ИК

И. К. Галетич

University of the Basque Country

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Vadim S. Shelkovsky

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

МВ

М. В. Косевич

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

Ludwik Adamowicz

University of Arizona

V. A. Sirenko

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

S. G. Stepanian

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

Nataly V. Shulyupina

Institute of Theoretical and Experimental Biophysics

A. V. Eremenko

Orel State University named after I.S. Turgenev

ИА

И. А. Господарев

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

K. V. Kravchenko

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

ВИ

В. И. Гришаев

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

Cooperative Institutions

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

National Academy of Sciences of Ukraine

Physicotechnical Institute

Physico-Technical Institute

University of Arizona

Russian Academy of Sciences

National Technical University "Kharkiv Polytechnic Institute"

University of the Basque Country

Institute of Theoretical and Experimental Biophysics

National Academy of Sciences

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Structure and energy of nucleic acid base–amino acid complexes: 1. 1-methyl-uracil-acrylamide

Journal of Molecular Structure (1999)

И. К. Галетич М. В. Косевич Vadim S. Shelkovsky S. G. Stepanian Yu. P. Blagoı̆

Uracil

Quantum chemical

10.1016/s0022-2860(98)00756-x

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Citations (16)

Study of Protein-Nucleic Acid Base Complexes Involving Amide Group

Springer eBooks (1997)

И. К. Галетич

Biopolymer

Amide

Nucleic acid structure

Nucleic acid analogue

10.1007/978-94-011-5622-6_165

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Citations (0)

Mass spectrometric andab initiostudy of the interaction between 9-methylguanine and amino acid amide group

Molecular Physics (2002)

И. К. Галетич S. G. STAPANIAN Vadim S. Shelkovsky М. В. Косевич Ludwik Adamowicz

The temperature dependent field ionization mass spectrometry method combined with ab initio calculations was used to determine the interaction energies and the structures of 9-methylguanine-acrylamide dimers. Acrylamide mimics the side chain amide group of the natural amino acids asparagine and glutamine. The experimental enthalpy of the dimer formation derived from the van't Hoff plot is −59.5 ± 3.8 kJ mol−1. The value is higher than interaction energies between acrylamide and other nucleic acid bases which were determined to be −57.0 for 1-methylcytosine, −52.0 for 9-methyladenine, and −40.6 kJ mol−1 for 1-methyl-uracil. In total, eight hydrogen bonded dimers formed by the three lowest energy 9-methylguanine tautomers and acrylamide were found in the quantum chemical calculations performed at the DFT/B3LYP/6-31++G∗∗ and MP2/6-31++G∗∗ levels of theory. The relative stability and the interaction energies of the dimers were calculated accounting for the basis set superposition error and the zero-point vibrational energy correction. The lowest energy dimer found in the calculations is formed by acrylamide (Ac) with the keto tautomer of 9-methylguanine (Gk). It is stabilized by two intermolecular H bonds, C6=O(Gk) · · · H—N(Ac) and Nl—H(Gk) · · ·O(Ac), and it is more stable than the second lowest energy dimer by ≈ 25 kJ mol−1. The calculated interaction energies of the lowest energy 9-methylguanine-acrylamide dimer are −65.0 kJ mol−1 and −67.7 kJ mol−1 at the MP2 and DFT levels of theory, respectively. The experimental enthalpy of the dimer formation is in good agreement with both the calculated interaction energies of the GkAc dimer and much higher than the interaction energies calculated for all other 9-methylguanine-acrylamide dimers. This proved that only one dimer was present in the experimental samples. To verify whether acrylamide is a good model of the amino acid-amide group, we performed direct calculations of the 9-methylguanine-glutamine dimers at the same levels of theory as used for the complexes involving acrylamide. The interaction energies found for the lowest energy 9-methylguanine-glutamine dimer are −65.1 kJ mon−1 (MP2/6-31++G∗∗) and −66.2 kJ mol−1 (DFT/B3LYP/6-31++G∗∗) and these values are very close (within 0.5 kJ mol−1) to the interaction energies obtained for the 9-methylguanine-acrylamide dimers.

Methyl group

Interaction energy

10.1080/00268970210149740

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Citations (4)

Mass spectrometric and computational study of complex formation of nucleic acid bases with acrylamide as a surrogate for asparagine and glutamine residues

Rapid Communications in Mass Spectrometry (1998)

И. К. Галетич Vadim S. Shelkovsky М. В. Косевич Yury P. Blagoy Nataly V. Shulyupina

In the context of the problem of nucleic acid–protein interactions, thermodynamic and geometrical parameters of complexes of methylated nucleic acid bases with acrylamide (as a model of the side chains of asparagine and glutamine) were investigated. Enthalpies of formation of nucleic acid base–acrylamide complexes, determined experimentally by means of temperature-dependent field ionization mass spectrometry, were in reasonable agreement with the interaction energies calculated theoretically using atom–atom potential functions. A stability order for base–acrylamide complexes was determined:m9Gua ≥ m21,4 Cyt ≥ m1 Cyt > m9 Ade > m31,4,4 Cyt > m1 Ura > m21,3 Thy.The geometries of the most energetically favourable complexes are determined and discussed. © 1998 John Wiley & Sons, Ltd.

