1
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Arandhara M, Ramesh SG. Nuclear quantum effects in gas-phase ethylene glycol. Phys Chem Chem Phys 2024; 26:19529-19542. [PMID: 38979630 DOI: 10.1039/d4cp00700j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Path integral molecular simulations are used to explore the nuclear quantum effects (NQEs) on the structure, dihedral landscape and infrared spectrum of ethylene glycol. The simulations are carried out on a new reaction surface Hamiltonian-based model potential energy surface, with special focus on the role of the OCCO and HOCC dihedrals. In contrast with classical simulations, we analyse how the intramolecular interactions between the OH groups change due to zero-point effects as well as temperature. These are found to be weak. The NQEs on the free energy profile along the OCCO dihedral are analysed, where notable effects are seen at low temperatures and found to be correlated with the radii of gyration of the atoms. Finally, the power spectrum of the molecule from path integral simulations is compared with the experimental infrared spectrum, yielding a good agreement of band positions.
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Affiliation(s)
- Mrinal Arandhara
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Sai G Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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2
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Lomas JS, Rosenberg RE. Cooperativity and intermolecular hydrogen bonding in donor‐acceptor complexes of phenol and polyhydroxybenzenes. J PHYS ORG CHEM 2023. [DOI: 10.1002/poc.4506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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3
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Akyeva AY, Kansuzyan AV, Vukich KS, Kuhn L, Saverina EA, Minyaev ME, Pechennikov VM, Egorov MP, Alabugin IV, Vorobyev SV, Syroeshkin MA. Remote Stereoelectronic Effects in Pyrrolidone- and Caprolactam-Substituted Phenols: Discrepancies in Antioxidant Properties Evaluated by Electrochemical Oxidation and H-Atom Transfer Reactivity. J Org Chem 2022; 87:5371-5384. [PMID: 35363496 DOI: 10.1021/acs.joc.2c00207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antioxidants are commonly evaluated via two main approaches, i.e., the ability to donate an electron and the ability to intercept free radicals. We compared these approaches by evaluating the properties of 11 compounds containing both antioxidant moieties (mono- and polyphenols) and auxiliary pharmacophores (pyrrolidone and caprolactam). Several common antioxidants, such as butylated hydroxytoluene (BHT), 2,3,5-trimethylphenol (TMP), quercetin, and dihydroquercetin, were added for comparison. The antioxidant properties of these compounds were determined by their rates of reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and their oxidation potentials from cyclic voltammetry. Although these methods test different chemical properties, their results correlate reasonably well. However, several exceptions exist where the two methods give opposite predictions! One of them is the different behavior of mono- and polyphenols: polyphenols can react with DPPH more than an order of magnitude faster than monophenols of a similar oxidation potential. The second exception stems from the size of a "bystander" lactam ring at the benzylic position. Although the phenols with a seven-membered lactam ring are harder to oxidize, the sterically nonhindered compounds react with DPPH about 2× faster than the analogous five-membered lactams. The limitations of computational methods, especially those based on a single parameter, are also evaluated and discussed.
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Affiliation(s)
- Anna Ya Akyeva
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia
| | | | - Katarina S Vukich
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia.,I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | | | | | | | - Mikhail P Egorov
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Stepan V Vorobyev
- Gubkin Russian State University of Oil and Gas, 65 Leninsky Prospect, 119991 Moscow, Russia
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4
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Bruckhuisen J, Dhont G, Roucou A, Jabri A, Bayoudh H, Tran TT, Goubet M, Martin-Drumel MA, Cuisset A. Intramolecular H-Bond Dynamics of Catechol Investigated by THz High-Resolution Spectroscopy of Its Low-Frequency Modes. Molecules 2021; 26:molecules26123645. [PMID: 34203730 PMCID: PMC8232127 DOI: 10.3390/molecules26123645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
Catechol is an oxygenated aromatic volatile organic compound and a biogenic precursor of secondary organic aerosols. Monitoring this compound in the gas phase is desirable due to its appreciable reactivity with tropospheric ozone. From a molecular point of view, this molecule is attractive since the two adjacent hydroxy groups can interchangeably act as donor and acceptor in an intramolecular hydrogen bonding due to the tunnelling between two symmetrically equivalent structures. Using synchrotron radiation, we recorded a rotationally-resolved Fourier Transform far-infrared (IR) spectrum of the torsional modes of the free and bonded -OH groups forming the intramolecular hydrogen bond. Additionally, the room temperature, pure rotational spectrum was measured in the 70–220 GHz frequency range using a millimeter-wave spectrometer. The assignment of these molecular transitions was assisted by anharmonic high-level quantum-chemical calculations. In particular, pure rotational lines belonging to the ground and the four lowest energy, vibrationally excited states were assigned. Splitting due to the tunnelling was resolved for the free -OH torsional state. A global fit combining the far-IR and millimeter-wave data provided the spectroscopic parameters of the low-energy far-IR modes, in particular those characterizing the intramolecular hydrogen bond dynamics.
