Chem 2023; 6:46. [PMID: 36869192 PMCID: PMC9984374 DOI: 10.1038/s42004-023-00835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.
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Affiliation(s)
- Amir Kotobi
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Gregor B. Vonbun-Feldbauer
- grid.6884.20000 0004 0549 1777Hamburg University of Technology, Institute of Advanced Ceramics, Hamburg, Germany
| | - Mariana Rossi
- grid.469852.40000 0004 1796 3508Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Piero Gasparotto
- grid.5991.40000 0001 1090 7501Scientific Computing Division, Paul Scherrer Institute, Villigen, Switzerland
| | - Christian Feiler
- grid.24999.3f0000 0004 0541 3699Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany
| | - Giel Berden
- grid.5590.90000000122931605Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- grid.5590.90000000122931605Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Bart Oostenrijk
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany ,grid.9026.d0000 0001 2287 2617The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Debora Scuderi
- grid.503243.3Institut de Chimie Physique, CNRS UMR8000, Université Paris-Saclay, Orsay, France
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany. .,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Robert H. Meißner
- grid.24999.3f0000 0004 0541 3699Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany ,grid.6884.20000 0004 0549 1777Hamburg University of Technology, Institute of Polymers and Composites, Hamburg, Germany
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4
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Clavaguéra C, Thaunay F, Ohanessian G. Manifolds of low energy structures for a magic number of hydrated sulfate: SO 42-(H 2O) 24. Phys Chem Chem Phys 2021; 23:24428-24438. [PMID: 34693943 DOI: 10.1039/d1cp03123f] [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
Low energy structures of SO42-(H2O)24 have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ mol-1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO42-(H2O)24 does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed.
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Affiliation(s)
- Carine Clavaguéra
- Institut de Chimie Physique, Université Paris-Saclay - CNRS, UMR 8000, 91405 Orsay, France.
| | - Florian Thaunay
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.
| | - Gilles Ohanessian
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.
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Antezana PE, Municoy S, Bellino MG, Martini MF, Desimone MF. Nanodelivery of the Gramicidin Peptide for Enhancing Antimicrobial Activity. EUR J LIPID SCI TECH 2021. [DOI: 10.1002/ejlt.202000389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pablo E. Antezana
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
| | - Sofia Municoy
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
| | - Martín G. Bellino
- Instituto de Nanociencia y Nanotecnología – Comisión Nacional de Energía Atómica y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. General Paz 1499, (1650) San Martín Argentina
| | - M. Florencia Martini
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
| | - Martín F. Desimone
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
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6
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Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
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Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
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7
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Affiliation(s)
- Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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8
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Roy TK, Nagornova NS, Boyarkin OV, Gerber RB. A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy. J Phys Chem A 2017; 121:9401-9408. [PMID: 29091429 DOI: 10.1021/acs.jpca.7b10357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry & Chemical Sciences, Central University of Jammu , Jammu, 180011 India
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University , Jerusalem 91904, Israel.,Department of Chemistry, University of California , Irvine, California 92697, United States.,Department of Chemistry, University of Helsinki , P.O. Box 55, 00014 Helsinki, Finland
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9
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Sahu N, Gadre SR. Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach. J Chem Phys 2017; 144:114113. [PMID: 27004868 DOI: 10.1063/1.4943966] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 310- and α-helix of acetyl(alanine)nNH2 (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm(-1) is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine)20 and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.
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Affiliation(s)
- Nityananda Sahu
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
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10
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Stamm A, Maué D, Schaly A, Schlicher S, Bartl J, Kubik S, Gerhards M. Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues. Phys Chem Chem Phys 2017; 19:10718-10726. [DOI: 10.1039/c6cp08696a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues were performed by applying combined IR/UV spectroscopy in the molecular beam and DFT calculations. The intrinsic structural properties especially with regard to the influence of different amino acid residues are fundamental for optimizing their binding ability.
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Affiliation(s)
- A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - A. Schaly
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Schlicher
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - J. Bartl
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Kubik
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
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Mahé J, Bakker DJ, Jaeqx S, Rijs AM, Gaigeot MP. Mapping gas phase dipeptide motions in the far-infrared and terahertz domain. Phys Chem Chem Phys 2017; 19:13778-13787. [DOI: 10.1039/c7cp00369b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vibrational signatures of Ac-Phe-AA-NH2 dipeptides are recorded and analysed in the far IR/THz spectral domain (100–800 cm−1, 3–24 THz), with the ‘AA’ amino acid chosen within the series ‘AA’ = Gly, Ala, Pro, Cys, Ser, Val. Phe stands for phenylalanine.
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Affiliation(s)
- Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Université Paris-Saclay
| | - Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Sander Jaeqx
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Université Paris-Saclay
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12
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Dunbar RC, Martens J, Berden G, Oomens J. Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate. Phys Chem Chem Phys 2016; 18:26923-26932. [DOI: 10.1039/c6cp03974j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.
