351
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Rozas I, Alkorta I, Elguero J. Hydrogen bonds and ionic interactions in Guanidine/Guanidinium complexes: a computational case study. Struct Chem 2008. [DOI: 10.1007/s11224-008-9377-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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352
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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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353
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Conformer stabilization of N-(5,7-dinitro-8-quinolinyl)-N-(4-nitrophenyl)amine. MENDELEEV COMMUNICATIONS 2008. [DOI: 10.1016/j.mencom.2008.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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354
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Martins F, Camps I, Doriguetto A, dos Santos M, Ellena J, Barbosa L. Crystal Structure of Garciniaphenone and Evidences on the Relationship between Keto-Enol Tautomerism and Configuration. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890143] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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355
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Piccoli PMB, Koetzle TF, Schultz AJ, Zhurova EA, Stare J, Pinkerton AA, Eckert J, Hadzi D. Variable Temperature Neutron Diffraction and X-Ray Charge Density Studies of Tetraacetylethane. J Phys Chem A 2008; 112:6667-77. [DOI: 10.1021/jp800204r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paula M. B. Piccoli
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Thomas F. Koetzle
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Arthur J. Schultz
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Elizabeth A. Zhurova
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Jernej Stare
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - A. Alan Pinkerton
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Juergen Eckert
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Dusan Hadzi
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
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356
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Zinck P, Gérard JF. Polyepoxide–water interactions: Influence of the chemical structure of the network. Polym Degrad Stab 2008. [DOI: 10.1016/j.polymdegradstab.2007.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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357
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Fillaux F, Cousson A, Archilla JFR, Tomkinson J. A neutron scattering study of strong-symmetric hydrogen bonds in potassium and cesium hydrogen bistrifluoroacetates: Determination of the crystal structures and of the single-well potentials for protons. J Chem Phys 2008; 128:204502. [DOI: 10.1063/1.2927353] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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358
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Krygowski TM, Zachara-Horeglad JE, Palusiak M, Pelloni S, Lazzeretti P. Relation between pi-electron localization/delocalization and H-bond strength in derivatives of omicron-hydroxy-schiff bases. J Org Chem 2008; 73:2138-45. [PMID: 18303912 DOI: 10.1021/jo7023174] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed investigations of electronic effects taking place within the molecular system of o-hydroxy Schiff bases have been performed. The analysis of geometry, local and global aromaticity, selected AIM-based parameters, and finally, pi-electron currents induced in the systems under consideration have been performed on the basis of quantum chemical calculations at the B3LYP/6-311+G** level of theory. The relation between localization/delocalization of pi-electrons within the whole system has been described. It has been shown that the character of the bond which is common to the phenylic ring and the quasi-ring formed as a result of H-bond formation has a crucial impact on the strength of H-bonding. The strongest H-bonds can be observed for the systems in which the sequence of formally single and double bonds within the H-bridged quasi-ring enable a pi-electronic coupling. These observations indicate that pi-electron effects play a fundamental role in the stabilization of the hydrogen bridge within omicron-hydroxy Schiff bases. Analysis of pi-ring currents induced by a magnetic field perpendicular to the molecular plane of selected analyzed systems confirms these conclusions.
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Affiliation(s)
- Tadeusz M Krygowski
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
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359
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Chierotti MR, Gobetto R. Solid-state NMR studies of weak interactions in supramolecular systems. Chem Commun (Camb) 2008:1621-34. [PMID: 18368147 DOI: 10.1039/b711551b] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The field of application of solid-state NMR to the study of supramolecular systems is growing rapidly, with many research groups involved in the development of techniques for the study of crystalline and amorphous phases. This Feature Article aims to provide an overview of the recent contributions of our research group to this field, paying particular attention to the study of the weak interactions such as hydrogen bonds in supramolecular systems through solid-state NMR investigations. The structure and dynamic behaviour of selected host-guest systems will be also discussed.
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Affiliation(s)
- Michele R Chierotti
- Università degli Studi di Torino, Dipartimento di Chimica I.F.M, Via P. Giuria 7, 10125 Torino, Italy
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360
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Bertolasi V, Ferretti V, Gilli P, Yao X, Li CJ. Substituent effects on keto–enol tautomerization of β-diketones from X-ray structural data and DFT calculations. NEW J CHEM 2008. [DOI: 10.1039/b714708b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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361
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Grabowski SJ. Hydrogen bonds assisted by π-electron delocalization – the influence of external intermolecular interactions on dimer of formic acid. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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362
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Wolstenholme DJ, Weigand JJ, M Cameron E, Cameron TS. The progression of strong and weak hydrogen bonds in a series of ethylenediammonium dithiocyanate derivatives—a new bonding protocol for macromolecules? Phys Chem Chem Phys 2008; 10:3569-77. [PMID: 18548163 DOI: 10.1039/b800108a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- David J Wolstenholme
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4J3.