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Affiliation(s)
- Jonas Bruckhuisen
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Guillaume Dhont
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Anthony Roucou
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Atef Jabri
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Hamdi Bayoudh
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Thi Thanh Tran
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Manuel Goubet
- UMR8523—PhLAM—Physique des Lasers Atomes et Molécules, Université de Lille, CNRS, F-59000 Lille, France;
| | | | - Arnaud Cuisset
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
- Correspondence:
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5
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Shangin PG, Krylova IV, Lalov AV, Kozmenkova AY, Saverina EA, Buikin PA, Korlyukov AA, Starikova AA, Nikolaevskaya EN, Egorov MP, Syroeshkin MA. Supramolecular D⋯A-layered structures based on germanium complexes with 2,3-dihydroxynaphthalene and N, N'-bidentate ligands. RSC Adv 2021; 11:21527-21536. [PMID: 35478811 PMCID: PMC9034134 DOI: 10.1039/d1ra02691g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/12/2021] [Indexed: 11/25/2022] Open
Abstract
The concept of using redox-active ligands, which has become extremely widespread in organometallic chemistry, is often considered from 'their effect on the metal center properties' point of view and 'how to modify the ligands'. In this paper, we present the reverse side of this effective approach - a dramatic change of redox properties of ligands under the influence of a redox-inert metal. Germanium derivatives based on 2,3-dihydroxynaphthalene (1) and N,N'-bidentate ligands, namely 2,2'-bipyridine (2) and 1,10-phenanthroline (3), were obtained and characterized by CV, UV-vis spectroscopy, DFT calculations and in the case of 3 X-ray diffraction. It was shown that the HOMO of the complexes is almost completely located on the naphthalene fragment while the LUMO is on the N,N-ligands. At the same time, there are no boundary molecular orbitals on the germanium atom, but it forms the axial part of the molecule holding two opposite motifs together. Moreover, it sharply affects the level of HOMO and LUMO. Derivatives 2 and 3 are more easily oxidized compared to 2,3-dihydroxynaphthalene by 0.31-0.34 V (7-8 kcal mol-1) and are more easily reduced compared to N,N-donors by 1.08-1.15 V (25-26.5 kcal mol-1). All this together makes it possible to form a system with a narrow HOMO/LUMO gap (∼2 eV). The crystal structure of 3 consists of alternating monomolecular easily oxidizing and easily reducing layers formed due to intermolecular interactions, in particular π-stacking. In addition, in contrast to 1 that starts to decompose noticeably at the temperatures from 200 °C, 2 and 3 have an extremely high thermal stability. They remain stable with no signs of decomposition and melting up to 400 °С. We believe that this approach to the formation of the supramolecular structure may present prospects for obtaining new functional materials.
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Affiliation(s)
- Pavel G Shangin
- N. D. Zelinsky Institute of Organic Chemistry 119991 Moscow Russia
| | - Irina V Krylova
- N. D. Zelinsky Institute of Organic Chemistry 119991 Moscow Russia
| | - Andrey V Lalov
- N. D. Zelinsky Institute of Organic Chemistry 119991 Moscow Russia
| | | | | | - Petr A Buikin
- A. N. Nesmeyanov Institute of Organoelement Compounds 119991 Moscow Russia
| | | | - Alyona A Starikova
- Institute of Physical and Organic Chemistry, Southern Federal University 344090 Rostov-on-Don Russia
| | | | - Mikhail P Egorov
- N. D. Zelinsky Institute of Organic Chemistry 119991 Moscow Russia
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I-Ting T, Montero-Campillo MM, Alkorta I, Elguero J, Yáñez M. Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives. Molecules 2021; 26:molecules26113401. [PMID: 34199746 PMCID: PMC8199991 DOI: 10.3390/molecules26113401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol−1 are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.
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Affiliation(s)
- Tsai I-Ting
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain;
| | - M. Merced Montero-Campillo
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain;
- Correspondence: (M.M.M.-C.); (I.A.); (M.Y.)
| | - Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain;
- Correspondence: (M.M.M.-C.); (I.A.); (M.Y.)
| | - José Elguero
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain;
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain;
- Correspondence: (M.M.M.-C.); (I.A.); (M.Y.)
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7
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Pandey SK, Arunan E. Effects of Multiple OH/SH Substitution on the H‐Bonding/Stability versus Aromaticity of Benzene Rings: From Computational Insights. ChemistrySelect 2021. [DOI: 10.1002/slct.202100689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarvesh Kumar Pandey
- Department of Inorganic and Physical Chemistry Indian Institute of Science Bangalore Bangalore 560 012 India
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur 208 016 India
| | - Elangannan Arunan
- Department of Inorganic and Physical Chemistry Indian Institute of Science Bangalore Bangalore 560 012 India
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8
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Lomas JS, Rosenberg RE, Brémond E. Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:957-968. [PMID: 32529717 DOI: 10.1002/mrc.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/06/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O-H⋯O-H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O-H⋯O-H bond paths, and an inner ring of bond paths, due to C-H⋯H-C hydrogen-hydrogen bonding, which result in a central ring critical point. The topological O-H⋯O-H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C-H⋯H-C hydrogen-hydrogen bonds can be as low as -0.4 kcal mol-1 .
