1
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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024; 45:1846-1869. [PMID: 38682874 DOI: 10.1002/jcc.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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2
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Pascariu M, Bernasconi L, Krzystyniak M, Taylor J, Rudić S. Comprehensive Analysis of Methyl-β-D-ribofuranoside: A Multifaceted Spectroscopic and Theoretical Approach. J Phys Chem A 2024; 128:2111-2120. [PMID: 38469744 PMCID: PMC10961842 DOI: 10.1021/acs.jpca.4c00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
This study presents a comprehensive analysis of the vibrational spectra of methyl-β-D-ribofuranoside. Employing a combination of inelastic neutron scattering, Raman, and infrared spectroscopy allows for the observation of all modes regardless of the selection rules. The experimental techniques were complemented by density functional theory computational methods using both gas-phase (Gaussian) and solid-state (CRYSTAL, CASTEP) approaches to provide an unambiguous assignment of the defining vibrational features. Two distinct structures of the molecule were identified in the unit cell, differentiated mainly by the orientation of the furanose ring O-H bonds. The low-energy region of the spectrum (<400 cm-1) is dominated by lattice vibrations and functional group rotation, while the midenergy region is dominated by out-of-plane bending motions of the furanose ring (400-900 cm-1) and by C-H bending in the methyl and methylene groups (1400-1600 cm-1). The high-energy region (>2800 cm-1) encompasses the C-H and O-H stretching modes and offers convincing evidence of at least one H-bonding interaction between the two structures of methyl-β-D-ribofuranoside.
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Affiliation(s)
- Matei Pascariu
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Leonardo Bernasconi
- Center
for Research Computing & Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Matthew Krzystyniak
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| | - James Taylor
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| | - Svemir Rudić
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
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3
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Galván I, Hassasfar A, Adams B, Petruccione F. Isotope effects on radical pair performance in cryptochrome: A new hypothesis for the evolution of animal migration: The quantum biology of migration. Bioessays 2024; 46:e2300152. [PMID: 37888800 DOI: 10.1002/bies.202300152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
Mechanisms occurring at the atomic level are now known to drive processes essential for life, as revealed by quantum effects on biochemical reactions. Some macroscopic characteristics of organisms may thus show an atomic imprint, which may be transferred across organisms and affect their evolution. This possibility is considered here for the first time, with the aim of elucidating the appearance of an animal innovation with an unclear evolutionary origin: migratory behaviour. This trait may be mediated by a radical pair (RP) mechanism in the retinal flavoprotein cryptochrome, providing essential magnetic orientation for migration. Isotopes may affect the performance of quantum processes through their nuclear spin. Here, we consider a simple model and then apply the standard open quantum system approach to the spin dynamics of cryptochrome RP. We changed the spin quantum number (I) and g-factor of hydrogen and nitrogen isotopes to investigate their effect on RP's yield and magnetic sensitivity. Strong differences arose between isotopes with I = 1 and I = 1/2 in their contribution to cryptochrome magnetic sensitivity, particularly regarding Earth's magnetic field strengths (25-65 µT). In most cases, isotopic substitution improved RP's magnetic sensitivity. Migratory behaviour may thus have been favoured in animals with certain isotopic compositions of cryptochrome.
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Affiliation(s)
- Ismael Galván
- Department of Evolutionary Ecology, National Museum of Natural Sciences, CSIC, Madrid, Spain
| | - Abbas Hassasfar
- Department of Physics, Stellenbosch University, Stellenbosch, South Africa
| | - Betony Adams
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- The Guy Foundation, Beaminster, Dorset, UK
| | - Francesco Petruccione
- Department of Physics, Stellenbosch University, Stellenbosch, South Africa
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
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4
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Pinillos P, Camiruaga A, Torres-Hernández F, Basterrechea FJ, Usabiaga I, Fernández JA. Exploring the interaction sites in glucose and galactose using phenol as a probe. Phys Chem Chem Phys 2023; 25:7205-7212. [PMID: 36846922 DOI: 10.1039/d2cp06036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.
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Affiliation(s)
- Paúl Pinillos
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Ander Camiruaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Fernando Torres-Hernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Francisco J Basterrechea
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Imanol Usabiaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - José A Fernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
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5
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Carlo MJ, Patrick AL. Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:14-25. [PMID: 34993503 PMCID: PMC8713122 DOI: 10.1016/j.jmsacl.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.