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363
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Larkin JD, Milkevitch M, Bhat KL, Markham GD, Brooks BR, Bock CW. Dimers of boroglycine and methylamine boronic acid: a computational comparison of the relative importance of dative versus hydrogen bonding. J Phys Chem A 2007; 112:125-33. [PMID: 18072757 DOI: 10.1021/jp076537h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Boronic acids are widely used in materials science, pharmacology, and the synthesis of biologically active compounds. In this Article, geometrical structures and relative energies of dimers of boroglycine, H2N-CH2-B(OH)2, and its constitutional isomer H3C-NH-B(OH)2, were computed using second-order Møller-Plesset perturbation theory and density functional theory; Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the MP2 calculations, and the Pople 6-311++G(d,p) basis set was employed for a majority of the DFT calculations. Effects of an aqueous environment were incorporated into the results using PCM and COSMO-RS methodology. The lowest-energy conformer of the H2N-CH2-B(OH)2 dimer was a six-membered ring structure (chair conformation; Ci symmetry) with two intermolecular B:N dative-bonds; it was 14.0 kcal/mol lower in energy at the MP2/aug-cc-pVDZ computational level than a conformer with the classic eight-centered ring structure (Ci symmetry) in which the boroglycine monomers are linked by a pair of H-O...H bonds. Compared to the results of MP2 calculations with correlation-consistent basis sets, DFT calculations using the PBE1PBE and TPSS functionals with the 6-311++G(d,p) basis set were significantly better at predicting relative conformational energies of the H2N-CH2-B(OH)2 and H3C-NH-B(OH)2 dimers than corresponding calculations using the BLYP, B3LYP, OLYP, and O3LYP functionals, particularly with respect to dative-bonded structures.
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Affiliation(s)
- Joseph D Larkin
- Department of Chemistry, Bloomsburg University of Pennsylvania, Bloomsburg, Pennsylvania 17815, USA. jlarkin@ bloomu.edu
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364
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Rodríguez-Cuamatzi P, Arillo-Flores OI, Bernal-Uruchurtu MI, Höpfl H. Experimental and Theoretical Analysis of the Hydrogen-bonding Motifs Formed Between the Carboxyl and the Carboxylate Group: Towards a Systematic Classification of their Supramolecular Motifs. Supramol Chem 2007. [DOI: 10.1080/10610270701474439] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- P. Rodríguez-Cuamatzi
- a Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, C.P. 62209, Cuernavaca, México
| | - O. I. Arillo-Flores
- a Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, C.P. 62209, Cuernavaca, México
| | - M. I. Bernal-Uruchurtu
- a Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, C.P. 62209, Cuernavaca, México
| | - H. Höpfl
- a Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, C.P. 62209, Cuernavaca, México
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365
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Rodríguez M, Santillan R, López Y, Farfán N, Barba V, Nakatani K, García Baéz EV, Padilla-Martínez II. N–H…O Assisted Structural Changes Induced on Ketoenamine Systems. Supramol Chem 2007. [DOI: 10.1080/10610270701534778] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- M. Rodríguez
- a Departamento de Química , Centro de Investigación y de Estudios Avanzados del IPN , México
| | - R. Santillan
- a Departamento de Química , Centro de Investigación y de Estudios Avanzados del IPN , México
| | - Y. López
- a Departamento de Química , Centro de Investigación y de Estudios Avanzados del IPN , México
| | - N. Farfán
- b Facultad de Quimica, Departamento de Quimica Orgánica , Universidad Nacional Autónoma de México , México D. F., 04510, México
| | - V. Barba
- c Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos , México
| | - K. Nakatani
- d Laboratoire de Photophysique et Photochimie Supramoléculaire et Macromoléculaire , Ecole Normale Supérieure de Cachan , France
| | - E. V. García Baéz
- e Departamento de Química , Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional , México
| | - I. I. Padilla-Martínez
- e Departamento de Química , Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional , México
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366
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Mariam YH, Musin RN. Transition from Moderate to Strong Hydrogen Bonds: Its Identification and Physical Bases in the Case of O−H···O Intramolecular Hydrogen Bonds. J Phys Chem A 2007; 112:134-45. [DOI: 10.1021/jp076668i] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yitbarek H. Mariam
- Department of Chemistry and Center for Theoretical Studies of Physical Systems, Clark Atlanta University, Atlanta, Georgia 30314
| | - Ryza N. Musin
- Department of Chemistry and Center for Theoretical Studies of Physical Systems, Clark Atlanta University, Atlanta, Georgia 30314
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367