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Affiliation(s)
- John S Lomas
- ITODYS, CNRS, Université de Paris, Paris, France
| | | | - Eric Brémond
- ITODYS, CNRS, Université de Paris, Paris, France
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9
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Lomas JS. Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H … OH and C─H … OH bonding interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:666-684. [PMID: 32201981 DOI: 10.1002/mrc.5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Université de Paris, Paris, France
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10
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Abstract
For 2-X-ethanols, where X = F, OH, or NH2, the gauche conformer is favored over the trans conformer by at least 2 kcal/mol. Initially, this preference, ΔE, was attributed to an intramolecular hydrogen bond, IMHB, between the OH and X groups. Over the years, this conclusion has been challenged by two major arguments. One claim is that the entirety of ΔE can be accounted for by the gauche effect. Against this, calculations using five different methods show that the maximum contribution of the gauche effect to ΔE is less than 1 kcal/mol. A second argument employs the quantum theory of atoms in molecules to contend that the absence of a bond critical point (BCP) between the OH and X groups in 2-X-ethanols denotes the lack of an IMHB. By looking at the 2-X-ethanols at fixed XCCO torsional angles ranging from 0° to 60°, it is shown that the BCP criterion is inconsistent with other properties such as energy, bond lengths, and stretching frequencies. These inconsistencies are removed when the theory of noncovalent interactions is used. The IMHBs in 2-X-ethanols are found to be similar in form but smaller in magnitude than their intermolecular counterparts. This work concludes that 2-X-ethanols form IMHBs.
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Affiliation(s)
- Robert E Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky 40508, United States
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11
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Wang J, Shao L, Yan P, Liu C, Liu X, Zhang XM. Are solvent effects important for intramolecular C—H···O
−
hydrogen bonding interactions? J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jinhu Wang
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Linjun Shao
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals ProcessShaoxing University Shaoxing China
| | - Peng Yan
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Chunli Liu
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Xuejing Liu
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Xian M. Zhang
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
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Jadżyn J, Swiergiel J. The viscous consequence of different trends in clustering of 1,2-diol and 1,n-diol molecules. Phys Chem Chem Phys 2018; 20:21640-21646. [PMID: 30101265 DOI: 10.1039/c8cp03687j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents the molecular basis for the quite different behavior of the viscosity of 1,2- and 1,n-diols in dependence of the length of the alkyl part of the molecules of these compounds. The experimental data on the dipolar orientational effects revealed a decidedly different role of that part of the molecules in creating a microstructure of both the hydrogen-bonded liquids. In the case of 1,n-diols, an increase in the alkyl radical length, i.e. an increasing of the distance between the OH groups within the molecule, highly stimulates molecular self-assembly in form of gradually longer and wider ribbon-like clusters. This effect yields a quite important increase in the viscosity of 1,n-diols as n increases. In the case of 1,2-diols, due to gradual separation of the hydrophilic and hydrophobic parts of the molecules, the situation is quite different. Two OH groups situated on one of the ends of the hydrocarbon radical form the clusters of a micelle-like shape, however, the dipole moment is not compensated. Along with an increase in the hydrocarbon part in 1,2-diol molecules, one only observes an increase in the intermolecular consolidation within the micelle-like entities. This manifests as a gradual decrease in the polarity of these clusters. So, actually, there are no relevant reasons for essential differences of viscosities in the series of 1,2-diols.
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Affiliation(s)
- Jan Jadżyn
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, PL-60-179 Poznań, Poland.
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13
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Cesari L, Canabady-Rochelle L, Mutelet F. Computational study of phenolic compounds-water clusters. Struct Chem 2018. [DOI: 10.1007/s11224-018-1081-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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de Lange JH, van Niekerk DME, Cukrowski I. FALDI-based decomposition of an atomic interaction line leads to 3D representation of the multicenter nature of interactions. J Comput Chem 2018; 39:973-985. [DOI: 10.1002/jcc.25175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/07/2017] [Accepted: 01/14/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Jurgens H. de Lange
- Department of Chemistry; Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road; Hatfield Pretoria 0002 South Africa
| | - Daniel M. E. van Niekerk
- Department of Chemistry; Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road; Hatfield Pretoria 0002 South Africa
| | - Ignacy Cukrowski
- Department of Chemistry; Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road; Hatfield Pretoria 0002 South Africa
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15
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16
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Cesari L, Canabady-Rochelle L, Mutelet F. Computational study on the molecular conformations of phenolic compounds. Struct Chem 2017. [DOI: 10.1007/s11224-017-1017-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Pandey SK, Manogaran D, Manogaran S, Schaefer HF. Quantification of Hydrogen Bond Strength Based on Interaction Coordinates: A New Approach. J Phys Chem A 2017; 121:6090-6103. [DOI: 10.1021/acs.jpca.7b04752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dhivya Manogaran
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Sadasivam Manogaran
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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18
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Jaiyong P, Bryce RA. Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet. Phys Chem Chem Phys 2017; 19:15346-15355. [DOI: 10.1039/c7cp02160g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adsorption of carbohydrates on graphene has the potential to improve graphene dispersibility in water. Here we assess the ability of DFTB-based and NDDO-based quantum chemical methods to model β-cyclodextrin conformations and interactions with graphene.
