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Nacsa AB, Kígyósi M, Czakó G. Protonation of serine: conformers, proton affinities and gas-phase basicities at the "gold standard" and beyond. Phys Chem Chem Phys 2023; 25:8891-8902. [PMID: 36916632 DOI: 10.1039/d3cp00612c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The potential energy surfaces (PESs) of serine and its protonated counterparts are investigated to determine the structures of the minima. A total of 95 neutral serine, 15 N-(amino-) and 46 O-(carbonyl-)protonated serine conformers are found. Their relative energies, geometries and harmonic vibrational frequencies are determined at the MP2/aug-cc-pVDZ level of theory. To obtain highly accurate thermodynamic values, further computations are performed: the ten conformers with the lowest relative energies from each molecule type (neutral, N- and O-protonated) are further optimized using the explicitly correlated CCSD(T)-F12a/cc-pVDZ-F12 method (for neutral serine, harmonic vibrational frequencies were also computed). In addition, auxiliary corrections were determined: basis-set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation and second-order Douglas-Kroll relativistic effects along with zero-point energy contributions. Two important thermodynamic parameters (at 298.15 K), proton affinity (PA)/gas-phase basicity (GB) are calculated considering the two different protonation sites: 218.05 ± 0.2/209.86 ± 0.6 kcal mol-1 and 205.87 ± 0.2/196.36 ± 0.3 kcal mol-1 for the amino and carbonyl sites, respectively. The uncertainty of the determined values was approximated based on various sources including auxiliary corrections, basis-set effects, harmonic vibrational frequencies.
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Affiliation(s)
- András B Nacsa
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Máté Kígyósi
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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2
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Wang Z, Dan G, Zhang R, Ma L, Lin K. Coupling and decoupling CH stretching vibration of methylene and methine in serine conformers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121829. [PMID: 36116413 DOI: 10.1016/j.saa.2022.121829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
In the molecules of the early Earth, as a building block of proteins, serine has enormous chemical and biological significance. The vibrational spectroscopy of CH bonds plays an important role in probing biomolecules. Whether the CH stretching vibration bands can be accurately assigned will affect the accuracy of the detection results. In this study, we employed the MP2/cc-pVTZ method to calculate the Raman spectra of 85 serine conformers and the corresponding species with deuterium in the CH stretching region from 2800 cm-1 to 3050 cm-1 and then recorded the movement of each atom and the dihedral angles, CH bond lengths, and Raman shifts before and after deuterium for each conformer. We directly observed that the stretching vibration of two CH bonds in the methylene group decoupled to vibrate independently in some conformers, and the stretching vibrations of methylene and methine could be strongly coupled in some conformers. Those results are inconsistent with the traditional understanding, which is generally believed that the CH stretching vibrations are mutually coupled in a single methyl or methylene group to generate symmetric and antisymmetric stretching vibrations, while for different methyl, methylene or methine groups, the CH stretching vibrations cannot be mutually coupled. Through the statistical analysis between several factors, we found that the level of local coupling in serine methylene was correlated with the bond length difference between two CH bonds. Our work provides a new understanding of the vibrational modes of hydrocarbon bonds and the coupling between different hydrocarbon groups.
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Affiliation(s)
- Zhiqiang Wang
- School of Physics, Xidian University, Xi'an 710071, PR China
| | - Guangyu Dan
- School of Physics, Xidian University, Xi'an 710071, PR China
| | - Ruiting Zhang
- School of Physics, Xidian University, Xi'an 710071, PR China
| | - Lin Ma
- School of Physics, Xidian University, Xi'an 710071, PR China
| | - Ke Lin
- School of Physics, Xidian University, Xi'an 710071, PR China; Interdisciplinary Research Center of Smart Sensor, Xidian University, Xi'an 710071, PR China.
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3
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Nacsa AB, Czakó G. Benchmark Ab Initio Determination of the Conformers, Proton Affinities, and Gas-Phase Basicities of Cysteine. J Phys Chem A 2022; 126:9667-9679. [PMID: 36524999 PMCID: PMC9806835 DOI: 10.1021/acs.jpca.2c07035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A systematic conformational mapping combined with literature data leads to 85 stable neutral cysteine conformers. The implementation of the same mapping process for the protonated counterparts reveals 21 N-(amino-), 64 O-(carbonyl-), and 37 S-(thiol-)protonated cysteine conformers. Their relative energies and harmonic vibrational frequencies are given at the MP2/aug-cc-pVDZ level of theory. Further benchmark ab initio computations are performed for the 10 lowest-lying neutral and protonated amino acid conformers (for each type) such as CCSD(T)-F12a/cc-pVDZ-F12 geometry optimizations (and frequency computations for cysteine) as well as auxiliary correction computations of the basis set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation effects, second-order Douglass-Kroll relativistic effects, and zero-point energy contributions. Boltzmann-averaged 0 (298.15) K proton affinity and [298.15 K gas-phase basicity] values of cysteine are predicted to be 214.96 (216.39) [208.21], 201.83 (203.55) [194.16], and 193.31 (194.74) [186.40] kcal/mol for N-, O-, and S-protonation, respectively, also considering the previously described auxiliary corrections.