10.1002/(sici)1097-0231(19981130)12:22<1761::aid-rcm358>3.0.co;2-8

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Citations (1)

Vibrational characteristics of the niobium dichalcogenide. Bulk samples and nanofilms

Superlattices and Microstructures (2009)

И. К. Галетич И. А. Господарев В. И. Гришаев A. V. Eremenko K. V. Kravchenko

Diselenide

Lattice (music)

Matrix element

10.1016/j.spmi.2009.03.008

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Citations (8)

Low frequensy peculiarities of phonon spectra of solid substitutional solution. Interaction beetwen fast acoustic phonons with quasi local vibrations

Scientific Herald of Uzhhorod University Series Physics (2010)

И. А. Господарев В. И. Гришаев А. В. Котляр K. V. Kravchenko Е. В. Манжелий

Phonon spectra of solid substitutional solution with finite concentration of impurities have been analyzed on the microscopical level. The phonon densities of states and local phonon densities of impurity atoms are calculated. The formation of quasilocal vibrations and their evolution with increasing of the concentration of impurities are investigated.

10.24144/2415-8038.2010.28.70-79

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Citations (0)

Experimental and Theoretical Study of Energetics of Complex Formation Between Nucleic Acid Bases and the Bases with Amide Group

Journal of Biomolecular Structure and Dynamics (1991)

V. I. Poltev Nataly V. Shulyupina В. И. Брусков A. B. Teplitsky Л. Ф. Суходуб

Abstract A number of nucleic acid base pairs and complexes between the bases and the amide group of acrylamide have been studied experimentally by using mass spectrometry and theoretically by the method of atom-atom potential function calculations. It has been found from temperature dependencies of peak intensities in mass spectra of m3 2,2,9Gua · m1Ura, m9 Ade · m1Cyt, m2.2.9 3 Gua · m1Gua · m1Cyt pairs that enthalpy values, ΔH, of the complex formation are equal to 14.2 ± 1.1, 13.5 ± 1.3 and 16.4 ± 1.4 kcal/M, respectively, and those of acrylamide with m13 2 Ura and m1 Thy corresponds to 9.7 ± 1.0 and 6.8 ± 0.6 kcal/M. There is a good agreement of the experimental data with calculations when taking into account both the amino-oxo and the amino-hydroxy tautomeric forms of guanine. A combined use of the data allows us to determine the energy, the modes of interaction and the structure of the complexes. The results are discussed in connection with the modelling of molecular structure of biopolymers by the method of classical potential functions, protein-nucleic acids recognition and fidelity of nucleic acids biosynthesis.

Amide

Base (topology)

10.1080/07391102.1991.10507896

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Citations (4)

Modeling of recognition sites of nucleic acid bases aaand amide side chains of amino acids. Combination of experimental and theoretical approaches

The European Physical Journal D (2002)

Vadim S. Shelkovsky S. G. Stepanian И. К. Галетич М. В. Косевич Ludwik Adamowicz

Nucleobase

Biomolecule

Side chain

Amide

Nucleic acid structure

10.1140/epjd/e2002-00144-9

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Citations (9)

Mass spectrometric and computational study of complex formation of nucleic acid bases with acrylamide as a surrogate for asparagine and glutamine residues

Rapid Communications in Mass Spectrometry (1998)

И. К. Галетич Vadim S. Shelkovsky М. В. Косевич Yury P. Blagoy Nataly V. Shulyupina

10.1002/(sici)1097-0231(19981130)12:22<1761::aid-rcm358>3.3.co;2-#

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Citations (0)

Matrix Sublimation Device for MALDI Mass Spectrometry Imaging

Analytical Chemistry (2018)

Roberto Fernández Jone Garate Lucía Martín‐Saiz И. К. Галетич José A. Fernández

Sublimation is a widely used method for matrix deposition in imaging mass spectrometry experiments. Still, most of the time, standard glass sublimators are used for this purpose, which do not enable optimal matrix deposition reproducibility, compromising inter-experiment comparison of the results. Here, we present an in-house designed stainless steel sublimator in which the parameters that have the strongest influence over matrix deposition reproducibility can be easily monitored. Using sections of human colon biopsies, we demonstrate the capabilities of this new prototype.

Sublimation

Mass spectrometry imaging

Matrix (chemical analysis)

10.1021/acs.analchem.8b04765

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Citations (27)