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Affiliation(s)
- Panichakorn Jaiyong
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
| | - Richard A. Bryce
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
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19
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Kumar Deb D, Sarkar B. Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule. Phys Chem Chem Phys 2017; 19:2466-2478. [DOI: 10.1039/c6cp08442g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study of the interaction energies and hydrogen bonding interaction of a gas-phase molecular complex between 2-hydroxy thiophenol and a water molecule.
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Affiliation(s)
- Debojit Kumar Deb
- Department of Chemistry
- Centre for Advanced Studies
- North-Eastern Hill University
- Shillong 793022
- India
| | - Biplab Sarkar
- Department of Chemistry
- Centre for Advanced Studies
- North-Eastern Hill University
- Shillong 793022
- India
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Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
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21
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Lomas JS, Joubert L, Maurel F. Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1 H NMR chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:805-814. [PMID: 27247256 DOI: 10.1002/mrc.4457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- John S Lomas
- ITODYS (UMR 7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, France
| | - François Maurel
- ITODYS (UMR 7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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22
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Impact of deformation energy on the hydrogen bonding interactions in gas phase 3-X catechol⋯H2O complexes (X = H, F, Cl, Br): The effect of approach of a water molecule. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Schrøder SD, Wallberg JH, Kroll JA, Maroun Z, Vaida V, Kjaergaard HG. Intramolecular Hydrogen Bonding in Methyl Lactate. J Phys Chem A 2015; 119:9692-702. [DOI: 10.1021/acs.jpca.5b04812] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sidsel D. Schrøder
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jens H. Wallberg
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jay A. Kroll
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Cooperative Institute for Research in Environmental Sciences, Boulder, Colorado 80309, United States
| | - Zeina Maroun
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Veronica Vaida
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Cooperative Institute for Research in Environmental Sciences, Boulder, Colorado 80309, United States
| | - Henrik G. Kjaergaard
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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24
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Das P, Das PK, Arunan E. Conformational stability and intramolecular hydrogen bonding in 1,2-ethanediol and 1,4-butanediol. J Phys Chem A 2015; 119:3710-20. [PMID: 25839224 DOI: 10.1021/jp512686s] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The gas-phase infrared spectra of 1,2-ED and 1,4-BD have been recorded at three different temperatures using a multipass gas cell of 6 m optical path length. DFT calculation has also been carried out using 6-311++G** and aug-cc-pVDZ basis sets to look for the existence of intramolecular hydrogen bonding in them from the red shift and infrared absorption intensity enhancement of the bonded O-H band compared to that of the free O-H band. Equilibrium population analysis with 10 conformers of 1,2-ED and 1,4-BD at experimental temperatures were carried out for the reconstruction of the observed vibrational spectra at that temperature using standard statistical relationships. The most abundant conformer at experimental temperatures was identified. In 1,2-ED a red shift of 45 cm(-1) in the intramolecularly interacting O-H stretching vibrational band position and no significant intensity enhancement compared to that of the free O-H have been observed. On the contrary, in one of the hydrogen-bonded conformers of 1,4-BD, a 124 cm(-1) red shift in the O-H stretching frequency and a 8.5 times intensity enhancement for the "bonded" O-H compared to that of the "free" O-H is seen. On the basis of this comparative study, we have concluded that strong intramolecular hydrogen bonding exists in 1,4-BD. But there appears to be weak intramolecular hydrogen bonding in 1,2-ED at temperatures of 303, 313, and 323 K in the gas phase. We have found that most stable hydrogen-bonded conformers of 1,4-BD are less populated than some of the non-hydrogen-bonded conformers. Even for the 1,4-BD, the relative population of the g'GG'Gt conformer, which has a strong intramolecular hydrogen bond, is less than what is predicted. Perhaps the intramolecular hydrogen bond plays a less significant role in the relative stability of the various conformers than what has been predicted from calculations and prevails in the literature.
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Affiliation(s)
- Prasanta Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Puspendu K Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - E Arunan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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25
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Cukrowski I, de Lange JH, Adeyinka AS, Mangondo P. Evaluating common QTAIM and NCI interpretations of the electron density concentration through IQA interaction energies and 1D cross-sections of the electron and deformation density distributions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Arunan E, Mani D. Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond. Faraday Discuss 2015; 177:51-64. [DOI: 10.1039/c4fd00167b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this discussion, we show that a static definition of a ‘bond’ is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan,Phys. Chem. Chem. Phys.2009,11, 8974) which showed a practical way to differentiate ‘hydrogen bonding’ from ‘van der Waals interaction’. We report results fromab initioand atoms in molecules theoretical calculations for a series of Rg⋯HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg⋯HX/DX complexes show that Rg⋯DX could have a ‘deuterium bond’ even when Rg⋯HX is not ‘hydrogen bonded’, according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an ‘intra-molecular hydrogen bond’ can appear during a normal mode vibration which is dominated by the O⋯O stretching, though a ‘bond’ is not found in the equilibrium structure. This dynamical ‘bond’ formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration ‘breaks’ an existing bond and in the later case, a vibration leads to ‘bond’ formation. In both cases, the molecule/complex stays bound irrespective of what happens to this ‘hydrogen bond’. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunanet al. Pure. Appl. Chem.2011,831637) and justify the inclusive nature of the definition.