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Key Words
- 2-AEP, 2-aminoethylphosphonic acid
- 2P1EA, 2-phenyl-1-ethanolamine
- CIVP, cryogenic ion vibrational predissociation spectroscopy
- CLIO, Centre Laser Infrarouge d’Orsay
- DFT, density functional theory
- FA, fluoroamphetamine
- FEL, free electron laser
- FELIX, Free Electron Laser for Infrared eXperiments
- FMA, fluoromethamphetamine
- FTICR, Fourier transform ion cyclotron resonance
- GC–MS, gas chromatography-mass spectrometry
- GSNO, S- nitro glutathione
- GlcNAc, n-Acetylglucosamine
- IR, infrared
- IR2MS3, infrared-infrared double-resonance multi-stage mass spectrometry
- IRMPD, infrared multiple photon dissociation (IRMPD)
- IRMPD-MS, infrared multiple photon dissociation spectroscopy mass spectrometry
- IRPD, infrared predissociation spectroscopy
- IVR, intramolecular vibrational redistribution
- Infrared multiple photon dissociation spectroscopy
- LC, liquid chromatography
- LC-MS, liquid chromatography-mass spectrometry
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MDA, methylenedioxyamphetamine
- MDMA, methylenedioxymethamphetamine
- MMC, methylmethcathinone
- MS/MS, tandem mass spectrometry
- MSn, multi-stage mass spectrometry
- Mass spectrometry
- Metabolites
- NANT, N-acetyl-N-nitrosotryptophan
- OPO/A, optical parametric oscillator/amplifier
- PTM, post-translational modification
- Pharmaceuticals
- Post-translational modifications
- SNOCys, S-nitrosocysteine
- UV, ultraviolet
- UV-IR, ultraviolet-infrared
- Vibrational spectroscopy
- cw, continuous wave
- α-PVP, alpha-pyrrolidinovalerophenone
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Affiliation(s)
- Matthew J. Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Amanda L. Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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6
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Fischer TLL, Bödecker MADI, Zehnacker A, Mata RA, Suhm MA. Setting up the HyDRA blind challenge for the microhydration of organic molecules. Phys Chem Chem Phys 2022; 24:11442-11454. [DOI: 10.1039/d2cp01119k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...
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7
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Yeni O, Schindler B, Moge B, Compagnon I. Rapid IRMPD (InfraRed multiple photon dissociation) analysis for glycomics. Analyst 2021; 147:312-317. [PMID: 34913933 DOI: 10.1039/d1an01870a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infrared vibrational spectroscopy in the gas phase has emerged as a powerful tool to determine complex molecular structures with high precision. Among the different approaches IRMPD (InfraRed multiple photon dissociation), which requires the use of an intense pulsed tuneable laser in the InfraRed (IR) domain, has been broadly applied to the study of complex (bio)molecules. Recently, it also emerged as a highly relevant approach for analytical purposes especially in the field of glycomics in which structural analysis is still a tremendous challenge. This opens the perspective to develop new analytical tools allowing for the determination of molecular structures with atomic precision, and to address advanced questions in the field. However, IRMPD experiments require non commercial equipment or/and long acquisition time which limits the data output. Here we show that it is possible to improve the IRMPD performances by optimizing the combination between a linear ion trap mass spectrometer and a high repetition tuneable laser. Two orders of magnitude are gained with this approach compared to the usual experiments ultimately leading to a completely resolved spectrum acquired in less than one minute. These results open the way to many new applications in glycomics with the possibility to include IRMPD in complex analytical workflows.
