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Li Y, Lau JKC, van Wieringen T, Martens J, Berden G, Oomens J, Hopkinson AC, Siu KWM, Chu IK. Structure and fragmentation chemistry of the peptide radical cations of glycylphenylalanylglycine (GFG). PLoS One 2024; 19:e0308164. [PMID: 39137228 PMCID: PMC11321575 DOI: 10.1371/journal.pone.0308164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024] Open
Abstract
Herein, we explore the generation and characterization of the radical cations of glycylphenylalanylglycine, or [GFG]•+, formed via dissociative electron-transfer reaction from the tripeptide to copper(II) within a ternary complex. A comprehensive investigation employing isotopic labeling, infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations elucidated the details and energetics in formation of the peptide radical cations as well as their dissociation products. Unlike conventional aromatic-containing peptide radical cations that primarily form canonical π-radicals, our findings reveal that 75% of the population of the experimentally produced [GFG]•+ precursors are [GFα•G]+, where the radical resides on the middle α-carbon of the phenylalanyl residue. This unexpected isomeric ion has an enthalpy of 6.8 kcal/mol above the global minimum, which has an N-terminal captodative structure, [Gα•FG]+, comprising 25% of the population. The [b₂-H]•+ product ions are also present in a ratio of 75/25 from [GFα•G]+/ [Gα•FG]+, the results of which are obtained from matches between the IRMPD action spectrum and predicted IR absorption spectra of the [b₂-H]•+ candidate structures, as well as from IRMPD isomer population analyses.
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Affiliation(s)
- Yinan Li
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Justin Kai-Chi Lau
- Department of Chemistry, York University, Toronto, ON, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Teun van Wieringen
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | | | - K. W. Michael Siu
- Department of Chemistry, York University, Toronto, ON, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
- Center for Mass Spectrometry Research and Clinical Application, Shandong Public Health Clinical Center Affiliated to Shandong University, Jinan, Shandong, China
| | - Ivan K. Chu
- Department of Chemistry, University of Hong Kong, Hong Kong, China
- Center for Mass Spectrometry Research and Clinical Application, Shandong Public Health Clinical Center Affiliated to Shandong University, Jinan, Shandong, China
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Lau JKC, Hopkinson AC, Siu KWM. Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study. J Phys Chem B 2024; 128:504-514. [PMID: 38190618 DOI: 10.1021/acs.jpcb.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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Rabus JM, Guan S, Schultz LM, Abutokaikah MT, Maître P, Bythell BJ. Protonated α- N-Acetyl Galactose Glycopeptide Dissociation Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1745-1752. [PMID: 36018613 DOI: 10.1021/jasms.2c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We recently provided mass spectrometric, H/D labeling, and computational evidence of pyranose to furanose N-acetylated ion isomerization reactions that occurred prior to glycosidic bond cleavage in both O- and N-linked glycosylated amino acid model systems (Guan et al. Phys. Chem. Chem. Phys., 2021, 23, 23256-23266). These reactions occurred irrespective of the glycosidic linkage stereochemistry (α or β) and the N-acetylated hexose structure (GlcNAc or GalNAc). In the present article, we test the generality of the preceding findings by examining threonyl α-GalNAc-glycosylated peptides. We utilize computational chemistry to compare the various dissociation and isomerization pathways accessible with collisional activation. We then interrogate the structure(s) of the resulting charged glycan and peptide fragments with infrared "action" spectroscopy. Isomerization of the original pyranose, the protonated glycopeptide [AT(GalNAc)A+H]+, is predicted to be facile compared to direct dissociation, as is the glycosidic bond cleavage of the newly formed furanose form, i.e., furanose oxazolinium ion structures are predicted to predominate. IR action spectra for the m/z 204, C8H14N1O5+, glycan fragment population support this prediction. The IR action spectra of the complementary m/z 262 peptide fragment were assigned as a mixture of the lowest-energy structures of [ATA+H]+ consistent with the literature. If general, the change to a furanose m/z 204 product ion structure fundamentally alters the ion population available for MS3 dissociation and glycopeptide sequence identification.
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Affiliation(s)
- Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Lauren M Schultz
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Philippe Maître
- Institut de Chimie Physique, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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Beran GJO, Greenwell C, Rezac J. Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy. Phys Chem Chem Phys 2022; 24:3695-3712. [DOI: 10.1039/d1cp04922d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Second-order Moller-Plesset perturbation theory (MP2) provides a valuable alternative to density functional theory for modeing problems in organic and biological chemistry. However, MP2 suffers from known limitations in the description...