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Affiliation(s)
- Elangannan Arunan
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore
- India 560012
| | - Devendra Mani
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore
- India 560012
- Department of Physical Chemistry II
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27
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Nagy PI. Competing intramolecular vs. intermolecular hydrogen bonds in solution. Int J Mol Sci 2014; 15:19562-633. [PMID: 25353178 PMCID: PMC4264129 DOI: 10.3390/ijms151119562] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/17/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, the University of Toledo, Toledo, OH 43606-3390, USA.
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28
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Butler M, Mañez PA, Cabrera GM, Maître P. Gas phase structure and reactivity of doubly charged microhydrated calcium(II)-catechol complexes probed by infrared spectroscopy. J Phys Chem A 2014; 118:4942-54. [PMID: 24963704 DOI: 10.1021/jp503789j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Doubly charged microhydrated adducts formed from catechol and calcium(II) were produced in the gas phase using electrospray ionization (ESI) appearing as the most important ions in the mass spectra recorded. The gas phase structures of [Ca(catechol)2(H2O)](2+) and [Ca(catechol)2(H2O)2](2+) have been assayed by IR multiphoton dissociation (IRMPD) spectroscopy, recording their vibrational spectra in the 3450-3750 cm(-1) range (OH stretching region) and in the 900-1700 cm(-1) fingerprint spectral region. The agreement between experimental and calculated IR spectra of the selected cluster ions confirmed the suitability of the proposed geometries. In addition, quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were performed for [Ca(catechol)2(H2O)](2+) to gain insight into the major routes of dissociation. The results suggest that loss of the water molecule is the lowest energy fragmentation channel followed by charge separation products and neutral loss of one catechol molecule, in agreement with the product ions observed upon collision-induced dissociation (CID).
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Affiliation(s)
- Matias Butler
- Departamento de Química Orgánica, UMyMFOR-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pabellón II, 3° piso, C1428EHA, Buenos Aires, Argentina
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Chen Y, Ozaki Y, Czarnecki MA. Molecular structure and hydrogen bonding in pure liquid ethylene glycol and ethylene glycol-water mixtures studied using NIR spectroscopy. Phys Chem Chem Phys 2014; 15:18694-701. [PMID: 24071663 DOI: 10.1039/c3cp52146j] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The molecular structure and hydrogen bonding of ethylene glycol (EG) and EG-water mixtures in the liquid phase were studied by using near-infrared (NIR) spectroscopy. The spectra were evaluated using a two-dimensional (2D) correlation approach, moving-window 2D correlation analysis and chemometric methods. The minor changes for the CH stretching bands indicate that the structures of pure liquid EG and EG-water mixtures are determined by the intermolecular hydrogen bonding through the OH groups. The analysis of the ν2 + ν3 combination band of water reveals that in EG-rich solutions the molecules of water are predominantly bonded with two molecules of EG and this cooperative hydrogen bonding is stronger than that in bulk water. Further increase in the water content leads to formation of small water clusters around OH groups of EG. Comparing results for the binary mixtures of water with different organic solvents one can conclude that the total amount and distribution of the polar groups are the most important factors determining the solubility of water in the organic phase. The distribution of these groups depends on the length and structure of the hydrocarbon chain. Due to high population and relatively uniform distribution of the OH groups of EG water has unlimited solubility in liquid EG.