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Affiliation(s)
| | - Jonathan Martens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Giel Berden
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
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14
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Yatsyna V, Bakker DJ, Feifel R, Rijs AM, Zhaunerchyk V. Aminophenol isomers unraveled by conformer-specific far-IR action spectroscopy. Phys Chem Chem Phys 2016; 18:6275-83. [DOI: 10.1039/c5cp07426f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Far-infrared action spectroscopy of aminophenol in the gas-phase revealed isomer- and conformer-specific vibrational signatures and provided the heights of NH2 inversion barrier.
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Affiliation(s)
- Vasyl Yatsyna
- University of Gothenburg
- Department of Physics
- 412 96 Gotheburg
- Sweden
- Radboud University
| | - Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Raimund Feifel
- University of Gothenburg
- Department of Physics
- 412 96 Gotheburg
- Sweden
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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15
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Pal S, Ghosh U, Ampapathi RS, Chakraborty TK. Recent Studies on Gramicidin S Analog Structure and Antimicrobial Activity. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/7081_2015_188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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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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17
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Roy TK, Kopysov V, Nagornova NS, Rizzo TR, Boyarkin OV, Gerber RB. Conformational Structures of a Decapeptide Validated by First Principles Calculations and Cold Ion Spectroscopy. Chemphyschem 2015; 16:1374-8. [DOI: 10.1002/cphc.201500085] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
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18
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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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19
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Gregori B, Guidoni L, Chiavarino B, Scuderi D, Nicol E, Frison G, Fornarini S, Crestoni ME. Vibrational Signatures of S-Nitrosoglutathione as Gaseous, Protonated Species. J Phys Chem B 2014; 118:12371-82. [DOI: 10.1021/jp5072742] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Leonardo Guidoni
- Dipartimento
di Scienza Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio 2, Coppito, L’Aquila I-64100, Italy
| | | | - Debora Scuderi
- Laboratoire
de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris-Sud, Batiment 350, 91405 Orsay Cedex, France
| | - Edith Nicol
- 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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20
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Carr JK, Wang L, Roy S, Skinner JL. Theoretical Sum Frequency Generation Spectroscopy of Peptides. J Phys Chem B 2014; 119:8969-83. [PMID: 25203677 PMCID: PMC4516311 DOI: 10.1021/jp507861t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Vibrational sum frequency generation (SFG) has become a very promising technique for the study of proteins at interfaces, and it has been applied to important systems such as anti-microbial peptides, ion channel proteins, and human islet amyloid polypeptide. Moreover, so-called "chiral" SFG techniques, which rely on polarization combinations that generate strong signals primarily for chiral molecules, have proven to be particularly discriminatory of protein secondary structure. In this work, we present a theoretical strategy for calculating protein amide I SFG spectra by combining line-shape theory with molecular dynamics simulations. We then apply this method to three model peptides, demonstrating the existence of a significant chiral SFG signal for peptides with chiral centers, and providing a framework for interpreting the results on the basis of the dependence of the SFG signal on the peptide orientation. We also examine the importance of dynamical and coupling effects. Finally, we suggest a simple method for determining a chromophore's orientation relative to the surface using ratios of experimental heterodyne-detected signals with different polarizations, and test this method using theoretical spectra.
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Affiliation(s)
- Joshua K Carr
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Lu Wang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Santanu Roy
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - James L Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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21
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Jaeqx S, Oomens J, Cimas A, Gaigeot MP, Rijs AM. Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born-Oppenheimer Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2014; 53:3663-6. [DOI: 10.1002/anie.201311189] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Indexed: 11/11/2022]
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22
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Jaeqx S, Oomens J, Cimas A, Gaigeot MP, Rijs AM. Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born-Oppenheimer Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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24
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Grebner C, Niebling S, Schmuck C, Schlücker S, Engels B. Force field-based conformational searches: efficiency and performance for peptide receptor complexes. Mol Phys 2013. [DOI: 10.1080/00268976.2013.826392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Navarro-Whyte L, Kellie JL, Lenz SAP, Wetmore SD. Hydrolysis of the damaged deoxythymidine glycol nucleoside and comparison to canonical DNA. Phys Chem Chem Phys 2013; 15:19343-52. [DOI: 10.1039/c3cp53217h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Grebner C, Kästner J, Thiel W, Engels B. A New Tabu-Search-Based Algorithm for Solvation of Proteins. J Chem Theory Comput 2012; 9:814-21. [DOI: 10.1021/ct300898d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| | - Johannes Kästner
- Universität
Stuttgart,
Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569
Stuttgart, Germany
| | - Walter Thiel
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an
der Ruhr, Germany
| | - Bernd Engels
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
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27
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Kang YK, Byun BJ. Computationally designed β-turn foldamers of γ-peptides based on 2-(aminomethyl)cyclohexanecarboxylic acid. Biopolymers 2012; 97:1018-25. [DOI: 10.1002/bip.22119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Pagba CV, Barry BA. Redox-Induced Conformational Switching in Photosystem-II-Inspired Biomimetic Peptides: A UV Resonance Raman Study. J Phys Chem B 2012; 116:10590-9. [DOI: 10.1021/jp303607b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Cynthia V. Pagba
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Bridgette A. Barry
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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