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Abstract
Enthalpies and free energies of reaction for small neutral and charged beryllium deuterides BeD, BeD2, and BeD3 that have been calculated are reported for a temperature range of 0 K to 1000 K. We discuss probable dissociation channels and possible ways of producing BeD by localizing the relevant transition states and by calculating corresponding rate constants. BeD and BeD+ are found to be the most stable ones among the considered compounds. BeD2 and \documentclass[12pt]{minimal}
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\begin{document}$$ {\mathrm{BeD}}_2^{+} $$\end{document}BeD2+ are more likely to decompose into Be0,+ + D2 than into BeD0,+ + D. The metastable BeD3 and \documentclass[12pt]{minimal}
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\begin{document}$$ {\mathrm{BeD}}_3^{+} $$\end{document}BeD3+ predominantly decompose into BeD0,+ + D2. In light of our results on the reaction energetics, we can interpret the pathways for production of BeD via BeD2 and BeD3 intermediates observed in molecular dynamics simulations.
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Affiliation(s)
- Ivan Sukuba
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstraße 25, A-6020, Innsbruck, Austria. .,Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, SK-84248, Bratislava, Slovakia.
| | - Alexander Kaiser
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstraße 25, A-6020, Innsbruck, Austria
| | - Stefan E Huber
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstraße 25, A-6020, Innsbruck, Austria
| | - Jan Urban
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, SK-84248, Bratislava, Slovakia
| | - Michael Probst
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstraße 25, A-6020, Innsbruck, Austria
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2
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Manzetti S, Lu T. The geometry and electronic structure of Aristolochic acid: possible implications for a frozen resonance. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3111] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sergio Manzetti
- Fjordforsk Institute of Science and Technology; Fresvik 6893 Norway
- Science for Life Laboratory, Department of Cell and Molecular Biology; University of Uppsala; Sweden
| | - Tian Lu
- Department of Chemistry and Chemical Engineering, School of Chemical and Biological Engineering; University of Science and Technology Beijing; Beijing 100083 People's Republic of China
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3
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Wang F, Pang W, Duffy P. Performance assessment of density functional theory-based models using orbital momentum distributions. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.647816] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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4
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Patil MP, Sharma AK, Sunoj RB. Importance of the Nature of α-Substituents in Pyrrolidine Organocatalysts in Asymmetric Michael Additions. J Org Chem 2010; 75:7310-21. [DOI: 10.1021/jo101592b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahendra P. Patil
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akhilesh K. Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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Flener-Lovitt C, Woon DE, Dunning TH, Girolami GS. A DFT and ab Initio Benchmarking Study of Metal−Alkane Interactions and the Activation of Carbon−Hydrogen Bonds. J Phys Chem A 2009; 114:1843-51. [DOI: 10.1021/jp9058033] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Charity Flener-Lovitt
- School of Chemical Sciences, 600 South Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - David E. Woon
- School of Chemical Sciences, 600 South Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Thom H. Dunning
- School of Chemical Sciences, 600 South Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Gregory S. Girolami
- School of Chemical Sciences, 600 South Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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Zottola MA, Beigel K, Soni SD, Lawrence R. Disulfides as Cyanide Antidotes: Evidence for a New In Vivo Oxidative Pathway for Cyanide Detoxification. Chem Res Toxicol 2009; 22:1948-53. [DOI: 10.1021/tx900258m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark A. Zottola
- United States Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Edgewood Area-Aberdeen Proving Ground, Maryland 21010, and Department of Chemistry, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, Alabama 35294
| | - Keith Beigel
- United States Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Edgewood Area-Aberdeen Proving Ground, Maryland 21010, and Department of Chemistry, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, Alabama 35294
| | - Sunil-Datta Soni
- United States Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Edgewood Area-Aberdeen Proving Ground, Maryland 21010, and Department of Chemistry, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, Alabama 35294
| | - Richard Lawrence
- United States Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Edgewood Area-Aberdeen Proving Ground, Maryland 21010, and Department of Chemistry, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, Alabama 35294
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A partial exploration of the potential energy surfaces of SCN and HSCN: Implications for the enzyme-mediated detoxification of cyanide. J Mol Graph Model 2009; 28:183-6. [DOI: 10.1016/j.jmgm.2009.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 06/27/2009] [Indexed: 11/22/2022]
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Patil MP, Sunoj RB. On the relative preference of enamine/iminium pathways in an organocatalytic Michael addition reaction. Chem Asian J 2009; 4:714-24. [PMID: 19353592 DOI: 10.1002/asia.200800351] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of the organocatalyzed Michael addition between propanal and methyl vinyl ketone is investigated using the density functional and ab intio methods. Different modes of substrate activation offered by a secondary amine (pyrrolidine) organocatalyst are reported. The electrophilic activation of enone (P-I) through the formation of an iminium ion, and nucleophilic activation of propanal (P-II) in the form of enamine have been examined by identifying the corresponding transition states. The kinetic preference for the formation of key intermediates is established in an effort to identify the competing pathways associated with the title reaction. A comparison of barriers associated with different pathways as well as intermediate formation allows us to provide a suitable mechanistic rationale for Michael addition reactions catalyzed by a secondary amine. The overall barriers for the C-C bond formation pathways involving enol or iminium intermediates are identified as higher than the enamine pathway. Additionally, the generation of iminium is found to be less favored as compared to enamine formation. The effect of co-catalyst/protic solvent on the energetics of the overall reaction is also studied using the cluster continuum approach. Significant reduction in the activation energies for each step of the reaction is predicted for the solvent-assisted models. The co-catalyst assisted addition of propanal-enamine to methyl vinyl ketone is identified as the most preferred pathway (P-IV) for the Michael addition reaction. The results are in concurrence with the available experimental reports on the rate acceleration by the use of a co-catalyst in this reaction.