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Ozen AS, Doruker P, Aviyente V. Effect of cooperative hydrogen bonding in azo-hydrazone tautomerism of azo dyes. J Phys Chem A 2007; 111:13506-14. [PMID: 18052263 DOI: 10.1021/jp0755645] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azo-hydrazone tautomerism in azo dyes has been modeled by using density functional theory (DFT) at the B3LYP/6-31+G(d,p) level of theory. The most stable tautomer was determined both for model compounds and for azo dyes Acid Orange 7 and Solvent Yellow 14. The effects of the sulfonate group substitution and the replacement of the phenyl group with naphthyl on the tautomer stability and on the behavior in solvent have been discussed. Intramolecular hydrogen bond energies have been estimated for the azo and hydrazone tautomers to derive a relationship between the tautomer stability and the hydrogen bond strength. The transition structures for proton transfer displayed resonance assisted strong hydrogen bonding properties within the framework of the electrostatic-covalent hydrogen bond model (ECHBM). Evolution of the intramolecular hydrogen bond with changing structural and environmental factors during the tautomeric conversion process has been studied extensively by means of the atoms-in-molecules (AIM) analysis of the electron density. The bulk solvent effect was examined using the self-consistent reaction field model. Special solute-solvent interactions were further investigated by means of quantum mechanical calculations after defining the first-solvation shell by molecular dynamics simulations. The effect of cooperative hydrogen bonding with solvent molecules on the tautomer stability has been discussed.
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Affiliation(s)
- Alimet Sema Ozen
- Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli, 34956 Tuzla, Istanbul, Turkey
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368
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The proton transfer reaction in malonaldehyde derivatives: Substituent effects and quasi-aromaticity of the proton bridge. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.09.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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369
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Sanz P, Mó O, Yáñez M, Elguero J. Non-resonance-assisted hydrogen bonding in hydroxymethylene and aminomethylene cyclobutanones and cyclobutenones and their nitrogen counterparts. Chemphyschem 2007; 8:1950-8. [PMID: 17676647 DOI: 10.1002/cphc.200700266] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The characteristics of intramolecular hydrogen bonds (IMHB) have been systematically analyzed for a series of 32 different enols of derivatives of cyclobutane, cyclobutene, and cyclobutadiene bearing oxygen and nitrogen functionalities, at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In those cases where two tautomers (interconnected by a hydrogen shift through the IMHB) exist, tautomer a, in which the HB-donor group (YH) is attached to the four-membered ring, is less stable than tautomer b, in which is the HB-acceptor (X) is the one attached to the four-membered ring. As expected the OH group behaves as a better HB-donor than the NH(2) group and the C==NH group as a better HB-acceptor than the C==O group, although the first effect clearly dominates. Accordingly, the expected IMHB strength follows the [donor, acceptor] trend: [OH,C==NH]>[OH,C==O]>[NH(2),C==NH]>[NH(2),C==O]. Quite unexpectedly, in all those compounds in which the functionality exhibiting the IMHB is unsaturated, the IMHB is weaker than in their saturated counterparts, verifying that the primary effect on the strength of the IMHB is the structure of the sigma-skeleton of the system. In the conjugated systems investigated here, the severe constraints imposed by the four-membered ring force the HB donor and acceptor to be far apart and the IMHB is rather weak. These geometrical constraints are less severe for the saturated analogues and the IMHB becomes stronger, confirming that the characteristics of the sigma-skeleton, and not the resonance-assisted hydrogen bond (RAHB) phenomenon, are the primary contributors to the strength of the IMHB in conjugated compounds.
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Affiliation(s)
- Pablo Sanz
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
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370
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Sevenard DV, Kazakova O, Lork E, Dülcks T, Chizhov DL, Röschenthaler GV. The structure of 4-phenyl-2,6-bis(trifluoroacetyl)cyclohexanone and its dilithium salt in the crystal state, solution and gas phase. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2007.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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371
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Bouchoux G. Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods. MASS SPECTROMETRY REVIEWS 2007; 26:775-835. [PMID: 17854059 DOI: 10.1002/mas.20151] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules.
