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Boča R, Imrich R, Štofko J, Vranovičová B, Rajnák C. Molecular properties of linear amino acids in water. Amino Acids 2024; 56:5. [PMID: 38300332 PMCID: PMC10834582 DOI: 10.1007/s00726-023-03365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/13/2023] [Indexed: 02/02/2024]
Abstract
Four linear amino acids of increased separation of the carboxyl and amino groups, namely glycine (aminoacetic acid), β-alanine (3-aminopropanoic acid), GABA (4-aminobutanoic acid) and DAVA (5-aminopentanoic acid), have been studied by quantum chemical ab initio and DFT methods including the solvent effect in order to get electronic structure and molecular descriptors, such as ionisation energy, electron affinity, molecular electronegativity, chemical hardness, electrophilicity index, dipole moment, quadrupole moment and dipole polarizability. Thermodynamic functions (zero-point energy, inner energy, enthalpy, entropy, and the Gibbs energy) were evaluated after the complete vibrational analysis at the true energy minimum provided by the full geometry optimization. Reaction Gibbs energy allows evaluating the absolute redox potentials on reduction and/or oxidation. The non-local non-additive molecular descriptors were compared along the series showing which of them behave as extensive, varying in match with the molar mass and/or separation of the carboxyl and amino groups. Amino acidic forms and zwitterionic forms of the substances were studied in parallel in order to compare their relative stability and redox properties. In total, 24 species were investigated by B3LYP/def2-TZVPD method (M1) including neutral molecules, molecular cations and molecular anions. For comparison, MP2/def2-TZVPD method (M2) with full geometry optimization and vibrational analysis in water has been applied for 12 species; analogously, for 24 substances, DLPNO-CCSD(T)/aug-cc-pVTZ method (M3) has been applied in the geometry obtained by MP2 and/or B3LYP. It was found that the absolute oxidation potential correlates with the adiabatic ionisation energy; the absolute reduction potential correlates with the adiabatic electron affinity and the electrophilicity index. In order to validate the used methodology with experimental vertical ionisation energies and vibrational spectrum obtained in gas phase, calculations were done also in vacuo.
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Affiliation(s)
- Roman Boča
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia.
| | - Richard Imrich
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Juraj Štofko
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Beáta Vranovičová
- Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Cyril Rajnák
- Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
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Boča R, Štofko J, Imrich R. Effect of Solvation on Glycine Molecules: A Theoretical Study. ACS OMEGA 2023; 8:28577-28582. [PMID: 37576642 PMCID: PMC10413822 DOI: 10.1021/acsomega.3c02972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/20/2023] [Indexed: 08/15/2023]
Abstract
Ab initio calculations of HF+MP2 and DFT-B3LYP quality have been used in calculating the molecular geometries and properties of neutral and charged molecules of glycine in amino acid as well as zwitterionic forms. A traditional set of molecular descriptors has been enriched by the molecular chemical potential, expressed via the Mulliken electronegativity, and Pearson's chemical hardness. In the global energy minimum, the complete vibrational analysis allowed evaluating the standard Gibbs energy and related thermodynamic quantities.
