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Dias HJ, Santos WH, Filho LCS, Crevelin EJ, McIndoe JS, Vessecchi R, Crotti AEM. Electrospray ionization tandem mass spectrometry of 4-aryl-3,4-dihydrocoumarins. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5062. [PMID: 38831552 DOI: 10.1002/jms.5062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024]
Abstract
We have investigated the gas-phase fragmentation reactions of 11 synthetic 4-aryl-3,4-dihydrocoumarins by electrospray ionization tandem mass spectrometry (ESI-MS/MS) on a quadrupole-time-of flight (Q-TOF) hybrid mass spectrometer. We have also estimated thermochemical data for the protonated coumarins (precursor ion A) and product ion structures by computational chemistry at a B3LYP level of theory to establish the ion structures and to rationalize the fragmentation pathways. The most abundant ions in the product ion spectra of coumarins 1-11 resulted from C8H8O2, CO2, C4H4O3, C8H10O3, C8H8O2, and CH3OH eliminations through retro-Diels-Alder (RDA) reactions, remote hydrogen rearrangements (β-eliminations), and β-lactone ring contraction. Although the investigated coumarins shared most of the fragmentation pathways, formation of a benzylic product ion and its corresponding tropylium ion was diagnostic of the substituents at ring C. The thermochemical data revealed that the nature and position of the substituents at ring C played a key role in the formation of this product ion and determined its relative intensity in the product ion spectrum. The results of this study contribute to knowledge of the gas-phase ion chemistry of this important class of organic compounds.
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Affiliation(s)
- Herbert J Dias
- Department of Chemistry, Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Goiano Federal Institute of Education, Science, and Technology, Campus Urutaí, Urutaí, Brazil
| | - William H Santos
- Department of Chemistry, Faculty of Sciences at Bauru, São Paulo State University, Bauru, Brazil
| | - Luis C S Filho
- Department of Chemistry, Faculty of Sciences at Bauru, São Paulo State University, Bauru, Brazil
| | - Eduardo J Crevelin
- Department of Chemistry, Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - J Scott McIndoe
- Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada
| | - Ricardo Vessecchi
- Department of Chemistry, Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Antônio E M Crotti
- Department of Chemistry, Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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Ariai J, Gellrich U. The entropic penalty for associative reactions and their physical treatment during routine computations. Phys Chem Chem Phys 2023; 25:14005-14015. [PMID: 37161492 DOI: 10.1039/d3cp00970j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.
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Affiliation(s)
- Jama Ariai
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| | - Urs Gellrich
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
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da Silva Borges L, Batista JHC, Bozzini L, Lourenço CD, Lopes NP, Clososki GC, Vessecchi R. Are benzoylium and nitrilium ions produced from substituted 2-arene-2-oxazolines during mass spectrometry? A study based on density functional theory calculations, quantum theory of atoms in molecules, and electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9449. [PMID: 36459945 DOI: 10.1002/rcm.9449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
RATIONALE Oxazolines are important compounds for drug development, synthesis, and pharmaceutical applications. Interest in analyzing and developing methods to characterize reaction products from these small heterocyclics has led us to study the gas-phase reactivity and fragmentation of seven 2-arene-2-oxazolines compounds using computational chemistry combined with mass spectrometry. METHOD Protonation sites were investigated using computed proton affinity, gas-phase basicity, and some quantum chemistry descriptors of reactivity; the B3LYP/6-31+G(d,p) computational model was used. Fragmentation mechanisms were suggested by employing data from collision-induced dissociation (CID), energy-resolved plots from MS/MS spectra, multiple-stage experiments, and survival-yield method. RESULTS Protonation studies based on quantum theory of atoms in molecules (QTAIM) and computational thermochemistry were useful to describe the reactivity of the investigated 2-arene-2-oxazolines, which can be protonated at the nitrogen atom. Three major fragmentation pathways were identified for the protonated molecules: formation of (a) benzoylium or (b) nitrilium ions through elimination of 71 and 72 u from the protonated molecules, respectively, and (c) elimination of 54 u from [M+H]+ . These pathways were exploited by the density functional theory calculations combined with QTAIM studies. CONCLUSIONS Our results can help in identifying 2-arene-2-oxazoline derivatives using electrospray ionization tandem mass spectrometry (ESI-MS/MS), which can be applied for monitoring reactions through the identified diagnostic ions (product ions). Also, we can suggest that benzoylium and nitrilium ions emerge during fragmentation under CID conditions.
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Affiliation(s)
- Letícia da Silva Borges
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - João Henrique Carvalho Batista
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Leandro Bozzini
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Celso Donizete Lourenço
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Norberto Peporine Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Giuliano Cesar Clososki
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
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Kaczorowska MA, Kaczmarek-Kędziera A, Ośmiałowski B. Tautomeric equilibrium, proton affinity and mass spectrometry fragmentation of flexible hydrogen-bonded precursors and rigid [Formula: see text] fluorescent dyes. Sci Rep 2021; 11:15995. [PMID: 34362952 PMCID: PMC8346630 DOI: 10.1038/s41598-021-94978-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
The stability of two groups of conformationally locked molecules, similar in topology, but differing only by the type of the bridge rigidifying their structure, is studied. The series of the less-rigid 2-phenacylheterocyclic compounds and their stiff difluoroboranyl derivatives are investigated for the determination of the effect of [Formula: see text]/S/O replacement in a five-membered heterocyclic ring and the presence of a strong electron-donating group on the tautomeric equilibrium, protonation affinity, and fragmentation pattern observed in the structural elucidation by means of mass spectrometry technique. The results of the [Formula: see text]B97X-D/6-311++G(d,p) calculations, the topological analysis of electron density as well as the experimental MS measurements show the importance of the number of heteroatoms, their properties, and location in the molecule for the rational design of the systems of desired stable tautomers or the favorable protonation sites. The obtained data allow for the understanding of the fundamentals of the novel highly fluorescent difluoroborates fragmentation behavior, vital for their structural elucidation with the application of high-resolution tandem mass spectrometry methods.
