Environmental effects on vibrational proton dynamics in H5O2+: DFT study on crystalline H5O2+ClO4−

Vener, Mikhail V.; Sauer, Joachim

doi:10.1039/b412795a

Cited by 53 publications

(31 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2 in Ref. 80 and is therefore used for the spectra reported below. A classical MD simulation gives a reasonable description of the IR spectrum of the liquid systems, 81,82 where a 0.5 fs time step is sufficient to produce reliable IR results for the ∼2000 cm −1 region.…”

Section: Computational Detailsmentioning

confidence: 99%

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Vener

Odinokov

Wehmeyer

et al. 2015

The Journal of Chemical Physics

View full text Add to dashboard Cite

Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.

show abstract

Section: Computational Detailsmentioning

confidence: 99%

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Vener

Odinokov

Wehmeyer

et al. 2015

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…The ab initio molecular dynamics is widely used to investigate the molecular properties of systems in various states of matter, e.g., solid state. [13][14][15][16][17] The time evolution of the molecular properties in the framework of the CPMD is performed on a potential energy surface obtained from electronic structure calculations, enabling studies of reaction pathways and realistic description of highly flexible systems, for which classical force fields are not appropriate. Boronic acids have been parametrized in the framework of the MM3 force field, 18 but our focus on the details of hydrogen bonding excludes the use of classical parametrization.…”

Section: Introductionmentioning

confidence: 99%

Structural and spectroscopic properties of an aliphatic boronic acid studied by combination of experimental and theoretical methods

Cyrański

Jezierska

Klimentowska

et al. 2008

The Journal of Chemical Physics

View full text Add to dashboard Cite

Boronic acids have emerged as one of the most useful class of organoboron molecules, with application in synthesis, catalysis, analytical chemistry, supramolecular chemistry, biology, and medicine. In this study, the structural and spectroscopic properties of n-butylboronic acid were investigated using experimental and theoretical approaches. X-ray crystallography method provided structural information on the studied compound in the solid state. Infrared and Raman spectroscopy served as tools for the data collection on vibrational modes of the analyzed system. Car-Parrinello molecular dynamics simulations in solid state were carried out at 100 and 293 K to investigate an environmental and temperature influence on molecular properties of the n-butylboronic acid. Analysis of interatomic distances of atoms involved in the intermolecular hydrogen bond was performed to study the proton motion in the crystal. Subsequently, Fourier transform of autocorrelation functions of atomic velocities and dipole moment was applied to study the vibrational properties of the compound. In addition, the inclusion of quantum nature of proton motion was performed for O-H stretching vibrational mode by application of the envelope method for intermolecular hydrogen-bonded system. The second part of the computational study consists of simulations performed in vacuo. Monomeric and dimeric forms of the n-butylboronic acid were investigated using density functional theory and Moller-Plesset second-order perturbation method. The basis set superposition error was estimated. Finally, atoms in molecules (AIM) theory was applied to study electron density topology and properties of the intermolecular hydrogen bond. Successful reproduction of the molecular properties of the n-butylboronic acid by computational methodologies, presented in the manuscript, indicates the way for future studies of large boron-containing organic systems of importance in biology or materials science.

show abstract

“…[33]. More recent investigations have focused on strongly H-bonded systems such as the Zundel cation in the crystalline phase [34].…”

mentioning

confidence: 99%

Vibrational Dynamics of the Double Hydrogen Bonds in Nucleic Acid Base Pairs

Yan

Kühn

2010

Hydrogen Bonding and Transfer in the Excited State

View full text Add to dashboard Cite

The structural selectivity of complementary pairing of nucleic acid bases in DNA signifies the importance of hydrogen bonding in biology [1,2]. This fact has triggered a host of investigations, starting with gasphase and microsolvation studies of the stability and spectroscopy of nucleic acid bases as the fundamental building blocks [3,4]. Here, the specific changes in the infrared (IR) spectrum owing to hydrogen bonding provide a sensitive means of identification of bonding patterns, not only in gas but also in condensed phase [5,6]. For isolated adenine-thymine pairs, for instance, which were studied in gas phase using the IR-UV double-resonance technique [7], evidence was found that Watson-Crick pairing is not very likely under these conditions. In order to identify the dominant tautomer, it was necessary to perform quantum dynamical simulations of IR spectra, including anharmonicity [8]. Anharmonicity of the potential energy surface is characteristic of hydrogen-bonded species. Together with the quantum nature of the problem, it makes hydrogen bond (HB) dynamics a challenging task even in gas phase [9][10][11]. The issue of preferential association of nucleobases carries over to solution-phase studies. In a seminal work, Rich and coworkers [12] studied the homo-and heteropairing of various adenine and uracil derivatives in deuterochloroform solution using IR spectroscopy. This work triggered investigations of a number of nucleic acid base pairs [13-17]; a review of IR bands in the 800-1800 cm À1 range in aqueous solution can be found in Ref. [18].Linear IR spectroscopy cannot disentangle the rich information on the HB dynamics that is encoded in the broad and often structured lineshapes of IR spectra, especially in the condensed phase. Ultrafast nonlinear IR spectroscopy, on the other hand, has been proven to provide the means for addressing this dynamical information, thus giving access to anharmonic couplings, fluctuation timescales and pathways of vibrational

show abstract

Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻

Cited by 53 publications

References 47 publications

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Structural and spectroscopic properties of an aliphatic boronic acid studied by combination of experimental and theoretical methods

Vibrational Dynamics of the Double Hydrogen Bonds in Nucleic Acid Base Pairs

Contact Info

Product

Resources

About