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Lau JKC, Esuon F, Berden G, Oomens J, Hopkinson AC, Ryzhov V, Siu KWM. Generation, Characterization, and Dissociation of Radical Cations Derived from Prolyl-glycyl-glycine. J Phys Chem B 2021; 125:6121-6129. [PMID: 34097420 DOI: 10.1021/acs.jpcb.1c01732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG•+) and its sequence ions [a3 + H]•+ and [b2 - H]•+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)]•2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG•+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a3 + H]•+ and [b2 - H]•+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG•+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a3 + H]•+ and [b2 - H]•+ ions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Francis Esuon
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, the Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, the Netherlands
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
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6
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Guan S, Bythell BJ. Size Dependent Fragmentation Chemistry of Short Doubly Protonated Tryptic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1020-1032. [PMID: 33779179 DOI: 10.1021/jasms.1c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tandem mass spectrometry of electrospray ionized multiply charged peptide ions is commonly used to identify the sequence of peptide(s) and infer the identity of source protein(s). Doubly protonated peptide ions are consistently the most efficiently sequenced ions following collision-induced dissociation of peptides generated by tryptic digestion. While the broad characteristics of longer (N ≥ 8 residue) doubly protonated peptides have been investigated, there is comparatively little data on shorter systems where charge repulsion should exhibit the greatest influence on the dissociation chemistry. To address this gap and further understand the chemistry underlying collisional-dissociation of doubly charged tryptic peptides, two series of analytes ([GxR+2H]2+ and [AxR+2H]2+, x = 2-5) were investigated experimentally and with theory. We find distinct differences in the preference of bond cleavage sites for these peptides as a function of size and to a lesser extent composition. Density functional calculations at two levels of theory predict that the threshold relative energies required for bond cleavages at the same site for peptides of different size are quite similar (for example, b2-yN-2). In isolation, this finding is inconsistent with experiment. However, the predicted extent of entropy change of these reactions is size dependent. Subsequent RRKM rate constant calculations provide a far clearer picture of the kinetics of the competing bond cleavage reactions enabling rationalization of experimental findings. The M06-2X data were substantially more consistent with experiment than were the B3LYP data.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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Mó O, Montero-Campillo MM, Yáñez M, Alkorta I, Elguero J. Are Anions of Cyclobutane Beryllium Derivatives Stabilized through Four-Center One-Electron Bonds? J Phys Chem A 2020; 124:1515-1521. [PMID: 31962049 DOI: 10.1021/acs.jpca.9b10187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-level G4 ab initio calculations allowed us to show that C4H4(BeX)4 (X = H, Cl) derivatives behave as rather efficient electron capturers due to their ability to trap the extra electron through the formation of a four-membered beryllium ring. This finding is in agreement with previous work showing the ability of highly electron-deficient atoms, such as beryllium, to lead to multicenter one-electron bonds. In our particular case, the formation of the four-center bond is characterized, in very good harmony, by different topological methods such as quantum theory of atoms in molecules (QTAIM), the electron localization function (ELF), and the noncovalent interactions (NCI) approach and is accompanied by large electron affinity values, around 300 kJ·mol-1, in the gas phase. Preliminary results may anticipate that the ability of groups of beryllium atoms to trap electrons decays on going to bigger systems.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid , Spain
| | - M Merced Montero-Campillo
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid , Spain
| | - Manuel Yáñez
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid , Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3 , E-28006 Madrid , Spain
| | - José Elguero
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3 , E-28006 Madrid , Spain
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Ferrer M, Montero-Campillo MM, Mó O, Yáñez M, Alkorta I, Elguero J. Bonding between electron-deficient atoms: strong Lewis-acid character preserved in X–Y–X (X = B, Al; Y = Be, Mg) bridges. NEW J CHEM 2020. [DOI: 10.1039/d0nj01803a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Beryllium bis(diazaborolyl) derivatives and their Mg and Al-containing analogues are stable compounds stabilized through covalent bonds between electron-deficient atoms, and behave as good Lewis acids.
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Affiliation(s)
- Maxime Ferrer
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - M. Merced Montero-Campillo
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Otilia Mó
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Manuel Yáñez
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
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Liu G, Zhang G, Zhang S, Xu Y, Yang X, Zhang X. Degradation and mechanism of microcystin-LR by PbCrO 4 nanorods driven by visible light. CHEMOSPHERE 2020; 239:124739. [PMID: 31527000 DOI: 10.1016/j.chemosphere.2019.124739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/22/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
This work focuses on the photocatalytic removal of recalcitrant organic pollutants in water treatment. Based on facile precipitation reaction, we fabricated a photocatalyst (PbCrO4) in single crystals that present evident response to visible light and employed the catalyst in the photocatalytic decomposition of microcystin-LR (MC-LR). In the degradation test using the nanorods with prepared PbCrO4 photocatalyst, a 100% removal efficiency (27 min reaction) and a kinetics constant of 0.1356 min-1 were achieved. Such a high performance of PbCrO4 in photocatalytic conversion of MC-LR was ascribed to its high carrier separation efficiency, positive valence band (VB) position, and good delocalization of VB and conduction band (CB). The test of electron spin-resonance resonance (ESR) demonstrated that excessive free OH radicals were produced during the PbCrO4 photocatalysis of MC-LR. The density functional theory (DFT) and LC/MS/MS technology were employed to ascertain the intermediates during the MC-LR photocatalytic degradation. The major intermediates were resulted from the attack of hydroxyl radicals to the ADDA side chains of MC-LR structure. This study provides a proof-of-concept strategy to develop effective photocatalysts to efficiently produce OH radicals for the visible-light induced photocatalytic degradation of MC-LR in water.
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Affiliation(s)
- Guoshuai Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600, GA, Delft, Netherlands
| | - Guoqiang Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
| | - Shuo Zhang
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600, GA, Delft, Netherlands
| | - Yangsen Xu
- International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Xun Yang
- School of Physics, Zhengzhou University, Zhengzhou, 450052, China
| | - Xuedong Zhang
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600, GA, Delft, Netherlands
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Chiu CC, Lin CK, Kuo JL. Improved agreement between experimental and computational results for collision-induced dissociation mass spectrometry of cation-tagged hexoses. Phys Chem Chem Phys 2020; 22:6928-6941. [DOI: 10.1039/d0cp00286k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low exact exchange DFT methods underestimate the dehydration barriers as the charge localization in such transition states is challenging to describe.
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Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Chih-Kai Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
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11
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Effect of solvent polarity on the potential energy surface in the SN2 reaction of F− + CH3Cl. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Bythell BJ, Rabus JM, Wagoner AR, Abutokaikah MT, Maître P. Sequence Ion Structures and Dissociation Chemistry of Deprotonated Sucrose Anions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2380-2393. [PMID: 30284205 DOI: 10.1007/s13361-018-2065-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B1-Y1 and C1-Z1 reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B1 and C1 product anions. For the C1 anions, barriers to interconversion of the pyranose [α-glucose-H]-, C1 anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol-1) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680-1720 cm-1. For the B1 anions, our transition structure calculations predict the presence of both deprotonated 1,6-anhydroglucose and carbon 2-ketone ((4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one) anion structures, with the latter predominating. This hypothesis is supported by our spectroscopic data which show diagnostic bands at 1600, 1674, and 1699 cm-1 (deprotonated carbon 2-ketone structures), and at ~ 1541 cm-1 (both types of structure) and RRKM rate calculations. The deprotonated carbon 2-ketone structures are also the lowest energy product B1 anions. Graphical Abstract ᅟ.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA.