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Affiliation(s)
- Małgorzata A. Kaczorowska
- Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Anna Kaczmarek-Kędziera
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87–100 Toruń, Poland
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87–100 Toruń, Poland
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Safi ZS, Wazzan N. Benchmark calculations of proton affinity and gas-phase basicity using multilevel (G4 and G3B3), B3LYP and MP2 computational methods of para-substituted benzaldehyde compounds. J Comput Chem 2021; 42:1106-1117. [PMID: 33871092 DOI: 10.1002/jcc.26538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 12/18/2022]
Abstract
This study presents the benchmark calculations of proton affinities (PAs) and gas-phase basicities (GBs) of 8-para substituted benzaldehyde compounds using the multilevel model chemistries (G3B3 and G4), density-functional quantum model (B3LYP) and ab initio model (MP2). The results show that the computed properties are strongly correlated with the available experimental data. The PAs and the GBs of other eight para-substituted benzaldehyde compounds, for which the experimental data does not currently exist, have been calculated using G3B3 and B3LYP methods. The correlations between the experimental PAs and GBs with the computed properties such as PA, GB, chemical properties (bond lengths, electron density and δ1 H NMR chemical shift) of the investigated benzaldehydes have been studied and statistically analyzed. The influence of the substituted groups has been discussed in terms of inductive effect and electron donating and electron withdrawing effect. The results obtained show that the chemical properties of the benzaldehyde compounds are controlled by the strong coupling between the CHO group and the nature of the para-substituent groups through the benzene ring as a conducting linkage.
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Affiliation(s)
- Zaki S Safi
- Chemistry Department, Faculty of Science, Al Azhar University-Gaza, Gaza, Palestine
| | - Nuha Wazzan
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Darii E, Gimbert Y, Alves S, Damont A, Perret A, Woods AS, Fenaille F, Tabet JC. First Direct Evidence of Interpartner Hydride/Deuteride Exchanges for Stored Sodiated Arginine/Fructose-6-phosphate Complex Anions within Salt-Solvated Structures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1424-1440. [PMID: 33929837 DOI: 10.1021/jasms.1c00040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mass spectrometric investigations of noncovalent binding between low molecular weight compounds revealed the existence of gas-phase (GP) noncovalent complex (NCC) ions involving zwitterionic structures. ESI MS is used to prove the formation of stable sodiated NCC anions between fructose (F6P) and arginine (R) moieties. Theoretical calculations indicate a folded solvated salt (i.e., sodiated carboxylate interacting with phosphate) rather than a charge-solvated form. Under standard CID conditions, [(F6P+R-H+Na)-H]- competitively forms two major product ions (PIs) through partner splitting [(R-H+Na) loss] and charge-induced cross-ring cleavage while preserving the noncovalent interactions (noncovalent product ions (NCPIs)). MS/MS experiments combined with in-solution proton/deuteron exchanges (HDXs) demonstrated an unexpected labeling of PIs, i.e., a correlated D-enrichment/D-depletion. An increase in activation time up to 3000 ms favors such processes when limited to two H/D exchanges. These results are rationalized by interpartner hydride/deuteride exchanges (⟨HDX⟩) through stepwise isomerization/dissociation of sodiated NCC-d11 anions. In addition, the D-enrichment/D-depletion discrepancy is further explained by back HDX with residual water in LTQ (selective for the isotopologue NCPIs as shown by PI relaxation experiments). Each isotopologue leads to only one back HDX unlike multiple HDXs generally observed in GP. This behavior shows that NCPIs are zwitterions with charges solvated by a single water molecule, thus generating a back HDX through a relay mechanism, which quenches the charges and prevents further back HDX. By estimating back HDX impact on D-depletion, the interpartner ⟨HDX⟩ complementarity was thus illustrated. This is the first description of interpartner ⟨HDX⟩ and selective back HDX validating salt-solvated structures.
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Affiliation(s)
- Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Yves Gimbert
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058 Grenoble, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Amina S Woods
- NIDA IRP, NIH Structural Biology Unit Cellular Neurobiology Branch, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- The Johns Hopkins University School of Medicine, Pharmacology and Molecular Sciences, Baltimore, Maryland 21205, United States
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Jean-Claude Tabet
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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Hirakawa T, Nishimoto CK, Komano A, Otsuka M, Negishi N, Miyaguchi H, Seto Y, Takeuchi K. Experimental study for adsorption and photocatalytic reaction of ethyl methylphosphonate molecule as organophosphorus compound adsorbed at surface of titanium dioxide under UV irradiation in ambient condition. RESEARCH ON CHEMICAL INTERMEDIATES 2021. [DOI: 10.1007/s11164-020-04389-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Vieira TM, Orenha RP, Crevelin EJ, Furtado SSP, Vessecchi R, Parreira RLT, Crotti AEM. Electrospray ionization tandem mass spectrometry of monoketone curcuminoids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 3:e8699. [PMID: 31845428 DOI: 10.1002/rcm.8699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/20/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Although monoketone curcuminoids (MKCs) have been largely investigated due to their biological activities, data on the gas-phase fragmentation reactions of protonated MKCs under collision-induced dissociation (CID) conditions are still scarce. Here, we combined electrospray ionization tandem mass spectrometry (ESI-MS/MS) data, multiple-stage mass spectrometry (MSn ), deuterium exchange experiments, accurate-mass data, and thermochemical data estimated by computational chemistry to elucidate and to rationalize the fragmentation pathways of eleven synthetic MKCs. METHODS The MKCs were synthesized by Claisen-Schmidt condensation under basic (1-9) or acidic (10-11) conditions. ESI-CID-MS/MS analyses and deuterium-exchange experiments were carried out on a triple quadrupole mass spectrometer. MSn analyses on an ion trap mass spectrometer helped to elucidate the fragmentation pathways. Accurate-mass data and thermochemical data, obtained at the B3LYP/6-31+G(d,p) level of theory, were used to support the ion structures. RESULTS The most intense product ions were the benzyl ions ([C7 H2 R1 R2 R3 R4 R5 ]+ ) and the acylium ions ([M + H - C8 H3 R1 R2 R3 R4 R5 ]+ ), which originated directly from the precursor ion as a result of two competitive hydrogen rearrangements. Product ions [M + H - H2 O]+ and [M + H - C6 HR1 R2 R3 R4 R5 ]+ , which are formed after Nazarov cyclization, were also common to all the analyzed compounds. In addition, •Br and •Cl eliminations were diagnostic for the presence of these halogen atoms at the aromatic ring, whereas •CH3 eliminations were useful to identify the methyl and methoxy groups attached to this same ring. Nazarov cyclization in the gas phase occurred for all the investigated MKCs and did not depend on the presence of the hydroxyl group at the aromatic ring. However, the presence and the position of a hydroxyl group at the aromatic rings played a key role in the Nazarov cyclization mechanism. CONCLUSIONS Our results reinforce some aspects of the fragmentation pathways previously published for 1,5-bis-(2-methoxyphenyl)-1,4-pentadien-3-one and 1,5-bis-(2-hydroxyphenyl)-1,4-pentadien-3-one. The alternative fragmentation mechanism proposed herein can explain the fragmentation of a wider diversity of monoketone curcuminoids.