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Affiliation(s)
- Yujing Chen
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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30
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Mackeprang K, Schrøder SD, Kjaergaard HG. Weak intramolecular OH⋯π hydrogen bonding in methallyl- and allyl-carbinol. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lane JR, Contreras-García J, Piquemal JP, Miller BJ, Kjaergaard HG. Are Bond Critical Points Really Critical for Hydrogen Bonding? J Chem Theory Comput 2013; 9:3263-6. [PMID: 26584086 DOI: 10.1021/ct400420r] [Citation(s) in RCA: 344] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph R. Lane
- Department of Chemistry, University
of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Julia Contreras-García
- UPMC Univ Paris 06, UMR 7616
CNRS, Laboratoire de Chimie Théorique, Case Courrier 137, 4
Place Jussieu, F-75005, Paris, France
| | - Jean-Philip Piquemal
- UPMC Univ Paris 06, UMR 7616
CNRS, Laboratoire de Chimie Théorique, Case Courrier 137, 4
Place Jussieu, F-75005, Paris, France
| | - Benjamin J. Miller
- Department of Chemistry, University
of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Henrik G. Kjaergaard
- Department of Chemistry, University
of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Oliveira BGD. Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H−δ⋯H+δdihydrogen bonds. Phys Chem Chem Phys 2013; 15:37-79. [DOI: 10.1039/c2cp41749a] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Nagy PI. Theoretical studies of the solvent effect on the conformation of the HO-C-C-X (X = F, NH2, NO2) moiety with competing intra- and intermolecular hydrogen bonds. J Phys Chem A 2012; 116:7726-41. [PMID: 22731938 DOI: 10.1021/jp304164g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Theoretical calculations up to the ab initio IEF-PCM/CCSD(T)/CBS//IEF-PCM/B3LYP/6-311++G** and IEF-PCM/B97D/aug-cc-pvtz levels have been performed for 2X-ethanol and 2X-phenol systems with X = F, NH(2), NO(2) in chloroform and aqueous solution. The calculated relative free energies by means of the IEF-PCM continuum dielectric method do not differ very much at the DFT and ab initio levels. Application of explicit solvent models and the FEP/MC method for determining relative solvation free energies causes, however, large deviations in the predicted equilibrium compositions, although the predominant conformation for the solute is generally in agreement with that from the corresponding IEF-PCM calculations. Existence of an intramolecular hydrogen bond (HB structure) for species with the HO-C-C-X moiety is preferred compared with a conformation when the hydrogen bond is disrupted (NoHB) for the considered F- and NO(2)-substituted molecules both in chloroform and aqueous solution. For 2NH(2)-ethanol, the HB structure is predominant in chloroform, whereas the 93:7 ratio for the OCCN trans/gauche species was obtained in aqueous solution. 2NH(2)-phenol exhibits a subtle equilibrium of the HB and NoHB conformations in both solvents. Potential of mean force calculations predict about a 10% solute association for the trans 2NH(2)-ethanol solute even in the fairly dilute 0.22 molar solution, whereas direct MC simulations do not support the maintenance of a doubly hydrogen-bonded dimer. Aqueous solution characteristics, as coordination numbers and numbers of strongly bound water molecules to the solute at T = 298 K and p = 1 atm, correspond reasonably to the derived molecular structures.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, USA.
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Varfolomeev MA, Klimovitskii AE, Abaidullina DI, Madzhidov TI, Solomonov BN. "Additive" cooperativity of hydrogen bonds in complexes of catechol with proton acceptors in the gas phase: FTIR spectroscopy and quantum chemical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 91:75-82. [PMID: 22366617 DOI: 10.1016/j.saa.2012.01.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 05/31/2023]
Abstract
Experimental study of hydrogen bond cooperativity in hetero-complexes in the gas phase was carried out by IR-spectroscopy method. Stretching vibration frequencies of O-H groups in phenol and catechol molecules as well as of their complexes with nitriles and ethers were determined in the gas phase using a specially designed cell. O-H groups experimental frequency shifts in the complexes of catechol induced by the formation of intermolecular hydrogen bonds are significantly higher than in the complexes of phenol due to the hydrogen bond cooperativity. It was shown that the cooperativity factors of hydrogen bonds in the complexes of catechol with nitriles and ethers in the gas phase are approximately the same. Quantum chemical calculations of the studied systems have been performed using density functional theory (DFT) methods. It was shown, that theoretically obtained cooperativity factors of hydrogen bonds in the complexes of catechol with proton acceptors are in good agreement with experimental values. Cooperative effects lead to a strengthening of intermolecular hydrogen bonds in the complexes of catechol on about 30%, despite the significant difference in the proton acceptor ability of the bases. The analysis within quantum theory of atoms in molecules was carried out for the explanation of this fact.
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Affiliation(s)
- Mikhail A Varfolomeev
- Department of Physical Chemistry, Chemical Institute, Kazan (Volga region) Federal University, Kremlevskaya 18, 420008 Kazan, Russia.
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Jabłoński M. Energetic and Geometrical Evidence of Nonbonding Character of Some Intramolecular Halogen···Oxygen and Other Y···Y Interactions. J Phys Chem A 2012; 116:3753-64. [DOI: 10.1021/jp300993b] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Mirosl̷aw Jabłoński
- Department of Quantum Chemistry, Nicolaus Copernicus University, 7-Gagarina
Street, PL-87 100 Toruń, Poland
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Dávalos JZ, Herrero R, Chana A, Guerrero A, Jiménez P, Santiuste JM. Energetics and structural properties, in the gas phase, of trans-hydroxycinnamic acids. J Phys Chem A 2012; 116:2261-7. [PMID: 22316076 DOI: 10.1021/jp2090439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have studied the energetics and structural properties of trans-cinnamic acid (CA), o-, m-, and p-coumaric acids (2-, 3-, and 4-hydroxycinnamic acids), caffeic acid (3,4-dihydroxycinnamic acid), ferulic acid (4-hydroxy-3-methoxycinnamic acid), iso-ferulic acid (3-hydroxy-4-methoxycinnamic acid), and sinapic acid (3,5-dimethoxy-4-hydroxycinnamic acid). The experimental values of Δ(f)H(m)°(g), determined (in kJ·mol(-1)) for CA (-229.8 ± 1.9), p-coumaric acid (-408.0 ± 4.4), caffeic acid (-580.0 ± 5.9), and ferulic acid (-566.4 ± 5.7), allowed us to derive Δ(f)H(m)°(g) of o-coumaric acid (-405.6 ± 4.4), m-coumaric acid (-406.4 ± 4.4), iso-ferulic acid (-565.2 ± 5.7), and sinapic acid (-698.8 ± 4.1). From these values and by use of isodesmic/homodesmotic reactions, we studied the energetic effects of π-donor substituents (-OH and -OCH(3)) in cinnamic acid derivatives and in the respective benzene analogues. Our results indicate that the interaction between -OCH(3) and/or -OH groups in hydroxycinnamic acids takes place without significant influence of the propenoic fragment.