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA
| | - Ashley R Wagoner
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA
| | - Philippe Maître
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
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13
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Chen L, Guo Y, Xu Z, Yang X. Multiscale Simulation of the Interaction and Adsorption of Ions on a Hydrophobic Graphene Surface. Chemphyschem 2018; 19:2954-2960. [PMID: 30142233 DOI: 10.1002/cphc.201800428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 11/07/2022]
Abstract
The adsorption of ions on a graphene surface is very important to control relevant graphene-based processes. In this work, a multiscale simulation was carried out to study the adsorption of Na+ /Cl- ions on graphene by combining quantum mechanics calculations and molecular dynamics (MD) simulations. The interaction energies of the ions with graphene were computed using density functional theory (DFT). It was found that the ions show strong interaction with a graphene cluster and the overwhelming portion of the interaction energy is the ion-π orbital interaction. The large orbital interaction can be ascribed to the two contributions arising from the ion-induced polarization of graphene and the charge transfer between ion and graphene. Their different contribution degrees reveal that the polarization effect plays a main role on the orbital interaction for ion adsorption. Comparatively, for Na/Cl atom adsorption, the charge transfer shows large part to the orbital interaction with weak atom-induced polarization. The obtained interaction energies were applied to develop new interaction potentials between ion and graphene, and then MD simulations were used to study the interfacial adsorption behavior of Na+ /Cl- aqueous solution onto the graphene surface. Due to enhanced ion-π interactions, Na+ /Cl- cooperatively demonstrates a strong ion adsorption layer through direct contact with the hydrophobic graphene surface. Our simulation result presents a new understanding of ion-graphene interactions.
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Affiliation(s)
- Luohao Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Yanan Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Zhijun Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Xiaoning Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering, Nanjing Tech University, Nanjing, 210009, China
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14
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Satpathy L, Sahu PK, Behera PK, Mishra BK. Solvent Effect on the Potential Energy Surfaces of the F - + CH 3CH 2Br Reaction. J Phys Chem A 2018; 122:5861-5869. [PMID: 29909618 DOI: 10.1021/acs.jpca.8b02687] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although substantial work has been undertaken on reaction pathways involved in base-promoted elimination reactions and bimolecular nucleophilic substitution reaction of F- on CH3CH2X (X = Cl, Br, I), the effect of solvents with varying dielectric constants on the stereochemistry of each of the reaction species involved across the reaction profile have not yet been clearly understood. The present investigation reports the effect of solvents on the potential energy surfaces (PES) and structures of the species appearing in the reaction pathway of F- with bromoethane. The PESs in the gas phase have been computed at MP2 level and CCSD(T) level. The performance of several hybrid density functional, such as B3LYP, M06, M06L, BHandH, X3LYP, M05, M05-2X, and M06-2X have also been investigated toward describing the elimination and nucleophilic substitution reactions. With respect to MAE values and to make the computation cost-effective, we have explored the implicit continuum solvent model, CPCM in solvents like cyclohexane, methanol, acetonitrile, dimethyl sulfoxide and water. The reactant complexes proceed through the subsequent steps to produce fluoroethane as the substitution product and ethylene as one of the elimination products. For elimination reaction both syn and anti elimination have been explored. The calculated relatives energies values, which are negative in the gas phase, are found to be positive in polar solvents since the point charge in the separated reactants are more stabilized than the dispersed charge in the transient complex, which has also been analyzed through NBO analysis.
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Affiliation(s)
- Lopamudra Satpathy
- Centre of Studies in Surface Science and Technology, School of Chemistry , Sambalpur University , Jyoti Vihar 768 019 , India
| | - Prabhat K Sahu
- Computational Modeling Research Laboratory , School of Chemistry Sambalpur University , Jyoti Vihar 768 019 , India
| | - Pradipta K Behera
- Centre of Studies in Surface Science and Technology, School of Chemistry , Sambalpur University , Jyoti Vihar 768 019 , India
| | - Bijay K Mishra
- Centre of Studies in Surface Science and Technology, School of Chemistry , Sambalpur University , Jyoti Vihar 768 019 , India
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15
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Alkorta I, Montero-Campillo MM, Elguero J, Yáñez M, Mó O. Trapping One Electron between Three Beryllium Atoms: Very Strong One-Electron Three-Center Bonds. Chemphyschem 2018; 19:1068-1074. [DOI: 10.1002/cphc.201701240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/26/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC); Juan de la Cierva, 3 E-28006 Madrid Spain
| | | | - José Elguero
- Instituto de Química Médica (CSIC); Juan de la Cierva, 3 E-28006 Madrid Spain
| | - Manuel Yáñez
- Dep. de Química; Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem); Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC; Cantoblanco E-28049 Madrid Spain
| | - Otilia Mó
- Dep. de Química; Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem); Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC; Cantoblanco E-28049 Madrid Spain
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16
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Mazière A, Chrostowska A, Darrigan C, Dargelos A, Graciaa A, Chermette H. Electronic structure of BN-aromatics: Choice of reliable computational tools. J Chem Phys 2017; 147:164306. [PMID: 29096486 DOI: 10.1063/1.4993297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The importance of having reliable calculation tools to interpret and predict the electronic properties of BN-aromatics is directly linked to the growing interest for these very promising new systems in the field of materials science, biomedical research, or energy sustainability. Ionization energy (IE) is one of the most important parameters to approach the electronic structure of molecules. It can be theoretically estimated, but in order to evaluate their persistence and propose the most reliable tools for the evaluation of different electronic properties of existent or only imagined BN-containing compounds, we took as reference experimental values of ionization energies provided by ultra-violet photoelectron spectroscopy (UV-PES) in gas phase-the only technique giving access to the energy levels of filled molecular orbitals. Thus, a set of 21 aromatic molecules containing B-N bonds and B-N-B patterns has been merged for a comparison between experimental IEs obtained by UV-PES and various theoretical approaches for their estimation. Time-Dependent Density Functional Theory (TD-DFT) methods using B3LYP and long-range corrected CAM-B3LYP functionals are used, combined with the ΔSCF approach, and compared with electron propagator theory such as outer valence Green's function (OVGF, P3) and symmetry adapted cluster-configuration interaction ab initio methods. Direct Kohn-Sham estimation and "corrected" Kohn-Sham estimation are also given. The deviation between experimental and theoretical values is computed for each molecule, and a statistical study is performed over the average and the root mean square for the whole set and sub-sets of molecules. It is shown that (i) ΔSCF+TDDFT(CAM-B3LYP), OVGF, and P3 are the most efficient way for a good agreement with UV-PES values, (ii) a CAM-B3LYP range-separated hybrid functional is significantly better than B3LYP for the purpose, especially for extended conjugated systems, and (iii) the "corrected" Kohn-Sham result is a fast and simple way to predict IEs.