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Affiliation(s)
- Oznur Yeni
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Baptiste Schindler
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Baptiste Moge
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Isabelle Compagnon
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
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8
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Carrà A, Spezia R. In Silico
Tandem Mass Spectrometer: an Analytical and Fundamental Tool. ACTA ACUST UNITED AC 2021. [DOI: 10.1002/cmtd.202000071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Andrea Carrà
- Agilent Technologies Italia Via Piero Gobetti 2/C 20063 Cernusco SN, Milano Italy
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique Sorbonne Université, UMR 7616 CNRS 4, Place Jussieu 75005 Paris France
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9
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Anggara K, Zhu Y, Delbianco M, Rauschenbach S, Abb S, Seeberger PH, Kern K. Exploring the Molecular Conformation Space by Soft Molecule-Surface Collision. J Am Chem Soc 2020; 142:21420-21427. [PMID: 33167615 PMCID: PMC7760097 DOI: 10.1021/jacs.0c09933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 01/08/2023]
Abstract
Biomolecules function by adopting multiple conformations. Such dynamics are governed by the conformation landscape whose study requires characterization of the ground and excited conformation states. Here, the conformational landscape of a molecule is sampled by exciting an initial gas-phase molecular conformer into diverse conformation states, using soft molecule-surface collision (0.5-5.0 eV). The resulting ground and excited molecular conformations, adsorbed on the surface, are imaged at the single-molecule level. This technique permits the exploration of oligosaccharide conformations, until now, limited by the high flexibility of oligosaccharides and ensemble-averaged analytical methods. As a model for cellulose, cellohexaose chains are observed in two conformational extremes, the typical "extended" chain and the atypical "coiled" chain-the latter identified as the gas-phase conformer preserved on the surface. Observing conformations between these two extremes reveals the physical properties of cellohexaose, behaving as a rigid ribbon that becomes flexible when twisted. The conformation space of any molecule that can be electrosprayed can now be explored.
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Affiliation(s)
- Kelvin Anggara
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Yuntao Zhu
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
| | - Martina Delbianco
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
| | - Stephan Rauschenbach
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sabine Abb
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Peter H. Seeberger
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin DE-14195, Germany
| | - Klaus Kern
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Institut
de Physique, École Polytechnique
Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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10
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Carrascosa E, Pellegrinelli RP, Rizzo TR, Muyskens MA. Cryogenic Infrared Action Spectroscopy Fingerprints the Hydrogen Bonding Network in Gas-Phase Coumarin Cations. J Phys Chem A 2020; 124:9942-9950. [DOI: 10.1021/acs.jpca.0c06430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Eduardo Carrascosa
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL, SB ISIC LCPM Station 6, CH-1015 Lausanne, Switzerland
| | - Robert P. Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL, SB ISIC LCPM Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL, SB ISIC LCPM Station 6, CH-1015 Lausanne, Switzerland
| | - Mark A. Muyskens
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan 49546, United States
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11
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12
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Sagiv L, Hirshberg B, Gerber RB. Hydrogenic Stretch Spectroscopy of Glycine–Water Complexes: Anharmonic Ab Initio Classical Separable Potential Calculations. J Phys Chem A 2019; 123:8377-8384. [DOI: 10.1021/acs.jpca.9b05378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lior Sagiv
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - Barak Hirshberg
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - R. Benny Gerber
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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13
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Garand E. Spectroscopy of Reactive Complexes and Solvated Clusters: A Bottom-Up Approach Using Cryogenic Ion Traps. J Phys Chem A 2018; 122:6479-6490. [DOI: 10.1021/acs.jpca.8b05712] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Etienne Garand
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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14
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Guanidinium/ammonium competition and proton transfer in the interaction of the amino acid arginine with the tetracarboxylic 18-crown-6 ionophore. Phys Chem Chem Phys 2018; 20:4067-4073. [DOI: 10.1039/c7cp07975c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The binding of arginine by the 18-crown-6 tetracarboxylic ionophore relies on extensive host–guest redistribution of electronic charge and proton transfer.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
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15
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Gastegger M, Behler J, Marquetand P. Machine learning molecular dynamics for the simulation of infrared spectra. Chem Sci 2017; 8:6924-6935. [PMID: 29147518 PMCID: PMC5636952 DOI: 10.1039/c7sc02267k] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022] Open
Abstract
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n-alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
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Affiliation(s)
- Michael Gastegger
- University of Vienna , Faculty of Chemistry , Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria . ; ; Tel: +43 1 4277 52764
| | - Jörg Behler
- Universität Göttingen , Institut für Physikalische Chemie , Theoretische Chemie , Tammannstr. 6 , 37077 Göttingen , Germany
| | - Philipp Marquetand
- University of Vienna , Faculty of Chemistry , Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria . ; ; Tel: +43 1 4277 52764
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16
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Isolated complexes of the amino acid arginine with polyether and polyamine macrocycles, the role of proton transfer. Phys Chem Chem Phys 2017; 19:31345-31351. [DOI: 10.1039/c7cp04270a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protonated arginine interacts with 12-crown-4 through the guanidinium side group. In the complex with the N-substituted analog cyclen, the dominant conformation is the result of the proton transfer from the carboxylic acid group of the amino acid to the macrocycle.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