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Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, 91120 Palaiseau, France.
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372
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Gilli P, Pretto L, Gilli G. PA/pKa equalization and the prediction of the hydrogen-bond strength: A synergism of classical thermodynamics and structural crystallography. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2007.05.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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373
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Do intramolecular halogen bonds exist? Ab initio calculations and crystal structures’ evidences. Struct Chem 2007. [DOI: 10.1007/s11224-007-9244-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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374
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Chan B, Del Bene JE, Radom L. Proton-Bound Homodimers: How Are the Binding Energies Related to Proton Affinities? J Am Chem Soc 2007; 129:12197-9. [PMID: 17877345 DOI: 10.1021/ja072690d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-level quantum chemical calculations [G3(MP2)-RAD//MP2/6-31+G(d,p)] have been employed to investigate the relationship between the binding energy (BE) of a substrate (X) and its protonated form [H-X]+ with the proton affinity (PA) of the substrate (X) in several series of protonated homodimers ([X...H-X]+). We find that for each series of closely related substrates, the binding energy (BE) is correlated with the proton affinity (PA) in an approximately quadratic manner. Thus, for a given series, the BE initially increases in magnitude with increasing PA, reaches a point of maximum binding, and then becomes smaller as the PA increases further. This behavior can be attributed to the competing effects of the exothermic partial protonation of the substrate and the endothermic partial deprotonation of the protonated substrate. As the PA increases, protonation of X contributes to increased binding but the penalty for partial deprotonation of [H-X]+ also increases. Once the PA becomes sufficiently high, the penalty for the partial deprotonation of [H-X]+ dominates, leading to maximum binding occurring at intermediate PA.
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Affiliation(s)
- Bun Chan
- School of Chemistry and Centre of Excellence in Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia.
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375
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Ln[(μ2-H)(H-mpdc)2](H-mpdc)2: Lanthanide infinite architectures with symmetric OHO hydrogen bonds (mpdc=2,6-dimethylpyridine-3,5-dicarboxylate). J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.11.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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376
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Do intramolecular halogen bonds exist? Ab initio calculations and crystal structures’ evidences. Struct Chem 2007. [DOI: 10.1007/s11224-007-9227-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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377
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Li ZJ, Abramov Y, Bordner J, Leonard J, Medek A, Trask AV. Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy. J Am Chem Soc 2007; 128:8199-210. [PMID: 16787084 DOI: 10.1021/ja0541332] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.
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Affiliation(s)
- Z Jane Li
- Pfizer Global Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, USA.
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378
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Woodford JN. Density Functional Theory and Atoms-in-Molecules Investigation of Intramolecular Hydrogen Bonding in Derivatives of Malonaldehyde and Implications for Resonance-Assisted Hydrogen Bonding. J Phys Chem A 2007; 111:8519-30. [PMID: 17683126 DOI: 10.1021/jp073098d] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A density functional theory (DFT) and atoms-in-molecules (AIM) analysis has been applied to the intramolecular hydrogen bonding in the enol conformers of malonaldehyde and its fluoro-, chloro-, cyano-, and nitro-substituted derivatives. With the B3LYP/6-311++G(2d,p) method, good agreement between the DFT geometries and published experimental structures has been found. The donor-acceptor distance was also varied in a series of constrained optimizations in order to determine if energetic, structural, and topological trends associated with intermolecular hydrogen bonding remain valid in the intramolecular case. At very short donor-acceptor distances (<2.24 A), the hydrogen is symmetrically located between donor and acceptor; at distances longer than this, the hydrogen bonding is no longer symmetric. The AIM methodology has been applied to explore the topology of the electron density in the intramolecular hydrogen bonds of the chosen model systems. Most AIM properties for intramolecular hydrogen bond distances longer than 2.24 A show smooth trends, consistent with intermolecular hydrogen bonds. Integrated AIM properties have also been used to explore the phenomenon of resonance-assisted hydrogen bonding (RAHB). It is shown that as the donor-acceptor distance is varied, pi-electron density is redistributed among the carbon atoms in the intramolecular hydrogen bond ring; however, contrary to prior studies, the integrated atomic charges on the donor-acceptor atoms were found to be insensitive to variation of hydrogen-bonding distance.
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Affiliation(s)
- Jeffrey N Woodford
- Department of Chemistry and Biochemistry, Eastern Oregon University, One University Boulevard, La Grande, Oregon 97850-2899, USA.