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Affiliation(s)
- Audrey Mazière
- Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Avenue de l'Université, 64000 Pau, France
| | - Anna Chrostowska
- Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Avenue de l'Université, 64000 Pau, France
| | - Clovis Darrigan
- Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Avenue de l'Université, 64000 Pau, France
| | - Alain Dargelos
- Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Avenue de l'Université, 64000 Pau, France
| | - Alain Graciaa
- Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Avenue de l'Université, 64000 Pau, France
| | - Henry Chermette
- Université de Lyon, Université Claude Bernard Lyon-1, ENS-Lyon, Institut des Sciences Analytiques, UMR CNRS 5280, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
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17
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Plaisance CP, van Santen RA, Reuter K. Constrained-Orbital Density Functional Theory. Computational Method and Applications to Surface Chemical Processes. J Chem Theory Comput 2017; 13:3561-3574. [PMID: 28657733 DOI: 10.1021/acs.jctc.7b00362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a method for performing density-functional theory (DFT) calculations in which one or more Kohn-Sham orbitals are constrained to be localized on individual atoms. This constrained-orbital DFT (CO-DFT) approach can be used to tackle two prevalent shortcomings of DFT: the lack of transparency with regard to the governing electronic structure in large (planewave based) DFT calculations and the limitations of semilocal DFT in describing systems with localized electrons or a large degree of static correlation. CO-DFT helps to address the first of these issues by decomposing complex orbital transformations occurring during elementary chemical processes into simpler and more intuitive transformations. The second issue is addressed by using the CO-DFT method to generate configuration states for multiconfiguration Kohn-Sham calculations. We demonstrate both of these applications for elementary reaction steps involved in the oxygen evolution reaction.
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Affiliation(s)
- Craig P Plaisance
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Rutger A van Santen
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven , Ceres Building, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Laboratory of Inorganic Materials Chemistry, Schuit Institute of Catalysis, Technische Universiteit Eindhoven , Helix Building, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
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18
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Mu X, Lau JKC, Lai CK, Siu KWM, Hopkinson AC, Chu IK. Isomerization versus dissociation of phenylalanylglycyltryptophan radical cations. Phys Chem Chem Phys 2017. [PMID: 28631796 DOI: 10.1039/c7cp02355c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four isomers of the radical cation of tripeptide phenylalanylglycyltryptophan, in which the initial location of the radical center is well defined, have been isolated and their collision-induced dissociation (CID) spectra examined. These ions, the π-centered [FGWπ˙]+, α-carbon- [FGα˙W]+, N-centered [FGWN˙]+ and ζ-carbon- [Fζ˙GW]+ radical cations, were generated via collision-induced dissociation (CID) of transition metal-ligand-peptide complexes, side chain fragmentation of a π-centered radical cation, homolytic cleavage of a labile nitrogen-nitrogen single bond, and laser induced dissociation of an iodinated peptide, respectively. The π-centered and tryptophan N-centered peptide radical cations produced almost identical CID spectra, despite the different locations of their initial radical sites, which indicated that interconversion between the π-centered and tryptophan N-centered radical cations is facile. By contrast, the α-carbon-glycyl radical [FGα˙W]+, and ζ-phenyl radical [Fζ˙GW]+, featured different dissociation product ions, suggesting that the interconversions among α-carbon, π-centered (or tryptophan N-centered) and ζ-carbon-radical cations have higher barriers than those to dissociation. Density functional theory calculations have been used to perform systematic mechanistic investigations on the interconversions between these isomers and to study selected fragmentation pathways for these isomeric peptide radical cations. The results showed that the energy barrier for interconversion between [FGWπ˙]+ and [FGWN˙]+ is only 31.1 kcal mol-1, much lower than the barriers to their dissociation (40.3 kcal mol-1). For the [FGWπ˙]+, [FGα˙W]+, and [Fζ˙GW]+, the barriers to interconversion are higher than those to dissociation, suggesting that interconversions among these isomers are not competitive with dissociations. The [z3 - H]˙+ ions isolated from [FGα˙W]+ and [Fζ˙GW]+ show distinctly different fragmentation patterns, indicating that the structures of these ions are different and this result is supported by the DFT calculations.