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17
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Avilés-Moreno JR, Gámez F, Berden G, Oomens J, Martínez-Haya B. Isolated alkali cation complexes of the antibiotic ionophore nonactin: correlation with crystalline structures. Phys Chem Chem Phys 2017; 19:14984-14991. [DOI: 10.1039/c7cp02438j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stabilization of the nonactin–Na+ complex in a S4 or C2 conformation constitutes a challenging benchmark for experimental and modelling methods.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Francisco Gámez
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
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18
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Bermúdez C, Peña I, Mata S, Alonso JL. Sweet Structural Signatures Unveiled in Ketohexoses. Chemistry 2016; 22:16829-16837. [DOI: 10.1002/chem.201603223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Celina Bermúdez
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
| | - Isabel Peña
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
| | - Santiago Mata
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
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19
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Seo J, Hoffmann W, Warnke S, Bowers MT, Pagel K, von Helden G. Die Erhaltung nativer Proteinstrukturen unter Ausschluss von Lösungsmittel: eine Untersuchung mit Hilfe der Kombination von Ionenmobilität mit Spektroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Waldemar Hoffmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry University of California Santa Barbara Santa Barbara CA 93106 USA
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie der Freien Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
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20
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Seo J, Hoffmann W, Warnke S, Bowers MT, Pagel K, von Helden G. Retention of Native Protein Structures in the Absence of Solvent: A Coupled Ion Mobility and Spectroscopic Study. Angew Chem Int Ed Engl 2016; 55:14173-14176. [PMID: 27545682 PMCID: PMC5113788 DOI: 10.1002/anie.201606029] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 11/18/2022]
Abstract
Can the structures of small to medium‐sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrometry techniques to be used to address problems relevant to structural biology. A combination of ion‐mobility mass spectrometry with infrared spectroscopy was used to investigate the secondary and tertiary structure of proteins carefully transferred from solution to the gas phase. The two proteins investigated are myoglobin and β‐lactoglobulin, which are prototypical examples of helical and β‐sheet proteins, respectively. The results show that for low charge states under gentle conditions, aspects of the native secondary and tertiary structure can be conserved.
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Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Waldemar Hoffmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie der, Freien Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
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21
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Threshold ionization spectroscopic investigation of supersonic jet-cooled, laser-desorbed Tryptophan. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.05.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Écija P, Uriarte I, Spada L, Davis BG, Caminati W, Basterretxea FJ, Lesarri A, Cocinero EJ. Furanosic forms of sugars: conformational equilibrium of methyl β-d-ribofuranoside. Chem Commun (Camb) 2016; 52:6241-4. [DOI: 10.1039/c6cc01180b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rotational spectrum of the isolated ribofuranoside unit, the biologically active sugar form, revealed two structures with a similar puckering to the RNA units in crystals.
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Affiliation(s)
- Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Iciar Uriarte
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Lorenzo Spada
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | | | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 1-40126 Bologna
- Italy
| | - Francisco J. Basterretxea
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
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23
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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24
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Marsh BM, Voss JM, Garand E. A dual cryogenic ion trap spectrometer for the formation and characterization of solvated ionic clusters. J Chem Phys 2015; 143:204201. [DOI: 10.1063/1.4936360] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brett M. Marsh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | - Jonathan M. Voss
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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25
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Gloaguen E, Tardivel B, Mons M. Gas phase double-resonance IR/UV spectroscopy of an alanine dipeptide analogue using a non-covalently bound UV-tag: observation of a folded peptide conformation in the Ac-Ala-NH2–toluene complex. Struct Chem 2015. [DOI: 10.1007/s11224-015-0690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Schindler B, Joshi J, Allouche AR, Simon D, Chambert S, Brites V, Gaigeot MP, Compagnon I. Distinguishing isobaric phosphated and sulfated carbohydrates by coupling of mass spectrometry with gas phase vibrational spectroscopy. Phys Chem Chem Phys 2015; 16:22131-8. [PMID: 25211353 DOI: 10.1039/c4cp02898h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An original application of the coupling of mass spectrometry with vibrational spectroscopy, used for the first time to discriminate isobaric bioactive saccharides with sulfate and phosphate functional modifications, is presented. Whereas their nominal masses and fragmentation patterns are undifferentiated by sole mass spectrometry, their distinctive OH stretching modes at 3595 cm(-1) and 3666 cm(-1), respectively, provide a reliable spectroscopic diagnostic for distinguishing their sulfate or phosphate functionalization. A detailed analysis of the 6-sulfated and 6-phosphated d-glucosamine conformations is presented, together with theoretical scaled harmonic spectra and anharmonic spectra (VPT2 and DFT-based molecular dynamics simulations). Strong anharmonic effects are observed in the case of the phosphated species, resulting in a dramatic enhancement of its phosphate diagnostic mode.