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379
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Grabowski SJ, Sokalski WA, Leszczynski J. Wide spectrum of H⋯H interactions: van der Waals contacts, dihydrogen bonds and covalency. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.042] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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380
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Grabowski SJ, Sokalski WA, Dyguda E, Leszczyński J. Quantitative classification of covalent and noncovalent H-bonds. J Phys Chem B 2007; 110:6444-6. [PMID: 16570938 DOI: 10.1021/jp0600817] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The covalent nature of interactions within various hydrogen bonded molecular aggregates has been characterized by the two entirely different computational methods: Bader analysis of the electron density and variation-perturbation partitioning of the intermolecular interaction energy. Analysis of 34 complexes representing different types of hydrogen bonds indicates that the proton-acceptor distance approximately 1.8 A and the ratio of delocalization and electrostatic terms approximately 0.45 constitutes approximately a borderline between covalent and noncovalent hydrogen bonds. The latter ratio could be used to characterize quantitatively the degree of the covalent nature of transition state interactions with active site residues, a quantity essential for an enzyme catalytic activity.
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381
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Parthasarathi R, Subramanian V, Sathyamurthy N. Hydrogen bonding without borders: an atoms-in-molecules perspective. J Phys Chem A 2007; 110:3349-51. [PMID: 16526611 DOI: 10.1021/jp060571z] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.
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382
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Dabbagh HA, Noroozi-Pesyan N, Najafi-Chermahini AR, Patrick BO, James BR. Diastereoselective formation of 18-membered ring BINOL-hydrogen phosphonate dimers - Quasi-covalent hydrogen bonds? CAN J CHEM 2007. [DOI: 10.1139/v07-060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diastereoselective syntheses of the unusual dimers, 4-heptyl-2-(2′-hydroxy-binaphthyl)hydrogen phosphonate (5) and the cyclohexyl analogue (7), are achieved by hydrolysis of 4-(3,5-dioxa-4-phosphacyclohepta[2,1-α;3,4-α′]-dinaphthalene-4-yloxy)heptane (4) and the cyclohexane analogue (6), respectively. Two out of eight possible pairs of monomers units are involved in the stereoselective formation of the dimer 5a of configuration BINOLR-PS:BINOLR-PS; this is determined by X-ray crystallographic data, which reveal a centrosymmetric, 18-membered ring structure with Ci symmetry, consisting of two monomers strongly hydrogen-bonded between the oxygen of P=O units and hydroxyl hydrogen atoms. Mass spectrometric, melting point, and thermal decomposition point data, as well as NMR data, support the presence of strong, quasi-covalent hydrogen bonds. Computational analysis suggests that the diastereoselectivity is controlled by molecularly constrained geometry of the monomer. Compound 7, although not characterized crystallographically, appears to be analogous to 5.Key words: 18-membered ring, phosphonate dimer, diastereoselectivity, hydrogen-bonds, computational analysis.
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383
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Collins KD, Neilson GW, Enderby JE. Ions in water: Characterizing the forces that control chemical processes and biological structure. Biophys Chem 2007; 128:95-104. [PMID: 17418479 DOI: 10.1016/j.bpc.2007.03.009] [Citation(s) in RCA: 433] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 03/09/2007] [Accepted: 03/10/2007] [Indexed: 11/29/2022]
Abstract
The continuum electrostatics model of Debye and Hückel [P. Debye and E. Hückel, On the theory of electrolytes. I. Freezing point depression and related phenomena., Phys. Z. 24 (1923) 185-206.] and its successors utilize a macroscopic dielectric constant and assume that all interactions involving ions are strictly electrostatic, implying that simple ions in water generate electric fields strong enough to orient water dipoles over long distances. However, solution neutron and X-ray diffraction indicate that even di- and tri-valent ions do not significantly alter the density or orientation of water more than two water molecules (5 A) away. Therefore the long range electric fields (generated by simple ions) which can be detected by various resonance techniques such as fluorescence resonance energy transfer over distances of 30 A (about 11 water diameters) or more must be weak relative to the strength of water-water interactions. Two different techniques indicate that the interaction of water with anions is by an approximately linear hydrogen bond, suggesting that the dominant forces on ions in water are short range forces of a chemical nature.
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Affiliation(s)
- Kim D Collins
- Center of Marine Biotechnology and Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201, USA.