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Affiliation(s)
- Xiaoyan Mu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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19
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Bythell BJ, Abutokaikah MT, Wagoner AR, Guan S, Rabus JM. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:688-703. [PMID: 27896699 DOI: 10.1007/s13361-016-1530-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/04/2023]
Abstract
We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies. Graphical Abstract ᅟ.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Ashley R Wagoner
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
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20
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Driant T, Nachon F, Ollivier C, Renard PY, Derat E. On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach. Chembiochem 2017; 18:666-675. [PMID: 28106328 DOI: 10.1002/cbic.201600646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 11/10/2022]
Abstract
Acetylcholinesterase (AChE), an enzyme of the serine hydrolase superfamily, is a mediator of signal transmission at cholinergic synapses by catalyzing acetylcholine cleavage into acetate and choline. This enzyme is vulnerable to covalent inhibition by organophosphate compounds (like VX). Covalent inhibition of AChE does not revert spontaneously. Known reactivator compounds have limited action in restoring catalytic activity. QM/MM simulations of VX-inhibited AChE reactivation by pralidoxime (2-PAM), a classical reactivator, were performed. These afforded a broad view of the effect of protonation states of active-site residues, and provide evidence for the role of Glu202, which needs to be protonated for reactivation to occur. In situ deprotonation of 2-PAM for both protonation states of Glu202 showed that His447 is able to deprotonate 2-PAM with the assistance of Glu202. Because the active site of serine hydrolases is highly conserved, this work provides new insights on the interplay between the catalytic triad residues and this glutamate, newly identified as protonatable.
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Affiliation(s)
- Thomas Driant
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91223, Brétigny-sur-Orge Cédex, France
| | - Cyril Ollivier
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Pierre-Yves Renard
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université Rouen-Normandie, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Etienne Derat
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
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21
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Grimme S, Bannwarth C. Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB). J Chem Phys 2016; 145:054103. [DOI: 10.1063/1.4959605] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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22
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Lamine W, Boughdiri S, Christ L, Morell C, Chermette H. Ill-advised self-interaction contribution in modelling anionic attack along a reaction path. Mol Phys 2016. [DOI: 10.1080/00268976.2015.1134828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Walid Lamine
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES19 Unité de recherche Physico-Chimie des Matériaux condensés, Tunis, Tunisia
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Salima Boughdiri
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES19 Unité de recherche Physico-Chimie des Matériaux condensés, Tunis, Tunisia
| | - Lorraine Christ
- Université de Lyon, Université Lyon 1(UCBL), IRCELYON, Villeurbanne, France
| | - Christophe Morell
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Henry Chermette
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
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23
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Bento AP, Solà M, Bickelhaupt FM. E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study. J Chem Theory Comput 2015; 4:929-40. [PMID: 26621234 DOI: 10.1021/ct700318e] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.
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Affiliation(s)
- A Patrícia Bento
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institut de Química Computacional, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Miquel Solà
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institut de Química Computacional, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institut de Química Computacional, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain
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24
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Bythell BJ, Harrison AG. Formation of a(1) ions directly from oxazolone b(2) ions: an energy-resolved and computational study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:774-781. [PMID: 25810075 DOI: 10.1007/s13361-015-1080-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
It is well-known that oxazolone b2 ions fragment extensively by elimination of CO to form a2 ions, which often fragment further to form a1 ions. Less well-known is that some oxazolone b2 ions may fragment directly to form a1 ions. The present study uses energy-resolved collision-induced dissociation experiments to explore the occurrence of the direct b2→a1 fragmentation reaction. The experimental results show that the direct b2→a1 reaction is generally observed when Gly is the C-terminal residue of the oxazolone. When the C-terminal residue is more complex, it is able to provide increased stability of the a2 product in the b2→a2 fragmentation pathway. Our computational studies of the relative critical reaction energies for the b2→a2 reaction compared with those for the b2→a1 reaction provide support that the critical reaction energies are similar for the two pathways when the C-terminal residue of the oxazolone is Gly. By contrast, when the nitrogen of the oxazolone ring in the b2 ion does not bear a hydrogen, as in the Ala-Sar and Tyr-Sar (Sar = N-methylglycine) oxazolone b2 ions, a1 ions are not formed but rather neutral imine elimination from the N-terminus of the b2 ion becomes a dominant fragmentation reaction. The M06-2X/6-31+G(d,p) density functional theory calculations are in general agreement with the experimental data for both types of reaction. In contrast, the B3LYP/6-31+G(d,p) model systematically underestimates the barriers of these SN2-like b2→a1 reaction. The difference between the two methods of barrier calculation are highly significant (P < 0.001) for the b2→a1 reaction, but only marginally significant (P = 0.05) for the b2→a2 reaction. The computations provide further evidence of the limitations of the B3LYP functional when describing SN2-like reactions.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, 63131, USA,
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25
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George J, Reimann C, Deringer VL, Bredow T, Dronskowski R. On the DFT Ground State of Crystalline Bromine and Iodine. Chemphyschem 2015; 16:728-32. [DOI: 10.1002/cphc.201402890] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Indexed: 11/09/2022]
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26
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García G, Atilhan M, Aparicio S. Assessment of DFT methods for studying acid gas capture by ionic liquids. Phys Chem Chem Phys 2015; 17:26875-91. [DOI: 10.1039/c5cp04283f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the first time, this work reports an analysis of the performance of Density Functional methods for studying acid gas capture (CO2 and SO2) by ionic liquids (ILs).