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Affiliation(s)
- Juan Z Dávalos
- Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain.
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Rodnikova MN, Solovei AB, Solonina IA. Structure of crystalline ethylene glycol and a model of its structural rearrangement during melting. RUSS J INORG CHEM+ 2012. [DOI: 10.1134/s0036023612020222] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Woldu AS, Mai J. Computation of the bond dissociation enthalpies and free energies of hydroxylic antioxidants using the ab initio Hartree-Fock method. Redox Rep 2012; 17:252-74. [PMID: 23339861 PMCID: PMC6837695 DOI: 10.1179/1351000212y.0000000030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION A new method for calculating theoretical bond dissociation enthalpy (BDE) and bond dissociation free energy (BDFE) of hydroxylic antioxidants is forwarded. BDE and BDFE may be understood as activation energies accompanying the formation of transition states, which may undergo downhill homolytic dissociation. The new method does not involve the complete fission of O-H bonds. METHOD Theoretical gas phase BDE values were calculated with the ab initio unrestricted Hartree-Fock (UHF) method, as changes in enthalpy between ground singlet states (GS) and triplet dissociative states (DS). Similarly, gas phase BDFEs were estimated from the corresponding changes in Gibbs free energy. The results were then compared with reliable experimental reports. RESULTS The proposed theoretical approach of BDE and BDFE determination was tested using 10 simple phenols, 5 flavonoids, and l-ascorbic acid derivatives. The agreement between our calculated gas phase results and the adopted experimental values were generally within 0.5 kcal mol(-1), with a very few exceptions. DISCUSSION Generally, steric interactions as well as intramolecular hydrogen bonding involving the dissociating OH group should be minimized in the GS. The DS are both electronically and vibrationally exited transition states. They have one unpaired electron on the carbon atom, which bears the homolytically dissociating OH group and are second order saddle points with a fixed CONCLUSION It was concluded that ab initio UHF was well suited for the estimation of gas phase BDE and BDFE. The method presented has a good potential for application across a range of hydroxylic antioxidants. Currently, work is underway to extend its application in other class of antioxidants.
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Affiliation(s)
- Ameha Seyoum Woldu
- Department of Pharmaceutical Chemistry and Pharmacognosy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
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Lomas JS, Maurel F, Adenier A. 1
H NMR study of the hetero-association of non-symmetrical diols with pyridine; GIAO/DFT calculations on diols. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1831] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Lomas JS. 1H NMR study of through-bond and through-space effects in the hetero-association of pyridine with alkane diols. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1716] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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41
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Chopra D, Guru Row TN, Arunan E, Klein RA. Crystalline ethane-1,2-diol does not have intra-molecular hydrogen bonding: Experimental and theoretical charge density studies. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.11.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gómez-Zaleta B, Gómez-Balderas R, Hernández-Trujillo J. Theoretical analysis of hydrogen bonding in catechol–n(H2O) clusters (n = 0…3). Phys Chem Chem Phys 2010; 12:4783-90. [DOI: 10.1039/b922203k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Alagona G, Ghio C, Nagy PI. The catalytic effect of water on the keto–enol tautomerism. Pyruvate and acetylacetone: a computational challenge. Phys Chem Chem Phys 2010; 12:10173-88. [DOI: 10.1039/c003999c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Estévez L, Otero N, Mosquera RA. Computational Study on the Stacking Interaction in Catechol Complexes. J Phys Chem A 2009; 113:11051-8. [DOI: 10.1021/jp906045f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Estévez
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
| | - Nicolás Otero
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
| | - Ricardo A. Mosquera
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
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Estévez L, Mosquera RA. Conformational and Substitution Effects on the Electron Distribution in a Series of Anthocyanidins. J Phys Chem A 2009; 113:9908-19. [DOI: 10.1021/jp904298z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Estévez
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
| | - Ricardo A. Mosquera
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
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Lomas JS, Cordier C. Diols as hydrogen bond acids:1H NMR study of the hetero-association of pyridine with sterically hindered EDOT diols. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1467] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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47
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Estévez L, Mosquera RA. Molecular structure and antioxidant properties of delphinidin. J Phys Chem A 2008; 112:10614-23. [PMID: 18821739 DOI: 10.1021/jp8043237] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory calculations were performed to evaluate the antioxidant activity of delphinidin, taking into account its acid/base equilibrium. The conformational behavior of both the isolated and the aqueous solvation species (simulated with the polarizable continuum model) were analyzed at the B3LYP/6-31++G(d,p) level, considering the cationic, neutral, and anionic forms, the latter two forms consisting of diverse tautomers. The analysis of their electron density distributions, using the quantum theory of atoms in molecules, reveals several facts that are not in line with their usual Lewis structures. The prototropic preferences observed in the gas phase and in solution are similar. Thus, in both phases, most stable tautomer of neutral delphinidin is obtained by deprotonating the hydroxyl at C4', and the most stable tautomer of the anion is obtained by deprotonating the hydroxyls at C4' and C5. All the planar conformers obtained display an intramolecular hydrogen bond (IHB) between O3 and H6'. Furthermore, the most stable tautomers of the neutral and anionic forms display two IHBs between O4' and H3' and H5'. To obtain ionization potentials (IPs) and homolytic O-H bond dissociation enthalpies (BDEs), the corresponding radical species were optimized at the UB3LYP level. Heterolytic O-H bond dissociation enthalpies (proton dissociation enthalpies, PDEs) were also computed. The expected important antioxidant activity can be justified from these results. IP, O-H BDE, and O-H PDE values suggest that one-step H atom transfer rather than sequential proton loss-electron transfer or electron transfer-proton transfer would be the most favored mechanisms for explaining the antioxidant activity of delphinidin in nonpolar solvents as well as in aqueous solution.