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27
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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28
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Brites V, Cimas A, Spezia R, Sieffert N, Lisy JM, Gaigeot MP. Stalking Higher Energy Conformers on the Potential Energy Surface of Charged Species. J Chem Theory Comput 2015; 11:871-83. [DOI: 10.1021/ct5008197] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vincent Brites
- LAMBE CNRS UMR8587, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Alvaro Cimas
- LAMBE CNRS UMR8587, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Riccardo Spezia
- LAMBE CNRS UMR8587, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Nicolas Sieffert
- Université Grenoble Alpes, DCM, 38000 Grenoble, France
- CNRS, DCM, 38000 Grenoble, France
| | - James M. Lisy
- Department
of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
- Institut Universitaire de France, 103 Blvd St Michel, 75005 Paris, France
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29
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Brites V, Lisy JM, Gaigeot MP. Infrared Predissociation Vibrational Spectroscopy of Li+(H2O)3–4Ar0,1 Reanalyzed Using Density Functional Theory Molecular Dynamics. J Phys Chem A 2015; 119:2468-74. [DOI: 10.1021/jp508699m] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V. Brites
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement,
LAMBE UMR 8587 CNRS, Université d’Evry Val d’Essonne, 91025 Evry, France
| | - J. M. Lisy
- Department
of Chemistry, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - M.-P. Gaigeot
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement,
LAMBE UMR 8587 CNRS, Université d’Evry Val d’Essonne, 91025 Evry, France
- Institut Universitaire de France IUF, 103 Blvd St Michel, 75005 Paris, France
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30
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Alauddin M, Biswal HS, Gloaguen E, Mons M. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides. Phys Chem Chem Phys 2014; 17:2169-78. [PMID: 25482851 DOI: 10.1039/c4cp04449e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.
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Affiliation(s)
- Mohammad Alauddin
- CEA, IRAMIS, Laboratoire Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
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31
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Leavitt CM, Moore KB, Raston PL, Agarwal J, Moody GH, Shirley CC, Schaefer HF, Douberly GE. Liquid Hot NAGMA Cooled to 0.4 K: Benchmark Thermochemistry of a Gas-Phase Peptide. J Phys Chem A 2014; 118:9692-700. [DOI: 10.1021/jp5092653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Paul L. Raston
- Department
of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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32
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Brites V, Nicely AL, Sieffert N, Gaigeot MP, Lisy JM. High energy conformers of M(+)(APE)(H2O)(0-1)Ar(0-1) clusters revealed by combined IR-PD and DFT-MD anharmonic vibrational spectroscopy. Phys Chem Chem Phys 2014; 16:13086-95. [PMID: 24852822 DOI: 10.1039/c4cp01275e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR-PD vibrational spectroscopy and DFT-based molecular dynamics simulations are combined in order to unravel the structures of M(+)(APE)(H2O)0-1 ionic clusters (M = Na, K), where APE (2-amino-1-phenyl ethanol) is commonly used as an analogue for the noradrenaline neurotransmitter. The strength of the synergy between experiments and simulations presented here is that DFT-MD provides anharmonic vibrational spectra that unambiguously help assign the ionic clusters structures. Depending on the interacting cation, we have found that the lowest energy conformers of K(+)(APE)(H2O)0-1 clusters are formed, while the lowest energy conformers of Na(+)(APE)(H2O)0-1 clusters can only be observed through water loss channel (i.e. without argon tagged to the clusters). Trapping of higher energy conformers is observed when the argon loss channel is recorded in the experiment. This has been rationalized by transition state energies. The dynamical anharmonic vibrational spectra unambiguously provide the prominent OH stretch due to the OH···NH2 H-bond, within 10 cm(-1) of the experiment, hence reproducing the 240-300 cm(-1) red-shift (depending on the interacting cation) from bare neutral APE. When this H-bond is not present, the dynamical anharmonic spectra provide the water O-H stretches as well as the rotational motion of the water molecule at finite temperature, as observed in the experiment.