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Hu X, Lenz-Himmer MO, Baldauf C. Better force fields start with better data: A data set of cation dipeptide interactions. Sci Data 2022; 9:327. [PMID: 35715420 PMCID: PMC9205945 DOI: 10.1038/s41597-022-01297-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.
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Affiliation(s)
- Xiaojuan Hu
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
| | | | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
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5
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Ferro-Costas D, Mosquera-Lois I, Fernández-Ramos A. TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids. J Cheminform 2021; 13:100. [PMID: 34952644 PMCID: PMC8710030 DOI: 10.1186/s13321-021-00578-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/08/2021] [Indexed: 11/10/2022] Open
Abstract
In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.
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Affiliation(s)
- David Ferro-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| | - Irea Mosquera-Lois
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Antonio Fernández-Ramos
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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6
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Owens A, Lane JR, Manley-Harris M, Marie Jensen A, Jørgensen S. Kinetics of conversion of dihydroxyacetone to methylglyoxal in New Zealand mānuka honey: Part V – The rate determining step. Food Chem 2019; 276:636-642. [DOI: 10.1016/j.foodchem.2018.10.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/11/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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7
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Shahriar I, Islam MKB, Iqfath M, Rahman A, Halim MA. Solvent effect on vibrational circular dichroism of chiral amino acids. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2419-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Silva WGDP, Braga CB, Rittner R. Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and 3JHH coupling constant analyses. Beilstein J Org Chem 2017; 13:925-937. [PMID: 28684974 PMCID: PMC5480334 DOI: 10.3762/bjoc.13.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 12/29/2022] Open
Abstract
The understanding of the conformational behavior of amino acids and their derivatives is a challenging task. Here, the conformational analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of 1H NMR and electronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into account the implicit solvent effects, according to the integral equation formalism polarizable continuum model (IEF-PCM), were obtained at the ωB97X-D/aug-cc-pVTZ level. The conformational preferences of the compounds in solution were also determined from experimental and theoretical 3JHH coupling constants analysis in different aprotic solvents. The results showed that the conformational stability of the esterified derivatives is not very sensitive to solvent effects, whereas the conformational equilibrium of the N-acetylated derivatives changes in the presence of solvent. According to the natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects.
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Affiliation(s)
- Weslley G D P Silva
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083−970, Campinas, SP, Brazil
| | - Carolyne B Braga
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083−970, Campinas, SP, Brazil
| | - Roberto Rittner
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083−970, Campinas, SP, Brazil
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9
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Jaidane NE. Structures and spectroscopy of medium size protonated ammonia clusters at different temperatures, H+(NH3)10–16. J Chem Phys 2017; 146:044305. [DOI: 10.1063/1.4974179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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11
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Mazmanian K, Sargsyan K, Grauffel C, Dudev T, Lim C. Preferred Hydrogen-Bonding Partners of Cysteine: Implications for Regulating Cys Functions. J Phys Chem B 2016; 120:10288-10296. [PMID: 27635780 DOI: 10.1021/acs.jpcb.6b08109] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrogen-bonding interactions of cysteine, which can serve as a hydrogen-bond donor and/or acceptor, play a central role in cysteine's diverse functional roles in proteins. They affect the balance between the neutral thiol (SH) or thiolate (S-) and the charge distribution in the rate-limiting transition state of a reaction. Despite their importance, no study has determined the preferred hydrogen-bonding partners of cysteine serving as a hydrogen-bond donor or acceptor. By computing the free energy for displacing a peptide backbone hydrogen-bonded to cysteine with amino acid side chains in various protein environments, we have evaluated how the strength of the hydrogen bond to the cysteine thiol/thiolate depends on its hydrogen-bonding partner and its local environment. The predicted hydrogen-bonding partners preferred by cysteine are consistent with the hydrogen-bonding interactions made by cysteines in 9138 nonredundant X-ray structures. Our results suggest a mechanism to regulate the reactivity of cysteines and a strategy to design drugs based on the hydrogen-bonding preference of cysteine.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University , Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
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12
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First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Sci Data 2016; 3:160009. [PMID: 26881946 PMCID: PMC4755128 DOI: 10.1038/sdata.2016.9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 01/15/2016] [Indexed: 11/24/2022] Open
Abstract
We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.