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Affiliation(s)
- Gregorio García
- Department of Chemistry
- University of Burgos
- 09001 Burgos
- Spain
| | - Mert Atilhan
- Department of Chemical Engineering
- Qatar University
- Doha
- Qatar
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27
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Bannwarth C, Grimme S. A simplified time-dependent density functional theory approach for electronic ultraviolet and circular dichroism spectra of very large molecules. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.023] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Wu Y, Genest A, Rösch N. Does the Preferred Mechanism of a Catalytic Transformation Depend on the Density Functional? Ethylene Hydrosilylation by a Metal Complex as a Case Study. J Phys Chem A 2014; 118:3004-13. [DOI: 10.1021/jp5010677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yin Wu
- Institut
für Siliciumchemie and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Alexander Genest
- Catalysis
Research Center and Department Chemie, Technische Universität München, 85747 Garching, Germany
- Institute
of High
Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Notker Rösch
- Catalysis
Research Center and Department Chemie, Technische Universität München, 85747 Garching, Germany
- Institute
of High
Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
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Grimme S. A simplified Tamm-Dancoff density functional approach for the electronic excitation spectra of very large molecules. J Chem Phys 2014; 138:244104. [PMID: 23822224 DOI: 10.1063/1.4811331] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two approximations in the Tamm-Dancoff density functional theory approach (TDA-DFT) to electronically excited states are proposed which allow routine computations for electronic ultraviolet (UV)- or circular dichroism (CD) spectra of molecules with 500-1000 atoms. Speed-ups compared to conventional time-dependent DFT (TD-DFT) treatments of about two to three orders of magnitude in the excited state part at only minor loss of accuracy are obtained. The method termed sTDA ("s" for simplified) employs atom-centered Löwdin-monopole based two-electron repulsion integrals with the asymptotically correct 1∕R behavior and perturbative single excitation configuration selection. It is formulated generally for any standard global hybrid density functional with given Fock-exchange mixing parameter ax. The method performs well for two standard benchmark sets of vertical singlet-singlet excitations for values of ax in the range 0.2-0.6. The mean absolute deviations from reference data are only 0.2-0.3 eV and similar to those from standard TD-DFT. In three cases (two dyes and one polypeptide), good mutual agreement between the electronic spectra (up to 10-11 eV excitation energy) from the sTDA method and those from TD(A)-DFT is obtained. The computed UV- and CD-spectra of a few typical systems (e.g., C60, two transition metal complexes, [7]helicene, polyalanine, a supramolecular aggregate with 483 atoms and about 7000 basis functions) compare well with corresponding experimental data. The method is proposed together with medium-sized double- or triple-zeta type atomic-orbital basis sets as a quantum chemical tool to investigate the spectra of huge molecular systems at a reliable DFT level.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany.
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Steinmetz M, Hansen A, Ehrlich S, Risthaus T, Grimme S. Accurate Thermochemistry for Large Molecules with Modern Density Functionals. Top Curr Chem (Cham) 2014. [DOI: 10.1007/128_2014_543] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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31
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Zhang J, Lourderaj U, Sun R, Mikosch J, Wester R, Hase WL. Simulation studies of the Cl- + CH3I SN2 nucleophilic substitution reaction: comparison with ion imaging experiments. J Chem Phys 2013; 138:114309. [PMID: 23534641 DOI: 10.1063/1.4795495] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the previous work of Mikosch et al. [Science 319, 183 (2008)], ion imaging experiments were used to study the Cl(-) + CH3I → ClCH3 + I(-) reaction at collision energies E(rel) of 0.39, 0.76, 1.07, and 1.9 eV. For the work reported here MP2(fc)/ECP/d direct dynamics simulations were performed to obtain an atomistic understanding of the experiments. There is good agreement with the experimental product energy and scattering angle distributions for the highest three E(rel), and at these energies 80% or more of the reaction is direct, primarily occurring by a rebound mechanism with backward scattering. At 0.76 eV there is a small indirect component, with isotropic scattering, involving formation of the pre- and post-reaction complexes. All of the reaction is direct at 1.07 eV. Increasing E(rel) to 1.9 eV opens up a new indirect pathway, the roundabout mechanism. The product energy is primarily partitioned into relative translation for the direct reactions, but to CH3Cl internal energy for the indirect reactions. The roundabout mechanism transfers substantial energy to CH3Cl rotation. At E(rel) = 0.39 eV both the experimental product energy partitioning and scattering are statistical, suggesting the reaction is primarily indirect with formation of the pre- and post-reaction complexes. However, neither MP2 nor BhandH/ECP/d simulations agree with experiment and, instead, give reaction dominated by direct processes as found for the higher collision energies. Decreasing the simulation E(rel) to 0.20 eV results in product energy partitioning and scattering which agree with the 0.39 eV experiment. The sharp transition from a dominant direct to indirect reaction as E(rel) is lowered from 0.39 to 0.20 eV is striking. The lack of agreement between the simulations and experiment for E(rel) = 0.39 eV may result from a distribution of collision energies in the experiment and/or a shortcoming in both the MP2 and BhandH simulations. Increasing the reactant rotational temperature from 75 to 300 K for the 1.9 eV collisions, results in more rotational energy in the CH3Cl product and a larger fraction of roundabout trajectories. Even though a ClCH3-I(-) post-reaction complex is not formed and the mechanistic dynamics are not statistical, the roundabout mechanism gives product energy partitioning in approximate agreement with phase space theory.