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Affiliation(s)
- V Brites
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, LAMBE UMR 8587 CNRS, Université d'Evry Val d'Essonne, 91025 Evry, France.
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33
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DiStasio RA, Gobre VV, Tkatchenko A. Many-body van der Waals interactions in molecules and condensed matter. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:213202. [PMID: 24805055 DOI: 10.1088/0953-8984/26/21/213202] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology, chemistry and physics. Starting with the exact expression for the electron correlation energy provided by the adiabatic connection fluctuation-dissipation theorem, we derive both pairwise and many-body interatomic methods for computing the long-range dispersion energy by considering a model system of coupled quantum harmonic oscillators within the random-phase approximation. By coupling this approach to density functional theory, the resulting many-body dispersion (MBD) method provides an accurate and efficient scheme for computing the frequency-dependent polarizability and many-body vdW energy in molecules and materials with a finite electronic gap. A select collection of applications are presented that ascertain the fundamental importance of these non-bonded interactions across the spectrum of intermolecular (the S22 and S66 benchmark databases), intramolecular (conformational energies of alanine tetrapeptide) and supramolecular (binding energy of the 'buckyball catcher') complexes, as well as molecular crystals (cohesive energies in oligoacenes). These applications demonstrate that electrodynamic response screening and beyond-pairwise many-body vdW interactions--both captured at the MBD level of theory--play a quantitative, and sometimes even qualitative, role in describing the properties considered herein. This work is then concluded with an in-depth discussion of the challenges that remain in the future development of reliable (accurate and efficient) methods for treating many-body vdW interactions in complex materials and provides a roadmap for navigating many of the research avenues that are yet to be explored.
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Affiliation(s)
- Robert A DiStasio
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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34
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Zehnacker A. Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies. INT REV PHYS CHEM 2014. [DOI: 10.1080/0144235x.2014.911548] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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DFT optimization and DFT-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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37
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Mayorkas N, Cohen S, Sachs H, Bar I. Photofragment ionization-loss stimulated Raman spectroscopy of a hydrated neurotransmitter: 2-phenylethylamine–water. RSC Adv 2014. [DOI: 10.1039/c4ra10493e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The first use of photofragment ionization-loss stimulated Raman spectroscopy, in a broad range, for structural studies of clusters is reported.
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Affiliation(s)
- Nitzan Mayorkas
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105, Israel
| | - Snir Cohen
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105, Israel
| | - Hanan Sachs
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105, Israel
| | - Ilana Bar
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105, Israel
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38
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Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
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Affiliation(s)
- Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV - EHU), Apartado 644, 48940, Bilbao, Spain,
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39
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Barry C, Cocinero EJ, Çarçabal P, Gamblin D, Stanca-Kaposta EC, Remmert SM, Fernández-Alonso MC, Rudić S, Simons JP, Davis BG. 'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks. J Am Chem Soc 2013; 135:16895-903. [PMID: 24127839 PMCID: PMC3901393 DOI: 10.1021/ja4056678] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Indexed: 12/11/2022]
Abstract
N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit -Man3GlcNAc2- lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal -GlcNAc-GlcNAc- unit acts as a rigid rod, while the central, and unusual, -Man-β-1,4-GlcNAc- linkage is more flexible and is modulated by the distal Man-α-1,3- and Man-α-1,6- branching units. Solvation stiffens the 'rod' but leaves the distal residues flexible, through a β-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies.