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Affiliation(s)
- Tatiana M Vieira
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, CEP 14040-901, Ribeirão Preto, SP, Brazil
| | - Renato P Orenha
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, CEP 14404-600, Franca, SP, Brazil
| | - Eduardo J Crevelin
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, CEP 14040-901, Ribeirão Preto, SP, Brazil
| | - Saulo S P Furtado
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, CEP 14404-600, Franca, SP, Brazil
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, CEP 14040-901, Ribeirão Preto, SP, Brazil
| | - Renato L T Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, CEP 14404-600, Franca, SP, Brazil
| | - Antônio E M Crotti
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, CEP 14040-901, Ribeirão Preto, SP, Brazil
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von Rudorff GF, von Lilienfeld OA. Rapid and accurate molecular deprotonation energies from quantum alchemy. Phys Chem Chem Phys 2020; 22:10519-10525. [PMID: 31960870 DOI: 10.1039/c9cp06471k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We assess the applicability of alchemical perturbation density functional theory (APDFT) for quickly and accurately estimating deprotonation energies. We have considered all possible single and double deprotonations in one hundred small organic molecules drawn at random from QM9 [Ramakrishnan et al., JCTC, 2015]. Numerical evidence is presented for 5160 deprotonated species at both HF/def2-TZVP and CCSD/6-31G* levels of theory. We show that the perturbation expansion formalism of APDFT quickly converges to reliable results: using CCSD electron densities and derivatives, regular Hartree-Fock calculations are outperformed at the second or third order for ranking all possible doubly or singly deprotonated molecules, respectively. CCSD single deprotonation energies are reproduced within 1.4 kcal mol-1 on average within third order APDFT. We introduce a hybrid approach where the computational cost of APDFT is reduced even further by mixing first order terms at a higher level of theory (CCSD) with higher order terms at a lower level of theory only (HF). We find that this approach reaches 2 kcal mol-1 accuracy in absolute deprotonation energies compared to CCSD at 2% of the computational cost of third order APDFT.
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Affiliation(s)
- Guido Falk von Rudorff
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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On the Use of Popular Basis Sets: Impact of the Intramolecular Basis Set Superposition Error. Molecules 2019; 24:molecules24203810. [PMID: 31652663 PMCID: PMC6832644 DOI: 10.3390/molecules24203810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022] Open
Abstract
The magnitude of intramolecular basis set superposition error (BSSE) is revealed via computing systematic trends in molecular properties. This type of error is largely neglected in the study of the chemical properties of small molecules and it has historically been analyzed just in the study of large molecules and processes dominated by non-covalent interactions (typically dimerization or molecular complexation and recognition events). In this work we try to provide proof of the broader prevalence of this error, which permeates all types of electronic structure calculations, particularly when employing insufficiently large basis sets.
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12
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Souza AA, Vessecchi R, Castro-Gamboa I, Furlan M. Combined use of tandem mass spectrometry and computational chemistry to study 2H-chromenes from Piper aduncum. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:634-642. [PMID: 31144377 DOI: 10.1002/jms.4378] [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: 01/06/2019] [Revised: 05/14/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Natural 2H-chromenes were isolated from the crude extract of Piper aduncum (Piperaceae) and analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS) applying collision-induced dissociation. Density functional theory (DFT) calculations were used to explain the preferred protonation sites of the 2H-chromenes based on thermochemical parameters, including atomic charges, proton affinity, and gas-phase basicity. After identifying the nucleophilic sites, the pathways were proposed to justify the formation of the diagnostic ions under ESI-MS/MS conditions. The calculated relative energy for each pathway was in good agreement with the energy-resolved plot obtained from ESI-MS/MS data. Moreover, the 2H-chromene underwent proton attachment on the prenyl moiety via a six-membered transition state. This behavior resulted in the formation of a diagnostic ion due to 2-methylpropene loss. These studies provide novel insights into gas-phase dissociation for natural benzopyran compounds, indicating how reactivity is correlated to the intrinsic acid-base equilibrium and structural aspects, including the substitution pattern on the aromatic moiety. Therefore, these results can be applied in the identification of benzopyran derivatives in a variety of biological samples.