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384
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Del Bene JE. Complexes with N-H(+)-P hydrogen bonds: structures, binding energies, and spin-spin coupling constants. J Phys Chem A 2007; 111:5509-14. [PMID: 17539616 DOI: 10.1021/jp0711491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab-initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of proton-bound complexes stabilized by N-H+-P hydrogen bonds and to investigate the nature of the proton-transfer coordinate in these systems. Double minima are found only when the difference between the protonation energies of the N and P bases is less than about 4 kcal/mol. The isomer in which the protonated nitrogen base is the donor lies lower on the potential surface and also has a greater binding energy relative to the corresponding isolated monomers. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been employed to obtain one- and two-bond spin-spin coupling constants across these hydrogen bonds. Two-bond coupling constants (2h)J(N-P) correlate with N-P distances, irrespective of whether the donor ion is N-H+ or P-H+. One-bond coupling constants (1)J(N-H) and (1h)J(H-P) for complexes stabilized by N-H+...P hydrogen bonds correlate with corresponding distances, but similar correlations are not found for (1)J(P-H) and (1h)J(H-N) for complexes with P-H+...N hydrogen bonds. Negative values of (1h)K(H-N) and (1h)K(H-P) indicate that the hydrogen bonds in these complexes are traditional. Comparisons are made with complexes stabilized by N-H+-N and P-H+-P hydrogen bonds.
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Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, OH 44555, USA.
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385
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Alía JM, Edwards HGM. Vibrational spectroscopic properties of hydrogen bonded acetonitrile studied by DFT. J Phys Chem A 2007; 109:7977-87. [PMID: 16834180 DOI: 10.1021/jp051892y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrational properties (band position, Infrared and Raman intensities) of the acetonitrile C[triple bond]N stretching mode were studied in 27 gas-phase medium intensity (length range: = 1.71-2.05 angstroms; -deltaE range = 13-48 kJ/mol) hydrogen-bonded 1:1 complexes of CH3CN with organic and inorganic acids using density functional theory (DFT) calculations [B3LYP-6-31++G(2d,2p)]. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in the OH stretching band of the acids were also considered. Experimentally observed blue-shifts of the C[triple bond]N stretching band promoted by the hydrogen bonding, which shortens the triple bond length, are very well reproduced and quantitatively depend on the hydrogen bond length. Both predicted enhancement of the infrared and Raman nu(C[triple bond]N) band intensities are in good agreement with the experimental results. Infrared band intensity increase is a direct function of the hydrogen bond energy. However, the predicted increase in the Raman band intensity increase is a more complex function, depending simultaneously on the characteristics of both the hydrogen bond (C[triple bond]N bond length) and the H-donating acid polarizability. Accounting for these two parameters, the calculated nu(C[triple bond]N) Raman intensities of the complexes are explained with a mean error of +/- 2.4%.
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Affiliation(s)
- Jose M Alía
- Departamento de Química-Física, E.U.I.T.A., Universidad de Castilla-La Mancha, Ronda de Calatrava 7, 13071 Ciudad Real, Spain.
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386
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Sanz P, Mó O, Yañez M, Elguero J. Resonance-assisted hydrogen bonds: a critical examination. Structure and stability of the enols of beta-diketones and beta-enaminones. J Phys Chem A 2007; 111:3585-91. [PMID: 17429952 DOI: 10.1021/jp067514q] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The characteristics of the intramolecular hydrogen bond (IMHB) for a series of 40 different enols of beta-diketones and their nitrogen counterparts have been systematically analyzed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In some cases, two tautomers may exist which are interconnected by a hydrogen shift through the IMHB. In tautomer a the HB donor group (YH) is attached to the six-membered ring, while in tautomer b the HB acceptor (X) is the one that is attached to the six-membered ring. We found that changing an O to a N favors the a tautomer when the atom is endo and the contrary when it is exo, while the presence of a double bond favors the a tautomers. As expected, the OH group behaves as a better HB donor than the NH2 group and the C=NH group as a better HB acceptor than the C=O group, although the first effect clearly dominates. Accordingly, the expected IMHB strength follows the [donor, acceptor] trend: [OH, C=NH] > [OH, C=O] > [NH2, C=NH] > [NH2, C=O]. For all those compounds in which the functionality exhibiting the IMHB is unsaturated (I-type), the IMHB is much stronger than in their saturated counterparts (II-type). However, when the systems of the II-type subset, which are saturated, are constrained to have the HB donor and the HB acceptor lying in the same plane and at the same distance as in the corresponding unsaturated analogue, the IMHB is of similar or even larger strength. Hence, we conclude that, at least for this series of unsaturated compounds, the resonance-assisted hydrogen bond effect is not the primary reason behind the strength of their IMHBs, which is simply a consequence of the structure of the sigma-skeleton of the system that keeps the HB donor and the HB acceptor coplanar and closer to each other.