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Affiliation(s)
- Jiaxu Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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Zvereva EE, Grimme S, Katsyuba SA, Burganov TI, Zagidullin AA, Milyukov VA, Sinyashin OG. Application of Time-Dependent Density Functional Theory and Optical Spectroscopy toward the Rational Design of Novel 3,4,5-Triaryl-1-R-1,2-diphospholes. J Phys Chem A 2013; 117:6827-34. [DOI: 10.1021/jp4043914] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elena E. Zvereva
- A.E. Arbuzov Institute of Organic
and Physical Chemistry, Kazan Scientific Centre, Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, 53115 Bonn,
Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, 53115 Bonn,
Germany
| | - Sergey A. Katsyuba
- A.E. Arbuzov Institute of Organic
and Physical Chemistry, Kazan Scientific Centre, Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Timur I. Burganov
- A.E. Arbuzov Institute of Organic
and Physical Chemistry, Kazan Scientific Centre, Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Almaz A. Zagidullin
- A.E. Arbuzov Institute of Organic
and Physical Chemistry, Kazan Scientific Centre, Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Vasily A. Milyukov
- A.E. Arbuzov Institute of Organic
and Physical Chemistry, Kazan Scientific Centre, Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Oleg G. Sinyashin
- A.E. Arbuzov Institute of Organic
and Physical Chemistry, Kazan Scientific Centre, Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
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33
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Sure R, Grimme S. Corrected small basis set Hartree-Fock method for large systems. J Comput Chem 2013; 34:1672-85. [PMID: 23670872 DOI: 10.1002/jcc.23317] [Citation(s) in RCA: 289] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 01/23/2023]
Abstract
A quantum chemical method based on a Hartree-Fock calculation with a small Gaussian AO basis set is presented. Its main area of application is the computation of structures, vibrational frequencies, and noncovalent interaction energies in huge molecular systems. The method is suggested as a partial replacement of semiempirical approaches or density functional theory (DFT) in particular when self-interaction errors are acute. In order to get accurate results three physically plausible atom pair-wise correction terms are applied for London dispersion interactions (D3 scheme), basis set superposition error (gCP scheme), and short-ranged basis set incompleteness effects. In total nine global empirical parameters are used. This so-called Hartee-Fock-3c (HF-3c) method is tested for geometries of small organic molecules, interaction energies and geometries of noncovalently bound complexes, for supramolecular systems, and protein structures. In the majority of realistic test cases good results approaching large basis set DFT quality are obtained at a tiny fraction of computational cost.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany
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34
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Brandenburg JG, Grimme S. Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction. Top Curr Chem (Cham) 2013; 345:1-23. [PMID: 24220994 DOI: 10.1007/128_2013_488] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße 4, 53115, Bonn, Germany,
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35
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Cuevas-Saavedra R, Chakraborty D, Rabi S, Cárdenas C, Ayers PW. Symmetric Nonlocal Weighted Density Approximations from the Exchange-Correlation Hole of the Uniform Electron Gas. J Chem Theory Comput 2012; 8:4081-93. [DOI: 10.1021/ct300325t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rogelio Cuevas-Saavedra
- Department
of Chemistry and
Chemical Biology, McMaster University,
Hamilton, Ontario, Canada
| | - Debajit Chakraborty
- Department
of Chemistry and
Chemical Biology, McMaster University,
Hamilton, Ontario, Canada
| | - Sandra Rabi
- Department
of Chemistry and
Chemical Biology, McMaster University,
Hamilton, Ontario, Canada
| | - Carlos Cárdenas
- Departamento de Física,
Facultad de Ciencias, Universidad de Chile, 653-Santiago, Chile
| | - Paul W. Ayers
- Department
of Chemistry and
Chemical Biology, McMaster University,
Hamilton, Ontario, Canada
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36
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Grimme S, Goerigk L, Fink RF. Spin-component-scaled electron correlation methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1110] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Marincean S, Rabago Smith M, Beltz L, Borhan B. Selectivity of labeled bromoethylamine for protein alkylation. J Mol Model 2012; 18:4547-56. [PMID: 22643979 DOI: 10.1007/s00894-012-1461-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 05/04/2012] [Indexed: 11/25/2022]
Abstract
Alkylation of cysteine residues has been used extensively for characterization of proteins and their mode of action in biological systems, research endeavors that are at the core of proteomics. Treatment with a simple alkylating agent such as [2-(13)C] bromoethylamine would result in labeled thialysine at the ε-position. This chemical modification of proteins would allow investigations via both (13)C NMR spectroscopy and mass spectrometry. However [2-(13)C] labeled bromoethylamine is not available commercially. We investigated its synthesis at acid pH with the goal of obtaining singly labeled bromoethylamine and understanding the mechanistic details of the reaction. Based on our experimental and theoretical results, bromination of [2-(13)C] labeled ethanolamine in acidic conditions takes place via exclusive attack of the nucleophile (HBr) at the hydroxyl bearing C. Moreover, hydrogen bonding guides the nucleophilic attack, resulting in no label scrambling of the bromoethylamine product. Protein alkylation at cysteine residue with the synthesized Br(13)CH(2)CH(2)NH(2)-HBr is successful. Ab initio calculations in which CH(3)SH serves as a model for the cysteine residue suggest that in gas phase intermolecular attack by the sulfur bearing nucleophile is favored over the intramolecular substitution by the amino group by 15.4 kJ mol(-1). Solution modeling shows that the trend is preserved at basic pH, which is the experimental one, but is reversed at neutral pH.
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Affiliation(s)
- Simona Marincean
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Rd., Dearborn, MI 48128, USA.