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Affiliation(s)
- Roman Boča
- University of SS Cyril and
Methodius, Faculty of Health Science, 917 01 Trnava, Slovakia
| | - Juraj Štofko
- University of SS Cyril and
Methodius, Faculty of Health Science, 917 01 Trnava, Slovakia
| | - Richard Imrich
- University of SS Cyril and
Methodius, Faculty of Health Science, 917 01 Trnava, Slovakia
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Boča R, Štofko J, Imrich R. Ab initio study of molecular properties of l-tyrosine. J Mol Model 2023; 29:245. [PMID: 37442864 PMCID: PMC10344843 DOI: 10.1007/s00894-023-05648-8] [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: 05/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
CONTEXT l-Tyrosine is a naturally occurring agent that acts as a precursor in biosynthesis of monoaminergic neurotransmitters in brain such as dopamine, adrenaline, noradrenaline, and hormones like thyroxine and triiodothyronine. While l-tyrosine in vacuo adopts the canonical aminoacid form with -NH2 and -COOH functional groups, from neutral solutions, is crystallizes in the zwitterionic form possessing -NH3+ and -COO- groups. As l-tyrosine is non-innocent agent with respect to redox processes, redox ability in water expressed by the absolute oxidation and reduction potentials is investigated. The cluster analysis applied to a set of nine related neurotransmitters and trace amines confirms that l-tyrosine is mostly similar to aminoacid forms of phenylalanine, octopamine, and noradrenaline. METHODS The energetic data at the Hartree-Fock MO-LCAO-SCF method has been conducted using def2-TZVP basis set, and improved by the many-body perturbation theory using the MP2 correction to the correlation energy. For the aminoacid form and the zwitterionic form of l-tyrosine, a set of molecular descriptors has been evaluated (ionization energy, electron affinity, molecular electronegativity, chemical hardness, electrophilicity index, dipole moment, quadrupole moment, and dipole polarizability). The solvent effect (CPCM) is very expressive to the zwitterionic form and alters the sign of the electron affinity from positive to negative values. In parallel, density-functional theory with B3LYP variant in the same basis set has been employed for full geometry optimization of the neutral and ionized forms of l-tyrosine allowing assessing the adiabatic (a) ionization/affinity processes. The complete vibrational analysis enables evaluating thermodynamic functions such as the inner energy, enthalpy, entropy, Gibbs energy, and consequently the absolute oxidation and reduction potentials. Of applied methods, the most reliable are B3LYP(a) results that account to the correlation energy and the electron and nuclear relaxation during the ionization/affinity processes.
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Affiliation(s)
- Roman Boča
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia.
| | - Juraj Štofko
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Richard Imrich
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
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Vranovičová B, Boča R. Ab initio study of the biogenic amino acids. J Mol Model 2021; 27:355. [PMID: 34792651 DOI: 10.1007/s00894-021-04976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022]
Abstract
Ten amino acids have been subjected to the quantum chemical calculations using the ab initio MO-LCAO-SCF calculations. When the geometry optimization started form the X-ray structure confirming the zwitterionic form, the ab initio calculations in vacuo result in the amino acid (canonical) form with the hydrogen atom attached not to the amine but to the carboxylate group. At the optimum geometry, a number of properties were evaluated: dipole moment, dipole polarizability, molecular surface, molecular volume, HOMO, LUMO, ionization energy, and electron affinity using the ΔSCF approach and their values corrected for electron correlation by the 2nd order perturbation theory (MP2). Also, the Mulliken electronegativity and Pearson hardness were evaluated. These properties have been mutually correlated by employing the statistical multivariate methods: the cluster analysis, the probabilistic neural network classifier, the principal component analysis, and the Pearson pair correlation. In addition, the molecular electrostatic potential mapped on the isovalue surface of charge density has been drawn. After the full vibrational analysis, thermodynamic properties at 300 K were evaluated: internal energy, entropy, and the free energy.
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Affiliation(s)
- Beata Vranovičová
- Department of Chemistry, Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Roman Boča
- Department of Chemistry, Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia.