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Affiliation(s)
- Pablo Sanz
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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387
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Zubatyuk RI, Volovenko YM, Shishkin OV, Gorb L, Leszczynski J. Aromaticity-controlled tautomerism and resonance-assisted hydrogen bonding in heterocyclic enaminone-iminoenol systems. J Org Chem 2007; 72:725-35. [PMID: 17253787 DOI: 10.1021/jo0616411] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The contribution of aromaticity and intramolecular hydrogen bonding to relative stability, for a set of (1H-azahetero-2-ylidene)-acetaldehyde and 2-azahetero-2-yl-ethanol tautomeric pairs, has been investigated by means of quantum chemical DFT and ab initio methods up to the MP4(SDTQ)/AUG-cc-pVDZ and MP2/AUG-cc-pVTZ levels of theory. It is found that the relative energy of the tautomers is governed by the change in the degree of heterocycle aromaticity upon intramolecular hydrogen transfer. An analysis of geometrical parameters of a hydrogen-bonded system reveals a clear relationship between the aromaticity of the heterocycle, the conjugation in a resonant spacer, and the strengths of the intramolecular hydrogen bonds. This allows the conclusion to be drawn that intramolecular N-H...O and O-H...N hydrogen bonds formed are found to be resonance-assisted and their strength is dependent on the pi-donating/accepting properties of the heterocycle. On the basis of the results of the calculations, a simple model describing the mechanism of resonance assistance of hydrogen bonding has been suggested.
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Affiliation(s)
- Roman I Zubatyuk
- STC "Institute for Single Crystals" NAS of Ukraine, 60 Lenina ave., Kharkiv, Ukraine
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388
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Grabowski SJ. Hydrogen Bonds with π and σ Electrons as the Multicenter Proton Acceptors: High Level ab Initio Calculations. J Phys Chem A 2007; 111:3387-93. [PMID: 17411022 DOI: 10.1021/jp070530i] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pi-electrons of acetylene and sigma-electrons of molecular hydrogen were investigated as Lewis bases in different complexes. Hence high level ab initio calculations were performed up to the MP2/6-311++G(3df,3pd) level of approximation. It was found that species analyzed possess characteristics typical for H-bonded systems. The Bader theory was additionally applied; bond paths between proton and pi-electrons of acetylene or sigma-electrons of molecular hydrogen were detected with the corresponding bond critical points attributed to the proton-acceptor interactions. Numerous correlations between topological, geometrical and energetic parameters were also found. For example, the H...pi or H...sigma interaction is stronger for the shorter corresponding distance between the proton and the middle of C[triple bond]C or H-H bond. It is connected with the greater elongation of C[triple bond]C or H-H bonds and the greater transfer of electron charge from the Lewis base to the Lewis acid.
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389
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Intramolecular NH⋯O resonance-assisted hydrogen bonds in crystal structures of oxaphosphinanes and chromones—DFT calculations and AIM analysis. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.07.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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390
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Simůnek P, Lusková L, Svobodová M, Bertolasi V, Lycka A, Machácek V. Synthesis and structure of some azo coupled cyclic beta-enaminones. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:330-9. [PMID: 17351971 DOI: 10.1002/mrc.1975] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The reaction of 3-phenylaminocyclopent-2-en-1-one with 4-methyl, 4-methoxy and 4-chlorobenzenediazonium tetrafluoroborates was used to prepare the azo coupling products 3a-c. It was found that these compounds are present in both CDCl(3) solution and solid phase practically exclusively as (E)-3-phenylamino-2-(4-subst.phenyldiazenyl)cyclopent-2-en-1-ones with N--H...N intramolecular hydrogen bond. The substitution of the phenyl residue of the diazonium salt has no effect on the position of the tautomeric equilibrium. On the other hand, the compounds 4a, b formed by the reaction of 3-phenylamino-1H-inden-1-one with 4-methylbenzene- or benzenediazonium tetrafluoroborates exist in CDCl(3) solution and in solid phase as hydrazone compounds. In the solution they occur as a mixture of three forms, out of which two were identified as E/Z isomers with different types of hydrogen bonds. Compound 5 formed by the reaction of 3-amino-5,5-dimethylcyclohex-2-en-1-one with 4-methoxybenzenediazonium tetrafluoroborate is converted into a stable hydrochloride 5.HCl on standing in CHCl(3) solution; this product exhibits a high degree of delocalization of the positive charge. Its structure was studied by means of X-ray.