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Affiliation(s)
- Conor
S. Barry
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emilio J. Cocinero
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - Pierre Çarçabal
- Institut
des Sciences Moléculaire d’Orsay-CNRS, Université Paris Sud, Bâtiment 210, 91405 Orsay Cedex, France
| | - David
P. Gamblin
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - E. Cristina Stanca-Kaposta
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - Sarah M. Remmert
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | | | - Svemir Rudić
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ United Kingdom
| | - Benjamin G. Davis
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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Ultraviolet and infrared spectroscopy of neutral and ionic non-covalent diastereomeric complexes in the gas phase. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2013. [DOI: 10.1007/s12210-013-0241-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gloaguen E, Loquais Y, Thomas JA, Pratt DW, Mons M. Spontaneous Formation of Hydrophobic Domains in Isolated Peptides. J Phys Chem B 2013; 117:4945-55. [DOI: 10.1021/jp401499x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric Gloaguen
- Laboratoire Francis Perrin, CNRS, INP & INC, URA 2453, F-91191 Gif-sur-Yvette, France
- Laboratoire Francis
Perrin, CEA, IRAMIS, URA 2453, F-91191
Gif-sur-Yvette, France
| | - Yohan Loquais
- Laboratoire Francis Perrin, CNRS, INP & INC, URA 2453, F-91191 Gif-sur-Yvette, France
- Laboratoire Francis
Perrin, CEA, IRAMIS, URA 2453, F-91191
Gif-sur-Yvette, France
| | - Jessica A. Thomas
- Department
of Biology and Chemistry, Purdue University North Central, Westville, Indiana
46391, United States
| | - David W. Pratt
- Department
of Chemistry, University of Vermont, Burlington,
Vermont 05405, United
States
| | - Michel Mons
- Laboratoire Francis Perrin, CNRS, INP & INC, URA 2453, F-91191 Gif-sur-Yvette, France
- Laboratoire Francis
Perrin, CEA, IRAMIS, URA 2453, F-91191
Gif-sur-Yvette, France
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Mahjoub A, Le Barbu-Debus K, Zehnacker A. Structural Rearrangement in the Formation of Jet-Cooled Complexes of Chiral (S)-1,2,3,4-Tetrahydro-3-isoquinolinemethanol with Methyl Lactate: Chirality Effect in Conformer Selection. J Phys Chem A 2013; 117:2952-60. [DOI: 10.1021/jp400998e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahmed Mahjoub
- Institut des Sciences Moléculaires d’Orsay
(ISMO), CNRS, UMR8214, Orsay F-91405, France,
and Université Paris-Sud, Orsay
F-91405, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d’Orsay
(ISMO), CNRS, UMR8214, Orsay F-91405, France,
and Université Paris-Sud, Orsay
F-91405, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d’Orsay
(ISMO), CNRS, UMR8214, Orsay F-91405, France,
and Université Paris-Sud, Orsay
F-91405, France
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Jackson G. Editorial – Topical Review. Mol Phys 2013. [DOI: 10.1080/00268976.2013.804281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Buchanan EG, Sibert EL, Zwier TS. Ground State Conformational Preferences and CH Stretch–Bend Coupling in a Model Alkoxy Chain: 1,2-Diphenoxyethane. J Phys Chem A 2013; 117:2800-11. [PMID: 23480677 DOI: 10.1021/jp400691a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Edwin L. Sibert
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
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Ciavardini A, Rondino F, Paladini A, Speranza M, Fornarini S, Satta M, Piccirillo S. The effect of fluorine substitution on chiral recognition: interplay of CH⋯π, OH⋯π and CH⋯F interactions in gas-phase complexes of 1-aryl-1-ethanol with butan-2-ol. Phys Chem Chem Phys 2013; 15:19360-70. [DOI: 10.1039/c3cp53215a] [Citation(s) in RCA: 6] [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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Çarçabal P, Cocinero EJ, Simons JP. Binding energies of micro-hydrated carbohydrates: measurements and interpretation. Chem Sci 2013. [DOI: 10.1039/c3sc50135c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Jin L, Simons JP, Gerber RB. Monosaccharide-Water Complexes: Vibrational Spectroscopy and Anharmonic Potentials. J Phys Chem A 2012; 116:11088-94. [DOI: 10.1021/jp303080k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lin Jin
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
- Institute of Chemistry
and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Gu Q, Knee JL. Communication: Spectroscopic measurement of the binding energy of a carboxylic acid-water dimer. J Chem Phys 2012; 136:171101. [DOI: 10.1063/1.4711862] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Quanli Gu
- Chemistry Department, University of Virginia, Charlottesville, Virginia 22904, USA
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
| | - J. L. Knee
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
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Hurtado P, Gámez F, Hamad S, Martínez–Haya B, Steill JD, Oomens J. Multipodal coordination of a tetracarboxylic crown ether with NH 4+: A vibrational spectroscopy and computational study. J Chem Phys 2012; 136:114301. [DOI: 10.1063/1.3693518] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Editorial. Mol Phys 2012. [DOI: 10.1080/00268976.2011.646415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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