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Affiliation(s)
- Amauri Alves Souza
- Universidade Estadual Paulista - UNESP, Instituto de Química, Rua Professor Francisco Degni, 55, Araraquara, SP, 14800-900, Brazil
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, SP, 14040-901, Brazil
| | - Ian Castro-Gamboa
- Universidade Estadual Paulista - UNESP, Instituto de Química, Rua Professor Francisco Degni, 55, Araraquara, SP, 14800-900, Brazil
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13
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Ghalami-Choobar B, Ghiami-Shomami A, Fereidoonzadeh M. Relative p K
a
of some anilinium derivatives in methanol, acetonitrile, and tetrahydrofurane solvents. J CHIN CHEM SOC-TAIP 2019. [DOI: 10.1002/jccs.201800139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Ali Ghiami-Shomami
- Department of Chemistry, Faculty of Science; University of Guilan; Rasht Iran
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14
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Dias HJ, Baguenard M, Crevelin EJ, Palaretti V, Gates PJ, Vessecchi R, Crotti AEM. Gas-phase fragmentation reactions of protonated benzofuran- and dihydrobenzofuran-type neolignans investigated by accurate-mass electrospray ionization tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:35-46. [PMID: 30362641 DOI: 10.1002/jms.4304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/12/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
We have investigated gas-phase fragmentation reactions of protonated benzofuran neolignans (BNs) and dihydrobenzofuran neolignans (DBNs) by accurate-mass electrospray ionization tandem and multiple-stage (MSn ) mass spectrometry combined with thermochemical data estimated by Computational Chemistry. Most of the protonated compounds fragment into product ions B ([M + H-MeOH]+ ), C ([B-MeOH]+ ), D ([C-CO]+ ), and E ([D-CO]+ ) upon collision-induced dissociation (CID). However, we identified a series of diagnostic ions and associated them with specific structural features. In the case of compounds displaying an acetoxy group at C-4, product ion C produces diagnostic ions K ([C-C2 H2 O]+ ), L ([K-CO]+ ), and P ([L-CO]+ ). Formation of product ions H ([D-H2 O]+ ) and M ([H-CO]+ ) is associated with the hydroxyl group at C-3 and C-3', whereas product ions N ([D-MeOH]+ ) and O ([N-MeOH]+ ) indicate a methoxyl group at the same positions. Finally, product ions F ([A-C2 H2 O]+ ), Q ([A-C3 H6 O2 ]+ ), I ([A-C6 H6 O]+ ), and J ([I-MeOH]+ ) for DBNs and product ion G ([B-C2 H2 O]+ ) for BNs diagnose a saturated bond between C-7' and C-8'. We used these structure-fragmentation relationships in combination with deuterium exchange experiments, MSn data, and Computational Chemistry to elucidate the gas-phase fragmentation pathways of these compounds. These results could help to elucidate DBN and BN metabolites in in vivo and in vitro studies on the basis of electrospray ionization ESI-CID-MS/MS data only.
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Affiliation(s)
- Herbert J Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Manon Baguenard
- Institut de Chimie, Université de Poitiers, Poitiers, France
| | - Eduardo J Crevelin
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vinicius Palaretti
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Paul J Gates
- School of Chemistry, University of Bristol, Bristol, UK
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Antônio E M Crotti
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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15
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Lee KH, Schnupf U, Sumpter BG, Irle S. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution. ACS OMEGA 2018; 3:16899-16915. [PMID: 31458314 PMCID: PMC6643604 DOI: 10.1021/acsomega.8b02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 05/12/2023]
Abstract
Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.
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Affiliation(s)
- Ka Hung Lee
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Bredesen
Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Udo Schnupf
- Department
of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
- E-mail: (U.S.)
| | - Bobby G. Sumpter
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan Irle
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- E-mail: (S.I.)
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16
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Reinhardt CR, Hu QH, Bresnahan CG, Hati S, Bhattacharyya S. Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations. ACS Catal 2018; 8:12015-12029. [PMID: 31583178 DOI: 10.1021/acscatal.8b04193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quinone reductases belong to the family of flavin-dependent oxidoreductases. With the redox active cofactor, flavin adenine dinucleotide, quinone reductases are known to utilize a 'ping-pong' kinetic mechanism during catalysis in which a hydride is bounced back and forth between flavin and its two substrates. However, the continuation of this catalytic cycle requires product displacement steps, where the product of one redox half-cycle is displaced by the substrate of the next half-cycle. Using improved hybrid quantum mechanical/molecular mechanical simulations, both the catalytic hydride transfer and the product displacement reactions were studied in NRH:quinone oxidoreductase 2. Initially, the self-consistent charge-density functional tight binding theory was used to describe flavin ring and the substrate atoms, while embedded in the molecular mechanically-treated solvated active site. Then, for each step of the catalytic cycle, a further improvement of energetics was made using density functional theory-based corrections. The present study showcases an integrated interplay of solvation, protonation, and protein matrix-induced polarization as the driving force behind the thermodynamic wheel of the 'ping-pong' kinetics. Reported here is the first-principles model of the 'ping-pong' kinetics that portrays how cyclic changes in the active site polarization and dynamics govern the oscillatory hydride transfer and product displacement in this enzyme.
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Affiliation(s)
- Clorice R. Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Quin H. Hu
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Caitlin G. Bresnahan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
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17
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Xiong J, Zhang C, Xu D. Catalytic mechanism of type C sialidase from Streptococcus pneumoniae: from covalent intermediate to final product. J Mol Model 2018; 24:297. [PMID: 30259133 DOI: 10.1007/s00894-018-3822-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/04/2018] [Indexed: 12/24/2022]
Abstract
Streptococcus pneumoniae is a Gram-positive human pathogenic bacterium, which is the main cause of pneumonia and meningitis in children and the elderly. Three sialidases (or neuraminidases) encoded from Streptococcus pneumoniae could catalyze the cleavage of sialic acid linkages. This mechanism is directly connected with infection, apoptosis, and signaling, and usually considered to be one of the critical virulence factors. Type C neuraminidase (NanC) is unique because its primary product of Neu5Ac2en is considered to be an inhibitor to the other two sialidases. Experimentally, there are two different pathways for the formation mechanism of Neu5Ac2en catalyzed by NanC. In this work, a combined quantum mechanical and molecular mechanical approach was employed in all calculations. Starting from the covalent sialylated intermediate, we first examined the reaction to Neu5Ac2en and found the reaction prefers a direct proton abstraction mechanism rather than the water mediated proton abstraction mechanism. Free energy profiles can confirm that Neu5Ac2en is the major product of NanC. Functional roles of some important residues were also investigated, e.g., D315 acts as the proton acceptor during the formation of Neu5Ac2en, while the general base for the hydrolytic reaction to Neu5Ac. This study can facilitate the understanding of the catalytic mechanism of NanC and has the potential to aid in future inhibitor design studies.