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13
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Jaidane NE. Structures and spectroscopy of protonated ammonia clusters at different temperatures. Phys Chem Chem Phys 2016; 18:26827-26843. [DOI: 10.1039/c6cp03240k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Campus Universitaire
- Tunis
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Campus Universitaire
- Tunis
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14
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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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15
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Fifen JJ, Dhaouadi Z, Nsangou M. Revision of the Thermodynamics of the Proton in Gas Phase. J Phys Chem A 2014; 118:11090-7. [DOI: 10.1021/jp508968z] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean Jules Fifen
- Department
of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire
de Spectroscopie Atomique et Moléculaire, Faculté des
Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire 1060, Tunis, Tunisia
| | - Mama Nsangou
- University of Maroua, P.O. Box, 46, Maroua, Cameroon
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16
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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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17
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Sengupta A, Ramabhadran RO, Raghavachari K. Accurate and Computationally Efficient Prediction of Thermochemical Properties of Biomolecules Using the Generalized Connectivity-Based Hierarchy. J Phys Chem B 2014; 118:9631-43. [DOI: 10.1021/jp505544y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Arkajyoti Sengupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | | | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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18
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Freeman F, Adesina IT, La JL, Lee JY, Poplawski AA. Conformers of cysteine and cysteine sulfenic acid and mechanisms of the reaction of cysteine sulfenic acid with 5,5-dimethyl-1,3-cyclohexanedione (dimedone). J Phys Chem B 2013; 117:16000-12. [PMID: 24274619 DOI: 10.1021/jp409022m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Equilibrium and molecular structures, relative energies of conformers of gaseous cysteine (Cys, C, Cys-SH) and gaseous cysteine sulfenic acid (Cys-SOH), and the mechanisms of the reaction of Cys-SOH with 3-hydroxy-5,5-dimethyl-2-cyclohexen-1-one, the enol tautomer of 5,5-dimethyl-1,3-cyclohexadione (dimedone), have been studied using BD(T), CCSD(T), and QCISD(T) with the cc-pVTZ basis set and using MP2 and the density functionals B3LYP, B3PW91, PBE1PBE, PBEh1PBE, M062X, CAM-B3LYP, and WB97XD with the 6-311+G(d,p) basis set. The structures of the six lowest energy conformers of gaseous Cys-SOH are compared with the six lowest energy conformers of gaseous cysteine (Cys-SH). The relative stability of the six lowest energy conformers of Cys-SH and Cys-SOH are influenced by the interplay among many factors including dispersive effects, electronic effects, electrostatic interactions, hydrogen bonds, inductive effects, and noncovalent interactions. The mechanism of the addition of the lowest energy conformer of cysteine sulfenic acid (Cys-SOH) to dimedone may proceed through a six-membered ring transition state structure and through cyclic hydrogen-bonded transition state structures with one water molecule (8-membered ring), with two water molecules (10-membered ring), and with three water molecules (12-membered ring). Inclusion of one and two water molecules in the transition state structures lowers the activation barrier, whereas inclusion of a third water molecule raises the activation barrier.
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Affiliation(s)
- Fillmore Freeman
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
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19
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Amorim Madeira PJ, Vaz PD, Bettencourt da Silva RJN, Florêncio MH. Can Semi-empirical Calculations Help Solve Mass Spectrometry Problems? Protonation Sites and Proton Affinities of Amino Acids. Chempluschem 2013; 78:1149-1156. [DOI: 10.1002/cplu.201300173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/19/2013] [Indexed: 11/10/2022]
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20
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Riffet V, Bouchoux G. Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base. Phys Chem Chem Phys 2013; 15:6097-106. [DOI: 10.1039/c3cp00043e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Michelson AZ, Chen M, Wang K, Lee JK. Gas-Phase Studies of Purine 3-Methyladenine DNA Glycosylase II (AlkA) Substrates. J Am Chem Soc 2012; 134:9622-33. [DOI: 10.1021/ja211960r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Zhachkina Michelson
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Mu Chen
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Kai Wang
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Jeehiun K. Lee
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
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22
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Roux MV, Notario R, Segura M, Chickos JS, Liebman JF. The enthalpy of formation of methionine revisited. J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.2961] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- María Victoria Roux
- Institute of Physical Chemistry “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Rafael Notario
- Institute of Physical Chemistry “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Marta Segura
- Perkin Elmer España S.L.; Ronda de Poniente 19, 28760 Tres Cantos Madrid Spain
| | - James S. Chickos
- Department of Chemistry and Biochemistry; University of Missouri-St. Louis; One University Boulevard St. Louis Missouri 63121-4499 USA
| | - Joel F. Liebman
- Department of Chemistry and Biochemistry; University of Maryland; Baltimore County Baltimore MD 21250 USA
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23
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Bouchoux G. Gas phase basicities of polyfunctional molecules. Part 3: Amino acids. MASS SPECTROMETRY REVIEWS 2012; 31:391-435. [PMID: 22611554 DOI: 10.1002/mas.20349] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed.
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Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91120 Palaiseau, France.
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