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Affiliation(s)
- Laura Estévez
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
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Lenain P, Mandado M, Mosquera RA, Bultinck P. Interplay Between Hydrogen Bond Formation and Multicenter π-Electron Delocalization: Intermolecular Hydrogen Bonds. J Phys Chem A 2008; 112:7898-904. [DOI: 10.1021/jp804346y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pieterjan Lenain
- Department of Physical Chemistry, University of Vigo, As Lagoas (Marcosende) sn, 36310 Vigo, Galicia, Spain, and Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium
| | - Marcos Mandado
- Department of Physical Chemistry, University of Vigo, As Lagoas (Marcosende) sn, 36310 Vigo, Galicia, Spain, and Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium
| | - Ricardo A. Mosquera
- Department of Physical Chemistry, University of Vigo, As Lagoas (Marcosende) sn, 36310 Vigo, Galicia, Spain, and Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium
| | - Patrick Bultinck
- Department of Physical Chemistry, University of Vigo, As Lagoas (Marcosende) sn, 36310 Vigo, Galicia, Spain, and Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium
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Rychlewska U, Waścinska N, Warżajtis B, Gawroński J. Role of the gauche effect and local 1,3-dipole–dipole interactions in stabilizing an unusual conformation of tartarodinitriles. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2008; 64:497-503. [DOI: 10.1107/s0108768108018272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 06/16/2008] [Indexed: 11/10/2022]
Abstract
This paper reports the synthesis, X-ray and NMR investigations of chiral and meso dinitriles of tartaric acid (tartarodinitriles) and their O,O′-diacetyl and O,O′-dibenzoyl derivatives. While in chiral tartaric acid its esters and NH amides the four-atom carbon chain is overwhelmingly trans, it is gauche in chiral tartarodinitriles. Conversely, meso-tartaric acid, its esters and amides display a tendency for the gauche conformation, but meso-tartarodinitriles usually have the trans conformation. The NMR studies of tartarodinitriles reveal the presence of a conformational equilibrium in solution with a preference for those conformers found in crystals. The gauche conformation of meso-tartarodinitriles seems to be stabilized by local dipolar interactions, intramolecular C—H...O hydrogen bonds and by a tendency for maximization of the gauche effect, the latter effect also operating in chiral tartarodinitriles. Stabilization of the trans conformers of tartarodinitriles in the crystals seems to originate from specific intermolecular interactions.
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Vila A, Mosquera RA. Atoms in molecules interpretation of the anomeric effect in the OCO unit. J Comput Chem 2007; 28:1516-1530. [PMID: 17330885 DOI: 10.1002/jcc.20585] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The conformational preferences of two model compounds for the O--CH2--O anomeric unit: methanediol and dimethoxymethane analyzed within the framework of the QTAIM theory provide a new interpretation of the anomeric effect. The characteristic stabilization of the gauche conformers of these compounds is accompanied by a progressive reduction of the electron population of the hydrogens of the central methylene as the number of their gauche interactions to lone pairs rises. The electron population removed from these atoms during the conformational change is gained in the gauche conformers by atoms of larger atomic number, which results in a more negative molecular energy. Also, the variations displayed by atomic populations and the QTAIM delocalization indexes are not keeping in line with the hyperconjugative model of the anomeric effect.
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Affiliation(s)
- Antonio Vila
- Departamento de Química Física, Universidade de Vigo, Facultade de Química, 36310-Vigo, Galicia, Spain
| | - Ricardo A Mosquera
- Departamento de Química Física, Universidade de Vigo, Facultade de Química, 36310-Vigo, Galicia, Spain
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