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Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, 610500, People's Republic of China
| | - Chunchun Zhang
- Analytical&Testing Center, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
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18
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Dias HJ, Bento MVB, da Silva ÉH, Saturnino-Júnior A, de Oliveira MF, Vessecchi R, Parreira RLT, Crotti AEM. Gas-phase fragmentation reactions of protonated cocaine: New details to an old story. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:203-213. [PMID: 29247586 DOI: 10.1002/jms.4053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/22/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Herbert J Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, SP, Brazil
| | - Mariana V B Bento
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, SP, Brazil
| | | | - Andrade Saturnino-Júnior
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, SP, Brazil
| | - Marcelo F de Oliveira
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Renato L T Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, SP, Brazil
| | - Antônio E M Crotti
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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19
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Lim CH, Holder AM, Hynes JT, Musgrave CB. Dihydropteridine/Pteridine as a 2H +/2e - Redox Mediator for the Reduction of CO 2 to Methanol: A Computational Study. J Phys Chem B 2017; 121:4158-4167. [PMID: 28375636 DOI: 10.1021/acs.jpcb.7b01224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Conflicting experimental results for the electrocatalytic reduction of CO2 to CH3OH on a glassy carbon electrode by the 6,7-dimethyl-4-hydroxy-2-mercaptopteridine have been recently reported [ J. Am. Chem. Soc. 2014 , 136 , 14007 - 14010 , J. Am. Chem. Soc. 2016 , 138 , 1017 - 1021 ]. In this connection, we have used computational chemistry to examine the issue of this molecule's ability to act as a hydride donor to reduce CO2. We first determined that the most thermodynamically stable tautomer of this aqueous compound is its oxothione form, termed here PTE. It is argued that this species electrochemically undergoes concerted 2H+/2e- transfers to first form the kinetic product 5,8-dihydropteridine, followed by acid-catalyzed tautomerization to the thermodynamically more stable 7,8-dihydropteridine PTEH2. While the overall conversion of CO2 to CH3OH by three successive hydride and proton transfers from this most stable tautomer is computed to be exergonic by 5.1 kcal/mol, we predict high activation free energies (ΔG‡HT) of 29.0 and 29.7 kcal/mol for the homogeneous reductions of CO2 and its intermediary formic acid product by PTE/PTEH2, respectively. These high barriers imply that PTE/PTEH2 is unable, by this mechanism, to homogeneously reduce CO2 on a time scale of hours at room temperature.
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Affiliation(s)
| | - Aaron M Holder
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - James T Hynes
- Chemistry Department, Ecole Normale Supérieure-PSL Research University, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 , Pasteur, 24 rue Lhomond, 75005 Paris, France
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20
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Darii E, Alves S, Gimbert Y, Perret A, Tabet JC. Meaning and consequence of the coexistence of competitive hydrogen bond/salt forms on the dissociation orientation of non-covalent complexes. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1047:45-58. [DOI: 10.1016/j.jchromb.2016.09.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 07/23/2016] [Accepted: 09/25/2016] [Indexed: 10/20/2022]
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21
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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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22
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Xiong J, Xu D. Insights into the Catalytic Mechanism of Unsaturated Glucuronyl Hydrolase of Bacillus sp. GL1. J Phys Chem B 2017; 121:931-941. [DOI: 10.1021/acs.jpcb.6b10501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
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23
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Martínez-Cifuentes M, Clavijo-Allancan G, Zuñiga-Hormazabal P, Aranda B, Barriga A, Weiss-López B, Araya-Maturana R. Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives. Int J Mol Sci 2016; 17:ijms17071071. [PMID: 27399676 PMCID: PMC4964447 DOI: 10.3390/ijms17071071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/10/2016] [Accepted: 06/28/2016] [Indexed: 11/16/2022] Open
Abstract
A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules.
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Affiliation(s)
- Maximiliano Martínez-Cifuentes
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Las Palmeras 3360, Casilla 9845, Santiago 7800003, Chile.
| | - Graciela Clavijo-Allancan
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
| | - Pamela Zuñiga-Hormazabal
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
| | - Braulio Aranda
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
| | - Andrés Barriga
- Unidad de Espectrometría de Masas, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont 964, Casilla 233, Santiago 8380494, Chile.
| | - Boris Weiss-López
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
| | - Ramiro Araya-Maturana
- Instituto de Química de Recursos Naturales, Universidad de Talca, Av. Lircay s/n, Casilla 747, Talca 3460000, Chile.
