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Penocchio E, Piccardo M, Barone V. Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route. J Chem Theory Comput 2015; 11:4689-707. [PMID: 26574259 DOI: 10.1021/acs.jctc.5b00622] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.
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Piccardo M, Penocchio E, Puzzarini C, Biczysko M, Barone V. Semi-Experimental Equilibrium Structure Determinations by Employing B3LYP/SNSD Anharmonic Force Fields: Validation and Application to Semirigid Organic Molecules. J Phys Chem A 2015; 119:2058-82. [DOI: 10.1021/jp511432m] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Matteo Piccardo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Emanuele Penocchio
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle Ricerche, Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca CNR,
UOS di Pisa, Via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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Lundell J, Olbert-Majkut A. Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt A:113-121. [PMID: 24094995 DOI: 10.1016/j.saa.2013.08.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/30/2013] [Indexed: 06/02/2023]
Abstract
The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be+8.0 kJ mol(-1) higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex structures were identified, with the most stable complex structure (T2A) also being the most abundant in the matrices. The difference between experiment and computational energetic order of the two complex structures of the same GA conformer is explained by contributions of deformation energy upon complexation and the effect of the environment. The computed BSSE-corrected interaction energies are for the two most stable complexes of the two GA conformers for T1A and T2A -42.11 and -45.03 kJ mol(-1), respectively, at the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level of theory.
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Affiliation(s)
- Jan Lundell
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.
| | - Adriana Olbert-Majkut
- Faculty of Chemistry, University of Wroclaw, F. Joliot Curie 14, 50-383 Wroclaw, Poland.
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Altnöder J, Krüger K, Borodin D, Reuter L, Rohleder D, Hecker F, Schulz RA, Nguyen XT, Preiß H, Eckhoff M, Levien M, Suhm MA. The Guinness Molecules for the Carbohydrate Formula. CHEM REC 2014; 14:1116-33. [DOI: 10.1002/tcr.201402059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Jonas Altnöder
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Kerstin Krüger
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Dmitriy Borodin
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Lennart Reuter
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Darius Rohleder
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Fabian Hecker
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Roland A. Schulz
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Xuan T. Nguyen
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Helen Preiß
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Marco Eckhoff
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Marcel Levien
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie; Georg-August-Universität Göttingen; Tammannstr. 6 D-37077 Göttingen Germany
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Olbert-Majkut A, Lundell J, Wierzejewska M. Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid. J Phys Chem A 2013; 118:350-7. [DOI: 10.1021/jp409982f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adriana Olbert-Majkut
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jan Lundell
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Maria Wierzejewska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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DING WANJIAN, NI LINGYAN, FANG WEIHAI, YU JIANGUO. THEORETICAL STUDY ON THE UNIMOLECULAR REACTIONS OF GLYOXYLIC ACID. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s021963360500174x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The potential energy surfaces of isomerization, decarboxylation, and decarbonylation reactions of glyoxylic acid have been characterized by the B3LYP/cc-pVTZ, B3LYP/aug-cc-pVTZ, and MP2/cc-pVTZ calculations. There is a relatively high barrier on the isomerization pathway from Tc to Tt , due to existence of the intramolecular H-bond in the Tc to Tt structures. The decarboxylation reaction proceeds mainly through a stepwise mechanism. The singlet hydroxyl carbene and carbon dioxide are formed in the first step, which is followed by isomerization of the carbene to formaldehyde in the second step. The thermal decarbonylation reaction of glyoxylic acid may take place at high temperature, due to a barrier of ~52 kcal/mol on the pathway.
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Affiliation(s)
- WAN-JIAN DING
- Department of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - LING-YAN NI
- Department of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - WEI-HAI FANG
- Department of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - JIAN-GUO YU
- Department of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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Kwon MK, Sung EM. Intramolecular Hydrogen Bonding in 2-Fluorocyclopropanemethanol and 2-Chlorocyclopropanemethanol as Studied by ab Initio Calculation. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2010. [DOI: 10.5012/jkcs.2010.54.3.275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Takahashi K, Plath KL, Axson JL, Nelson GC, Skodje RT, Vaida V. Dynamics and spectroscopy of vibrational overtone excited glyoxylic acid and 2,2-dihydroxyacetic acid in the gas-phase. J Chem Phys 2010; 132:094305. [DOI: 10.1063/1.3327839] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Plath KL, Axson JL, Nelson GC, Takahashi K, Skodje RT, Vaidaa V. Gas-phase vibrational spectra of glyoxylic acid and its gem diol monohydrate. Implications for atmospheric chemistry. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11144-009-5528-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Buemi G. DFT study of the hydrogen bond strength and IR spectra of formic, oxalic, glyoxylic and pyruvic acids in vacuum, acetone and water solution. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1543] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Demaison J, Herman M, Liévin J. Anharmonic force field ofcis- andtrans-formic acid from high-levelab initiocalculations, and analysis of resonance polyads. J Chem Phys 2007; 126:164305. [PMID: 17477600 DOI: 10.1063/1.2722752] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quadratic, cubic, and semidiagonal quartic force fields of cis- and trans-formic acid have been calculated using three different levels of theory. They all give satisfactory results, including the one at the lowest level of theory which is the MP2 method employing a basis set of triple-zeta quality. The results are used to theoretically analyze resonance polyads, including the one involving the 4(1), 5(1), 6(1), 8(1), 7(1)9(1), and 9(2) vibrational states. A semiexperimental equilibrium structure is derived from experimental ground state rotational constants and rovibrational interaction parameters calculated from the ab initio force field. The ab initio structure calculated at the CCSD(T) level of theory using a basis set of quintuple-zeta quality is in excellent agreement with the semiexperimental structure.