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38
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Beg H, De SP, Ash S, Misra A. Use of polarizability and chemical hardness to locate the transition state and the potential energy curve for double proton transfer reaction: A DFT based study. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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39
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Arbuznikov AV, Kaupp M. Importance of the correlation contribution for local hybrid functionals: Range separation and self-interaction corrections. J Chem Phys 2012; 136:014111. [DOI: 10.1063/1.3672080] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Grimme S, Hujo W, Kirchner B. Performance of dispersion-corrected density functional theory for the interactions in ionic liquids. Phys Chem Chem Phys 2012; 14:4875-83. [DOI: 10.1039/c2cp24096c] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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41
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Rougeau N, Teillet-Billy D, Sidis V. On the PES for the interaction of an H atom with an H chemisorbate on a graphenic platelet. Phys Chem Chem Phys 2011; 13:17579-87. [PMID: 21892489 DOI: 10.1039/c1cp22202c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Motivated by the problem of H(2) formation in diffuse clouds of the interstellar medium (ISM), we study the effect of including van der Waals-type corrections in DFT calculations on the entrance PES of the Eley-Rideal reaction H(b) + H(a)-GR → H(b)-H(a) + GR for a graphenic surface GR. The present calculations make use of the PBE-D3 dispersion corrected functional of Grimme et al. (2010) and are carried out on cluster models of graphenic surfaces: C(24)H(12) and C(54)H(18). To assess the soundness of the chosen functional we start by revisiting the H-GR adsorption potential. We find a satisfactory on top physisorption well (43-48 meV) correctly located at an H-GR distance of 3 Å. We then revisit the H(b)-H(a)-GR system using both the PW91 and PBE functionals. Our calculations do not reproduce the tiny potential barrier reported earlier for large H(b)distances from the surface. The barrier in the calculations of Sidis et al. (2000) and Morisset et al. (2003, 2004) has been traced to their previous use of an LSDA + POSTSCF PW91 procedure rather than the genuine PW91 one. The new PBE-D3 PES for the H(b)-H(a)-GR system is reported as a function of the H(b) distance to the surface and its impact parameter relative to the H(a) chemisorbate for the so-called "fixed puckered" ("diabatic" or "sudden") approach. The results are discussed in relation to recent experimental and theoretical work.
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Affiliation(s)
- N Rougeau
- Institut des Sciences Moléculaires d'Orsay, CNRS - Univ. Paris-Sud 11, F91405 Orsay Cedex, France.
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42
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Affiliation(s)
- Alexis T. Bell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720; ,
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Hargis JC, Vöhringer-Martinez E, Woodcock HL, Toro-Labbé A, Schaefer HF. Characterizing the Mechanism of the Double Proton Transfer in the Formamide Dimer. J Phys Chem A 2011; 115:2650-7. [DOI: 10.1021/jp111834v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jacqueline C. Hargis
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Esteban Vöhringer-Martinez
- Laboratorio de Química Teórica Computacional (QTC), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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44
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Goerigk L, Grimme S. A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions. Phys Chem Chem Phys 2011; 13:6670-88. [PMID: 21384027 DOI: 10.1039/c0cp02984j] [Citation(s) in RCA: 1310] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Lars Goerigk
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
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45
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Bythell BJ, Csonka IP, Suhai S, Barofsky DF, Paizs B. Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine. J Phys Chem B 2010; 114:15092-105. [PMID: 20973555 PMCID: PMC3664278 DOI: 10.1021/jp108452y] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.
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Affiliation(s)
- Benjamin J. Bythell
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Chemistry, Oregon State University, Corvallis, Oregon, USA
| | - István P. Csonka
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Sándor Suhai
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | | | - Béla Paizs
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
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46
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Rangelov MA, Petrova GP, Yomtova VM, Vayssilov GN. Catalytic Role of Vicinal OH in Ester Aminolysis: Proton Shuttle versus Hydrogen Bond Stabilization. J Org Chem 2010; 75:6782-92. [DOI: 10.1021/jo100886p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Miroslav A. Rangelov
- Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, Str. Acad. G. Bontchev, Bl. 9, 1113 Sofia, Bulgaria
| | - Galina P. Petrova
- Faculty of Chemistry, University of Sofia, Boulevard James Bouchier 1, 1164 Sofia, Bulgaria
| | - Vihra M. Yomtova
- Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, Str. Acad. G. Bontchev, Bl. 9, 1113 Sofia, Bulgaria
| | - Georgi N. Vayssilov
- Faculty of Chemistry, University of Sofia, Boulevard James Bouchier 1, 1164 Sofia, Bulgaria
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47
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Hansen N, Kerber T, Sauer J, Bell AT, Keil FJ. Quantum Chemical Modeling of Benzene Ethylation over H-ZSM-5 Approaching Chemical Accuracy: A Hybrid MP2:DFT Study. J Am Chem Soc 2010; 132:11525-38. [DOI: 10.1021/ja102261m] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Niels Hansen
- Department of Chemical Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany, and Department of Chemical Engineering, University of California, Berkeley, California 94720-1462
| | - Torsten Kerber
- Department of Chemical Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany, and Department of Chemical Engineering, University of California, Berkeley, California 94720-1462
| | - Joachim Sauer
- Department of Chemical Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany, and Department of Chemical Engineering, University of California, Berkeley, California 94720-1462
| | - Alexis T. Bell
- Department of Chemical Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany, and Department of Chemical Engineering, University of California, Berkeley, California 94720-1462
| | - Frerich J. Keil
- Department of Chemical Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany, and Department of Chemical Engineering, University of California, Berkeley, California 94720-1462
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48
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Zein S, Poor Kalhor M, Chibotaru LF, Chermette H. Density functional estimations of Heisenberg exchange constants in oligonuclear magnetic compounds: Assessment of density functional theory versus ab initio. J Chem Phys 2009; 131:224316. [DOI: 10.1063/1.3264570] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Goerigk L, Grimme S. A General Database for Main Group Thermochemistry, Kinetics, and Noncovalent Interactions − Assessment of Common and Reparameterized (meta-)GGA Density Functionals. J Chem Theory Comput 2009; 6:107-26. [DOI: 10.1021/ct900489g] [Citation(s) in RCA: 348] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Lars Goerigk
- Theoretische Organische Chemie, Organisch-Chemisches Institut, Universität Münster, Corrensstrasse 40 and NRW Graduate School of Chemistry, Universität Münster, Wilhelm-Klemm-Strasse 10, D-48149 Münster, Germany
| | - Stefan Grimme
- Theoretische Organische Chemie, Organisch-Chemisches Institut, Universität Münster, Corrensstrasse 40 and NRW Graduate School of Chemistry, Universität Münster, Wilhelm-Klemm-Strasse 10, D-48149 Münster, Germany
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50
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Competing gas-phase fragmentation pathways of asparagine-, glutamine-, and lysine-containing protonated dipeptides. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0658-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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