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24
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Quantum chemical theory calculations on the mechanism of the homogeneous, unimolecular gas-phase elimination kinetics of selected diazirines. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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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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26
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Nam K, Cui Q, Gao J, York DM. Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms. J Chem Theory Comput 2015; 3:486-504. [PMID: 26637030 DOI: 10.1021/ct6002466] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations. The model, designated AM1/d-PhoT, is parametrized for H, O, and P atoms to reproduce high-level density-functional results from a recently constructed database of quantum calculations for RNA catalysis ( http://theory.chem.umn.edu/Database/QCRNA ), including geometries and relative energies of minima, transition states and reactive intermediates, dipole moments, proton affinities, and other relevant properties. The model is tested in the gas phase and in solution using a QM/MM potential. The results indicate that the method provides significantly higher accuracy than MNDO/d, AM1, and PM3 methods and, for the transphosphorylation reactions, is in close agreement with the density-functional calculations at the B3LYP/6-311++G(3df,2p) level with a reduction in computational cost of 3-4 orders of magnitude. The model is expected to have considerable impact on the application of semiempirical QM/MM methods to transphosphorylation reactions in solution, enzymes, and ribozymes and to ultimately facilitate the design of improved next-generation multiscale quantum models.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Qiang Cui
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Darrin M York
- Department of Chemistry and Supercomputing Institute and the Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
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27
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Jin R, Liu S, Lan Y. Distortion–interaction analysis along the reaction pathway to reveal the reactivity of the Alder-ene reaction of enes. RSC Adv 2015. [DOI: 10.1039/c5ra10345b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The reactivity of uncatalyzed Alder-ene type reactions of hetero-substituted propylene is interpreted by distortion–interaction analysis of both the transition states and the complete reaction pathways.
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Affiliation(s)
- Rui Jin
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing 400030
- China
| | - Song Liu
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing 400030
- China
| | - Yu Lan
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing 400030
- China
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28
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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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29
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Govender KK, Naidoo KJ. Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations. J Chem Theory Comput 2014; 10:4708-17. [DOI: 10.1021/ct500373p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Krishna K. Govender
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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30
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Govender K, Gao J, Naidoo KJ. AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems. J Chem Theory Comput 2014; 10:4694-4707. [PMID: 26120288 DOI: 10.1021/ct500372s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A semiempirical method based on the AM1/d Hamiltonian is introduced to model chemical glycobiological systems. We included in the parameter training set glycans and the chemical environment often found about them in glycoenzymes. Starting with RM1 and AM1/d-PhoT models we optimized H, C, N, O, and P atomic parameters targeting the best performing molecular properties that contribute to enzyme catalyzed glycan reaction mechanisms. The training set comprising glycans, amino acids, phosphates and small organic model systems was used to derive parameters that reproduce experimental data or high-level density functional results for carbohydrate, phosphate and amino acid heats of formation, amino acid proton affinities, amino acid and monosaccharide dipole moments, amino acid ionization potentials, water-phosphate interaction energies, and carbohydrate ring pucker relaxation times. The result is the AM1/d-Chemical Biology 1 or AM1/d-CB1 model that is considerably more accurate than existing NDDO methods modeling carbohydrates and the amino acids often present in the catalytic domains of glycoenzymes as well as the binding sites of lectins. Moreover, AM1/d-CB1 computed proton affinities, dipole moments, ionization potentials and heats of formation for transition state puckered carbohydrate ring conformations, observed along glycoenzyme catalyzed reaction paths, are close to values computed using DFT M06-2X. AM1/d-CB1 provides a platform from which to accurately model reactions important in chemical glycobiology.
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Affiliation(s)
- Krishna Govender
- Scientific Computing Research Unit, University of Cape Town, Rondebosch 7701, South Africa ; Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Jiali Gao
- State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun, Jilin Province 130012, China ; Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kevin J Naidoo
- Scientific Computing Research Unit, University of Cape Town, Rondebosch 7701, South Africa ; Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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31
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Gaus M, Lu X, Elstner M, Cui Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. J Chem Theory Comput 2014; 10:1518-1537. [PMID: 24803865 PMCID: PMC3985940 DOI: 10.1021/ct401002w] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 01/06/2023]
Abstract
We report the parametrization of the approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The parametrization is done in a framework consistent with our previous 3OB set established for O, N, C, and H, thus the resulting parameters can be used to describe a broad set of organic and biologically relevant molecules. The 3d orbitals are included in the parametrization, and the electronic parameters are chosen to minimize errors in the atomization energies. The parameters are tested using a fairly diverse set of molecules of biological relevance, focusing on the geometries, reaction energies, proton affinities, and hydrogen bonding interactions of these molecules; vibrational frequencies are also examined, although less systematically. The results of DFTB3/3OB are compared to those from DFT (B3LYP and PBE), ab initio (MP2, G3B3), and several popular semiempirical methods (PM6 and PDDG), as well as predictions of DFTB3 with the older parametrization (the MIO set). In general, DFTB3/3OB is a major improvement over the previous parametrization (DFTB3/MIO), and for the majority cases tested here, it also outperforms PM6 and PDDG, especially for structural properties, vibrational frequencies, hydrogen bonding interactions, and proton affinities. For reaction energies, DFTB3/3OB exhibits major improvement over DFTB3/MIO, due mainly to significant reduction of errors in atomization energies; compared to PM6 and PDDG, DFTB3/3OB also generally performs better, although the magnitude of improvement is more modest. Compared to high-level calculations, DFTB3/3OB is most successful at predicting geometries; larger errors are found in the energies, although the results can be greatly improved by computing single point energies at a high level with DFTB3 geometries. There are several remaining issues with the DFTB3/3OB approach, most notably its difficulty in describing phosphate hydrolysis reactions involving a change in the coordination number of the phosphorus, for which a specific parametrization (3OB/OPhyd) is developed as a temporary solution; this suggests that the current DFTB3 methodology has limited transferability for complex phosphorus chemistry at the level of accuracy required for detailed mechanistic investigations. Therefore, fundamental improvements in the DFTB3 methodology are needed for a reliable method that describes phosphorus chemistry without ad hoc parameters. Nevertheless, DFTB3/3OB is expected to be a competitive QM method in QM/MM calculations for studying phosphorus/sulfur chemistry in condensed phase systems, especially as a low-level method that drives the sampling in a dual-level QM/MM framework.
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Affiliation(s)
- Michael Gaus
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xiya Lu
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstr.