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Affiliation(s)
- J Demaison
- Laboratoire de Chimie quantique et Photophysique, Université libre de Bruxelles (U.L.B), CP160/09, Avenue F.D. Roosevelt 50, B-1050 Brussels, Belgium.
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Demaison J, Császár AG, Kleiner I, Møllendal H. Equilibrium vs Ground-State Planarity of the CONH Linkage. J Phys Chem A 2007; 111:2574-86. [PMID: 17388342 DOI: 10.1021/jp067278j] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Planarity of the XC(=)NHY linkage has been investigated in unprecedented detail in a number of relatively simple compounds, including formamide (X = Y = H), acetamide (X = CH3, Y = H), urea (X = NH2, Y = H), carbamic acid (X = OH, Y = H), and methyl carbamate (X = OCH3, Y = H). Reliable estimates of the equilibrium structures of formamide, cyanamide, acetamide, urea, carbamic acid, methylamine, dimethyl ether, and methyl carbamate are derived, mostly for the first time. It is shown that formamide, considered prototypical for the amide linkage, is not typical as it has a planar equilibrium amide linkage corresponding to a single-minimum inversion potential around N. In contrast, several molecules containing the CONH linkage seem to have a pyramidalized nitrogen at equilibrium and a double-minimum inversion potential with a very small inversion barrier allowing for an effectively planar ground-state structure. Observables of rotational spectroscopy, including ground-state inertial defects, quadrupole coupling and centrifugal distortion constants, and dipole moment components, as well as equilibrium C=O and C-N bond lengths are reviewed in their ability to indicate the planarity of the effective and possibly the equilibrium structures.
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Affiliation(s)
- Jean Demaison
- Laboratoire de Physique des Lasers, Atomes et Molécules, UMR CNRS 8523, Université de Lille I, 59655 Villeneuve d'Ascq Cedex, France.
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Møllendal H, Leonov A, de Meijere A. A Microwave and Quantum Chemical Study of the Conformational Properties and Intramolecular Hydrogen Bonding of 1-Fluorocyclopropanecarboxylic Acid. J Phys Chem A 2005; 109:6344-50. [PMID: 16833977 DOI: 10.1021/jp050924e] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The structural and conformational properties of 1-fluorocyclopropanecarboxylic acid have been explored by microwave spectroscopy and a series of ab initio (MP2/6-311++G(d,p) level), density functional theory (B3LYP/aug-cc-pVTZ level), and G3 quantum chemical calculations. Four "stable" conformers, denoted conformers I-IV, were found in the quantum chemical calculations, three of which (conformers I -III) were predicted to be low-energy forms. Conformer I was in all the quantum chemical calculations predicted to have the lowest energy, conformer III to have the second lowest energy, and conformer II to have the third lowest energy. Conformers II and III were calculated to have relatively large dipole moments, while conformer I was predicted to have a small dipole moment. The microwave spectrum was investigated in the 18-62 GHz spectral range. The microwave spectra of conformers II and III were assigned. Conformer I was not assigned presumably because its dipole moment is comparatively small. Conformer II is stabilized by an intramolecular hydrogen bond formed between the fluorine atom and the hydrogen atom of the carboxylic acid group. Conformer III has a synperiplanar orientation for the F-C-C=O and H-O-C=O chains of atoms. Its dipole moment is: mua = 3.4(10), mub = 10.1(13), and muc = 0.0 (assumed) and mu(tot) = 10.6(14) x 10(-30) C m [3.2(4) D]. Several vibrationally excited states of the lowest torsional mode of each of II and III were also assigned. The hydrogen-bonded conformer II was found to be 2.7(2) kJ/mol less stable than III by relative intensity measurements. Absolute intensity measurements were used to show that the unassigned conformer I is the most abundant form present at a concentration of roughly 65% at room temperature. Conformer I was estimated to be ca. 5.0 kJ/mol more stable than the hydrogen-bonded rotamer (conformer II) and ca. 2.3 kJ/mol more stable than conformer III. The best agreement with the theoretical calculations is found in the MP2 calculations, which predict conformer I to be 5.1 kJ/mol more stable than III and 1.7 kJ/mol more stable than II.
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Affiliation(s)
- Harald Møllendal
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315 Oslo, Norway.
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Demaison J, Boggs JE, Rudolph H. Ab initio anharmonic force field and ab initio and experimental equilibrium structures of formyl chloride. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2003.10.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Møllendal H, Leonov A, de Meijere A. Intramolecular hydrogen bonding in (1-fluorocyclopropyl)methanol as studied by microwave spectroscopy and quantum chemical calculations. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2003.11.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Demyk K, Petitprez D, Demaison J, Møllendal H, Wlodarczak G. Rotational spectrum, hyperfine structure and structure of 2-azetidinone. Phys Chem Chem Phys 2003. [DOI: 10.1039/b307958a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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