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Correlation of electrochemical parameters for the redox couple Fe(III)/Fe(II) in the presence of amino acids and catecholamines. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.113920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chen BY, Lin YH, Wu YC, Hsueh CC. Deciphering Electron-Shuttling Characteristics of Neurotransmitters to Stimulate Bioelectricity-Generating Capabilities in Microbial Fuel Cells. Appl Biochem Biotechnol 2020; 191:59-73. [PMID: 31989437 DOI: 10.1007/s12010-020-03242-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/08/2020] [Indexed: 01/18/2023]
Abstract
This first-attempt study used electrochemical methods to quantitatively assess electron-shuttling capabilities of different neurotransmitters crucial to catecholamine biosynthesis in human brain. As prior studies mentioned, aromatics bearing ortho- or para-dihydroxybenzenes could reveal promising electroactivities to stimulate bioenergy generation in microbial fuel cells (MFCs). This feasibility study extended to investigate the electrochemical characteristics of catecholamines and trace amines (e.g., 14 model compounds selected from neurotransmitters) synthesized by human brain via cyclic voltammetry methods (CVs) and MFCs. Dopamine (DA), levodopa (L-DOPA), epinephrine (EP), norepinephrine (NP), and 3,4-dihydroxyphenylacetic acid (DOPAC) would perform the electron-shuttling characteristics, and the rest would not. In particular, DA formed by decarboxylation of L-DOPA could exhibit relatively higher electrochemical activities than their precursors. In addition, carboxylic acids formed by deamination and carboxylation of trace monoamines would reveal more significant reductive potential (Epc); however, their oxidative electric currents seemed to be reduced. That is, chemical structure significantly influenced whether the electrochemical characteristics could be effectively expressed. This work also clearly revealed that neurotransmitters with ortho-dihydroxybenzenes exhibited promising stimulation to bioelectricity-generating capabilities of MFCs in the ranking of DA ~ EP > NP > L-DOPA > DOPAC. This was consistent with ES behaviors as CV analyses indicated.
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Affiliation(s)
- Bor-Yann Chen
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan, 26047, Taiwan, Republic of China.
| | - Yu-Hsiu Lin
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan, 26047, Taiwan, Republic of China
| | - Yun-Chen Wu
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan, 26047, Taiwan, Republic of China
| | - Chung-Chuan Hsueh
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan, 26047, Taiwan, Republic of China.
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Kovalska N, Pfaffeneder-Kmen M, Tsyntsaru N, Mann R, Henrikas Cesiulis, Hansal W, Kautek W. The role of glycine in the iron-phosphorous alloy electrodeposition. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.03.203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yin W, Huang L, Pedersen EB, Frandsen C, Hansen HCB. Glycine buffered synthesis of layered iron(II)-iron(III) hydroxides (green rusts). J Colloid Interface Sci 2017; 497:429-438. [DOI: 10.1016/j.jcis.2016.11.076] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 11/26/2022]
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Yin W, Strobel BW, B Hansen HC. Amino Acid-Assisted Dehalogenation of Carbon Tetrachloride by Green Rust: Inhibition of Chloroform Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3445-3452. [PMID: 28244752 DOI: 10.1021/acs.est.6b06244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Layered FeII-FeIII hydroxides (green rusts, GRs) are promising reactants for reductive dechlorination of chlorinated solvents due to high reaction rates and the opportunity to inject reactive slurries of the compounds into contaminant plumes. However, it is necessary to develop strategies that reduce the formation of toxic byproducts such as chloroform (CF). In this study, carbon tetrachloride (CT) dehalogenation by the chloride form of GR (GRCl) was tested in the presence of glycine (GLY) and other selected amino acids. GLY, alanine (ALA), and serine (SER) all resulted in remarkable suppression of CF formation with only ∼10% of CF recovery while sarcosine (SAR) showed insignificant effects. For two nonamino acid buffers, TRIS had little effect while HEPES resulted in a 40 times lower rate constant compared to experiments in which no buffer was added. The FeII complexing properties of the amino acids and buffers caused variable extents of GRCl dissolution which was linearly correlated with CF suppression and dehalogenation rate. We hypothesize that the CF suppression seen for amino acids is caused by stabilization of carbene intermediates via the carbonyl group. Different effects on CF suppression and CT dehalogenation rate were expected because of the different structural and chemical properties of the amino acids.
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Affiliation(s)
- Weizhao Yin
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen , Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark
| | - Bjarne W Strobel
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen , Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark
| | - Hans Christian B Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen , Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark
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Oxidation properties of dopamine at and near physiological conditions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-015-1560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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