12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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32
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Liu S, Lei Y, Qi X, Lan Y. Reactivity for the Diels–Alder Reaction of Cumulenes: A Distortion-Interaction Analysis along the Reaction Pathway. J Phys Chem A 2014; 118:2638-45. [DOI: 10.1021/jp411914u] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Song Liu
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400030, China
| | - Yu Lei
- Department
of Emergency, First Hospital, Jilin University, Changchun, China
| | - Xiaotian Qi
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400030, China
| | - Yu Lan
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400030, China
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33
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Yang Q, Xing H, Bao Z, Su B, Zhang Z, Yang Y, Dai S, Ren Q. One of the Distinctive Properties of Ionic Liquids over Molecular Solvents and Inorganic Salts: Enhanced Basicity Stemming from the Electrostatic Environment and “Free” Microstructure. J Phys Chem B 2014; 118:3682-8. [DOI: 10.1021/jp500790r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Qiwei Yang
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Huabin Xing
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zongbi Bao
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Baogen Su
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhiguo Zhang
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Yiwen Yang
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Sheng Dai
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37966, United States
| | - Qilong Ren
- Key Laboratory
of Biomass Chemical Engineering of Ministry of Education, Department
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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34
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Bartholow TG, Sanford BL, Cao B, Schmit HL, Johnson JM, Meitzner J, Bhattacharyya S, Musier-Forsyth K, Hati S. Strictly conserved lysine of prolyl-tRNA Synthetase editing domain facilitates binding and positioning of misacylated tRNA(Pro.). Biochemistry 2014; 53:1059-68. [PMID: 24450765 PMCID: PMC3986007 DOI: 10.1021/bi401279r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
To ensure high fidelity in translation, many aminoacyl-tRNA synthetases, enzymes responsible for attaching specific amino acids to cognate tRNAs, require proof-reading mechanisms. Most bacterial prolyl-tRNA synthetases (ProRSs) misactivate alanine and employ a post-transfer editing mechanism to hydrolyze Ala-tRNA(Pro). This reaction occurs in a second catalytic site (INS) that is distinct from the synthetic active site. The 2'-OH of misacylated tRNA(Pro) and several conserved residues in the Escherichia coli ProRS INS domain are directly involved in Ala-tRNA(Pro) deacylation. Although mutation of the strictly conserved lysine 279 (K279) results in nearly complete loss of post-transfer editing activity, this residue does not directly participate in Ala-tRNA(Pro) hydrolysis. We hypothesized that the role of K279 is to bind the phosphate backbone of the acceptor stem of misacylated tRNA(Pro) and position it in the editing active site. To test this hypothesis, we carried out pKa, charge neutralization, and free-energy of binding calculations. Site-directed mutagenesis and kinetic studies were performed to verify the computational results. The calculations revealed a considerably higher pKa of K279 compared to an isolated lysine and showed that the protonated state of K279 is stabilized by the neighboring acidic residue. However, substitution of this acidic residue with a positively charged residue leads to a significant increase in Ala-tRNA(Pro) hydrolysis, suggesting that enhancement in positive charge density in the vicinity of K279 favors tRNA binding. A charge-swapping experiment and free energy of binding calculations support the conclusion that the positive charge at position 279 is absolutely necessary for tRNA binding in the editing active site.
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Affiliation(s)
- Thomas G Bartholow
- Department of Chemistry, University of Wisconsin-Eau Claire , Eau Claire, Wisconsin, 54702, United States
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35
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Zheng M, Xu D. Catalytic Mechanism of Hyaluronate Lyase from Spectrococcus pneumonia: Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies. J Phys Chem B 2013; 117:10161-72. [DOI: 10.1021/jp406206s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Zheng
- MOE Key Laboratory of Green
Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Dingguo Xu
- MOE Key Laboratory of Green
Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
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36
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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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37
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Steinbrecher T, Latzer J, Case DA. Revised AMBER parameters for bioorganic phosphates. J Chem Theory Comput 2012; 8:4405-4412. [PMID: 23264757 DOI: 10.1021/ct300613v] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report AMBER force field parameters for biological simulations involving phosphorylation of serine, threonine or tyrosine. The initial parameters used RESP fitting for the atomic partial charges and standard values for all other parameters such as Lennard-Jones coefficients. These were refined with the aid of a thermodynamic cycle consisting of experimentally determined pKa values, solvation energies from molecular dynamics free energy simulations, and gas phase basicities from QM calculations. A polarization energy term was included to account for the charge density change between the gas-phase and solution, and solvation free energies were determined using thermodynamic integration. Parameter adjustment is required to obtain consistent thermodynamic results with better balanced electrostatic interactions between water and the phosphate oxygens. To achieve this we modified the phosphate oxygen radii. A thermodynamically consistent parameter set can be derived for monoanions and requires an increase of the van der Waals phosphate oxygen radii of approximately 0.09 Å. Larger, residue-specific radii appear to be needed for dianions. The revised parameters developed here should be of particular interest for environments where simulations of multiple protonation states may be of interest.
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Affiliation(s)
- T Steinbrecher
- Institute for Physical Chemistry, Kaiserstr 12, University Karlsruhe, KIT, 76131 Karlsruhe, Germany, and Dept. of Chemistry and Chemical Biology, and BioMaPS Institute, 174 Frelinghuysen Road, Rutgers University, Piscataway, NJ 08854
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38
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Gupta M, da Silva EF, Svendsen HF. Modeling Temperature Dependency of Amine Basicity Using PCM and SM8T Implicit Solvation Models. J Phys Chem B 2012; 116:1865-75. [DOI: 10.1021/jp2116017] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Mayuri Gupta
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim,
Norway
| | - Eirik F. da Silva
- Process Technology, SINTEF Materials and Chemistry, Trondheim, Norway
| | - Hallvard F. Svendsen
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim,
Norway
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39
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Riccardi D, Zhu X, Goyal P, Yang S, Hou G, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4458-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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40
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Zevatskii YE, Samoilov DV. Modern methods for estimation of ionization constants of organic compounds in solution. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2011. [DOI: 10.1134/s1070428011100010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Lan Y, Zou L, Cao Y, Houk KN. Computational Methods To Calculate Accurate Activation and Reaction Energies of 1,3-Dipolar Cycloadditions of 24 1,3-Dipoles. J Phys Chem A 2011; 115:13906-20. [DOI: 10.1021/jp207563h] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yu Lan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Lufeng Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Yang Cao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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42
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Heimdal J, Kaukonen M, Srnec M, Rulíšek L, Ryde U. Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods. Chemphyschem 2011; 12:3337-47. [PMID: 21960467 DOI: 10.1002/cphc.201100339] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Indexed: 11/10/2022]
Abstract
We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.
