51
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Gurinov AA, Lesnichin SB, Limbach HH, Shenderovich IG. How short is the strongest hydrogen bond in the proton-bound homodimers of pyridine derivatives? J Phys Chem A 2014; 118:10804-12. [PMID: 25327551 DOI: 10.1021/jp5082033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bond geometries in the proton-bound homodimers of ortho-unsubstituted and ortho-methylsubstituted pyridine derivatives in aprotic polar solution were estimated using experimental NMR data. Within the series of homodimers studied the hydrogen bond lengths depend on the proton affinity of pyridines and--at least for the ortho-methylsubstituted pyridines--on the pKa of the conjugate acids in an approximately quadratic manner. The shortest possible hydrogen bond in the homodimers of ortho-unsubstituted pyridines is characterized by the N···N distance of 2.613 Å. Steric repulsion between the methyl groups of the ortho-methylsubstituted pyridines becomes operative at an N···N distance of ∼2.7 Å and limits the closest approach to 2.665 Å.
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Affiliation(s)
- Andrey A Gurinov
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany
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52
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Bartosik A, Wiśniewska M, Makowski M. Potentials of mean force for hydrophobic interactions between hydrocarbons in water solution: dependence on temperature, solute shape, and solute size. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Angelika Bartosik
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Marta Wiśniewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
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53
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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54
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Repič M, Purg M, Vianello R, Mavri J. Examining Electrostatic Preorganization in Monoamine Oxidases A and B by Structural Comparison and pKa Calculations. J Phys Chem B 2014; 118:4326-32. [DOI: 10.1021/jp500795p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Matej Repič
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
| | - Miha Purg
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
| | - Robert Vianello
- Quantum
Organic Chemistry Group, Ruđer Bošković Institute, Bijenička
cesta 54, HR−10000 Zagreb, Croatia
| | - Janez Mavri
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
- EN−FIST Centre of Excellence, Dunajska 156, SI−1000 Ljubljana, Slovenia
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55
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Monoamine oxidase A and B substrates: probing the pathway for drug development. Future Med Chem 2014; 6:697-717. [DOI: 10.4155/fmc.14.23] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Drug-discovery and -development efforts focused on the MAOs have increased at an accelerated rate over the past decade. Since the first crystal structure of human MAO-B was solved in 2002, over 40 additional structures have been reported and have helped define new, or confirm speculative, binding modes of inhibitors. The detailed mechanism of the MAO-catalyzed oxidation of amine substrates has not been fully elucidated, but its significance is central in the development of new mechanism-based inactivators. Novel fungal MAO-N variants derived from directed evolution strategies are enabling the production of new chiral amine products. Robust assays have been established for measuring MAO status in tissue and cells, while improved MAO radioligands are being deployed for PET imaging studies. This review will attempt to highlight the more recent and salient aspects of MAO research in drug discovery and development, with emphasis on substrates 'probing the pathway'.
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56
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Angelina EL, Andujar SA, Tosso RD, Enriz RD, Peruchena NM. Non-covalent interactions in receptor-ligand complexes. A study based on the electron charge density. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3250] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Emilio L. Angelina
- Lab. Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Av. Libertad 5470 Corrientes 3400 Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Sebastián A. Andujar
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Rodrigo D. Tosso
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Ricardo D. Enriz
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Nélida M. Peruchena
- Lab. Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Av. Libertad 5470 Corrientes 3400 Argentina
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57
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Abad E, Zenn RK, Kästner J. Reaction Mechanism of Monoamine Oxidase from QM/MM Calculations. J Phys Chem B 2013; 117:14238-46. [DOI: 10.1021/jp4061522] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Enrique Abad
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Roland K. Zenn
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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58
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A comparative computational investigation on the proton and hydride transfer mechanisms of monoamine oxidase using model molecules. Comput Biol Chem 2013; 47:181-91. [PMID: 24121676 DOI: 10.1016/j.compbiolchem.2013.08.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022]
Abstract
Monoamine oxidase (MAO) enzymes regulate the level of neurotransmitters by catalyzing the oxidation of various amine neurotransmitters, such as serotonin, dopamine and norepinephrine. Therefore, they are the important targets for drugs used in the treatment of depression, Parkinson, Alzeimer and other neurodegenerative disorders. Elucidation of MAO-catalyzed amine oxidation will provide new insights into the design of more effective drugs. Various amine oxidation mechanisms have been proposed for MAO so far, such as single electron transfer mechanism, polar nucleophilic mechanism and hydride mechanism. Since amine oxidation reaction of MAO takes place between cofactor flavin and the amine substrate, we focus on the small model structures mimicking flavin and amine substrates so that three model structures were employed. Reactants, transition states and products of the polar nucleophilic (proton transfer), the water-assisted proton transfer and the hydride transfer mechanisms were fully optimized employing various semi-empirical, ab initio and new generation density functional theory (DFT) methods. Activation energy barriers related to these mechanisms revealed that hydride transfer mechanism is more feasible.
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59
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Yang X, Xie H, Chen J, Li X. Anionic Phenolic Compounds Bind Stronger with Transthyretin than Their Neutral Forms: Nonnegligible Mechanisms in Virtual Screening of Endocrine Disrupting Chemicals. Chem Res Toxicol 2013; 26:1340-7. [DOI: 10.1021/tx4001557] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xianhai Yang
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hongbin Xie
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xuehua Li
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
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60
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Quantum-chemical approach to determining the high potency of clorgyline as an irreversible acetylenic monoamine oxidase inhibitor. J Neural Transm (Vienna) 2013; 120:875-82. [DOI: 10.1007/s00702-013-1016-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/23/2013] [Indexed: 01/18/2023]
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61
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Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013; 9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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62
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Vianello R, Repič M, Mavri J. How are Biogenic Amines Metabolized by Monoamine Oxidases? European J Org Chem 2012. [DOI: 10.1002/ejoc.201201122] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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