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Affiliation(s)
- Mahendra P Patil
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Patil M, Sunoj R. The Role of Noninnocent Solvent Molecules in Organocatalyzed Asymmetric Michael Addition Reactions. Chemistry 2008; 14:10472-85. [DOI: 10.1002/chem.200800877] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Patil MP, Sunoj RB. Insights on co-catalyst-promoted enamine formation between dimethylamine and propanal through ab initio and density functional theory study. J Org Chem 2007; 72:8202-15. [PMID: 17900139 DOI: 10.1021/jo071004q] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.
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Affiliation(s)
- Mahendra P Patil
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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11
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On the application of the counterpoise correction for the basis set superposition error in geometry optimization calculations of molecular systems: some inconsistent results. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0345-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Yang T, Su G, Ning C, Deng J, Wang F, Zhang S, Ren X, Huang Y. New Diagnostic of the Most Populated Conformer of Tetrahydrofuran in the Gas Phase. J Phys Chem A 2007; 111:4927-33. [PMID: 17511427 DOI: 10.1021/jp066299a] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The most populated conformer of tetrahydrofuran (C(4)H(8)O) has been diagnosed as the Cs conformer in the present study, jointly using experimental electron momentum spectroscopy (EMS) and quantum mechanics. Our B3LYP/6-311++G** model indicates that the C1 conformation, which is one of the three possible conformations of tetrahydrofuran produced by pseudorotation in the gas phase, is a transition state due to its imaginary frequencies, in agreement with the prediction from a recent ab initio MP2/aug-cc-pVTZ study (J. Chem. Phys. 2005, 122, 204303). The study has identified the fingerprint of the highest occupied molecular orbital (HOMO) of the C(s) (12a') conformer as the most populated conformer. The identification of the C(s) structure, therefore, leads to the orbital-based assignment of the ionization binding energy spectra of tetrahydrofuran for the first time, on the basis of the outer valence Green function OVGF/6-31G* model and the density functional theory (DFT) SAOP/ET-PVQZ model. The present study explores an innovative approach to study molecular stabilities. It also indicates that energetic properties are not always the most appropriate means to study conformer-rich biological systems.
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Affiliation(s)
- Tiecheng Yang
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People's Republic of China
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Reply to the comment on ‘Pople versus Dunning basis-sets for group IA metal hydrides and some other second row hydrides: The case against a De Facto standard’ by R.A. Klein and M.A. Zottola [Chem. Phys. Lett. 419 (2006) 254–258]. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Feller D, Peterson KA. Comment on ‘Pople versus Dunning basis sets for group IA metal hydrides and some other second row hydrides: The case against a De Facto standard’ by R.A. Klein and M.A. Zottola [Chem. Phys. Lett. 419 (2006) 254–258]. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.09.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Li H, Le Roy RJ. An accurate ab initio potential energy surface and calculated spectroscopic constants for BeH2, BeD2, and BeHD. J Chem Phys 2006; 125:44307. [PMID: 16942142 DOI: 10.1063/1.2212933] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A three-dimensional potential energy surface for the ground electronic state of BeH(2) has been determined by three-dimensional spline interpolation over 6864 symmetry-unique ab initio points calculated at the icMRCI/aug-cc-pV5Z level and corrected for core-electron correlation computed at the MR-ACPF/cc-pCV5Z level. Calculated spectroscopic constants of BeH(2) and BeD(2) are in excellent agreement with recent experimental results: for 11 bands of BeH(2) and 5 bands of BeD(2) the root mean square (rms) band origin discrepancies were only 0.15(+/-0.09) and 0.46(+/-0.19) cm(-1), respectively, and the rms relative discrepancies in the inertial rotational constants (B([v])) were only 0.028% and 0.023%, respectively. Spectral constants for BeHD were predicted using the same potential surface. The effect of different interpolation methods on predicted potential function values and on the calculated level energies and spectroscopic constants has been examined.
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Affiliation(s)
- Hui Li
- Guelph-Waterloo Centre for Graduate Work in Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Klein RA. Single point calculations using geometries derived at a lower level of theory: Caveats to be observed in using compound levels of theory or ‘double-barrelling’. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.04.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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