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Affiliation(s)
- Jimmy Heimdal
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00 Lund, Sweden
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43
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Vessecchi R, Lopes JNC, Lopes NP, Galembeck SE. Application of the Atoms in Molecules Theory and Computational Chemistry in Mass Spectrometry Analysis of 1,4-Naphthoquinone Derivatives. J Phys Chem A 2011; 115:12780-8. [DOI: 10.1021/jp203912d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
| | - José N. C. Lopes
- Lychnoflora Pesquisa e Desenvolvimento em Produtos Naturais LTDA, Av. dos Bandeirantes 3900, Incubadora Supera - Campus da USP, 14040-903 Ribeirão Preto - SP, Brazil
| | - Norberto P. Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
| | - Sérgio E. Galembeck
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
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44
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Vessecchi R, Naal Z, Lopes JNC, Galembeck SE, Lopes NP. Generation of naphthoquinone radical anions by electrospray ionization: solution, gas-phase, and computational chemistry studies. J Phys Chem A 2011; 115:5453-60. [PMID: 21561138 DOI: 10.1021/jp202322n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(•-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q+15](-) was described as being a reaction between the solvent system and the radical anion, Q(•-). The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses.
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Affiliation(s)
- Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP 14040-901, Brasil.
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45
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Goyal P, Elstner M, Cui Q. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B 2011; 115:6790-805. [PMID: 21526802 DOI: 10.1021/jp202259c] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The self-consistent charge density functional tight-binding (SCC-DFTB) method has been actively employed to study proton-transfer processes in biological systems. Recent studies in the literature employing SCC-DFTB reported that the method favors the Zundel form of the hydrated proton over the Eigen form, both in gas-phase water clusters and in bulk water, in disagreement with both higher-level calculations and experimental data. In this work, we explore the performance of SCC-DFTB for protonated gas-phase water clusters and bulk water (the latter both with and without an excess proton) with a modified O-H repulsive potential reported in our earlier work and with on-site third-order expansion of the DFT energy. Our results show that, with the proper set of published parameters, SCC-DFTB does correctly favor the Eigen form of the hydrated proton as compared to the Zundel form, both in gas-phase clusters and in the bulk; the amphiphilic character of the hydrated proton discussed in the literature has also been observed. The analyses do, however, bring forth remaining limitations in terms of the solvation structure around the hydrated proton as well as the structure of bulk water, which can guide future improvements of the method.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry, University of Wisconsin, Madison, Madison, Wisconsin 53706, United States
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Gaus M, Cui Q, Elstner M. DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput 2011. [PMID: 23204947 DOI: 10.1021/ct100684s] [Citation(s) in RCA: 671] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around a reference density. In the present study we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomolecular systems. Remaining challenges and possible solutions are also briefly discussed.
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Zevatskii YE, Samoilov DV. Empirical method for consideration of solvent effect on the dissociation constants of carboxylic acids. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2011. [DOI: 10.1134/s1070428008010065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Moser A, Range K, York DM. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis. J Phys Chem B 2010; 114:13911-21. [PMID: 20942500 PMCID: PMC2970571 DOI: 10.1021/jp107450n] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benchmark quantum calculations of proton affinities and gas-phase basicities of molecules relevant to biochemical processes, particularly acid/base catalysis, are presented and compared for a variety of multilevel and density functional quantum models. Included are nucleic acid bases in both keto and enol tautomeric forms, ribose in B-form and A-form sugar pucker conformations, amino acid side chains and backbone molecules, and various phosphates and phosphoranes, including thio substitutions. This work presents a high-level thermodynamic characterization of biologically relevant protonation states and provides a benchmark database for development of next-generation semiempirical and approximate density functional quantum models and parametrization of methods to predict pK(a) values and relative solvation energies.
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Affiliation(s)
- Adam Moser
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
| | - Kevin Range
- Department of Chemistry, Lock Haven University of Pennsylvania, Lock Haven, PA 17745, USA
| | - Darrin M. York
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854-8087, USA
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Vessecchi R, Emery FS, Galembeck SE, Lopes NP. Fragmentation studies and electrospray ionization mass spectrometry of lapachol: protonated, deprotonated and cationized species. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2101-2108. [PMID: 20552691 DOI: 10.1002/rcm.4625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization mass spectrometric analysis of lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone) was accomplished in order to elucidate the gas-phase dissociation reactions of this important biologically active natural product. The occurrence of protonated and cationized species in the positive mode and of deprotonated species in the negative mode was explored by means of collision-induced dissociation (CID) experiments. For the protonated molecule, the H(2)O and C(4)H(8) losses occur by two competitive channels. For the deprotonated molecule, the even-electron rule is not conserved, and the radicalar species are eliminated by formation of distonic anions. The fragmentation mechanism for each ion was suggested on the basis of computational thermochemistry. Atomic charges, relative energies, and frontier orbitals were employed aiming at a better understanding of the gas-phase reactivity of lapachol. Potential energy surfaces for fragmentation reactions were obtained by the B3LYP/6-31+G(d,p) model.
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Affiliation(s)
- Ricardo Vessecchi
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brasil
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Alongi KS, Shields GC. Theoretical Calculations of Acid Dissociation Constants: A Review Article. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2010. [DOI: 10.1016/s1574-1400(10)06008-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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