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Affiliation(s)
- Petr Simůnek
- University of Pardubice, Department of Organic Chemistry, Pardubice, Czech Republic.
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391
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Overgaard J, Turel I, Hibbs DE. Experimental electron density study of a complex between copper(II) and the antibacterial quinolone family member ciprofloxacin. Dalton Trans 2007:2171-8. [PMID: 17514338 DOI: 10.1039/b700248c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An experimental charge density study of a 1 : 1 complex of Cu-cfx (cfx = ciprofloxacin), 1 [Cu(cfx)(H(2)O)(3)]SO4.2H(2)O, has been performed using single-crystal X-ray diffraction data collected at 100 K using conventional Mo Kalpha radiation. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the electron density with the atoms in molecules (AIM) approach. The copper atom binds to two oxygen atoms in one end of the zwitterionic form of the cfx molecule, in addition to forming bonds with three water molecules, forming a square pyramidal coordination geometry. AIM decomposition of the experimental electron density establishes that the copper atom binds more strongly to the cfx molecule than to the water molecules, suggesting that the latter can be detached leaving behind a reactive, water-free Cu-cfx complex available for interaction with e.g. a macromolecular site. AIM analysis of the extensive hydrogen bond pattern reveals that the positively charged N-end of the zwitterionic cfx forms a relatively strong N-H-O hydrogen bond implying that this region of cfx may play an important role in the docking process in the active site. Visualisation and statistics of selected density derived properties on the molecular surface of the isolated cfx molecule vs its metal complexed counterpart points out regions of potential reactivity. The effect of the fluorine atom is to expand the negative region of the electrostatic potential, while the nitrogen end is heavily electropositive and willingly donates to--for molecular docking purposes--relatively strong hydrogen bonding. The Cu atom is highlighted as a potentially highly reactive site which is likely to interact strongly with any given negative ligand.
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Affiliation(s)
- Jacob Overgaard
- Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000, Aarhus C..
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392
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Mammino L, Kabanda MM. Model structures for the study of acylated phloroglucinols and computational study of the caespitate molecule. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.10.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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393
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Savko M, Kaščáková S, Mojzeš P, Jancura D, Miškovský P, Uličný J. Ground and excited state properties of naphthazarin: Absorption spectroscopy and theoretical modeling study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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394
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Vener MV, Manaev AV, Egorova AN, Tsirelson VG. QTAIM study of strong H-bonds with the O-H...a fragment (A=O, N) in three-dimensional periodical crystals. J Phys Chem A 2007; 111:1155-62. [PMID: 17253671 DOI: 10.1021/jp067057d] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relationship between the d(H...A) distance (A=O, N) and the topological properties at the H...A bond critical point of 37 strong (short) hydrogen bonds occurring in 26 molecular crystals are analyzed using the quantum theory of atoms in molecules (QTAIM). Ground-state wave functions of the three-dimensional periodical structures representing the accurate experimental geometries calculated at the B3LYP/6-31G** level of approximation were used to obtain the QTAIM electron density characteristics. The use of an electron-correlated method allowed us to reach the quantitatively correct values of electron density rhob at the H...A bond critical point. However, quite significant differences can appear for small absolute values of the Laplacian (<0.5 au). The difference between the H...O and H...N interactions is described using the rhob versus d(H...A) dependence. It is demonstrated that the values of parameters in this dependence are defined by the nature of the heavy atom forming the H...A bond. An intermediate (or transit) region separating the shared and closed-shell interactions is observed for the H-bonded crystals in which the bridging proton can move from one heavy atom to another. The crystalline environment changes the location of the bridging proton in strong H-bonded systems; however, the d(O-H)/d(H...O) ratio is approximately the same for both the gas-phase complexes and molecular crystals with a linear or near-linear O-H...O bond.
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Affiliation(s)
- M V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, Moscow 125047, Russia
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395
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Chemical insight into electron density and wave functions: software developments and applications to crystals, molecular complexes and materials science. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0208-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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396
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Šimůnek P, Svobodová M, Bertolasi V, Pretto L, Lyčka A, Macháček V. Structure and tautomerism of azo coupling products from N-alkylenaminones derived from acetylacetone and benzoylacetone in solid phase and in solution. NEW J CHEM 2007. [DOI: 10.1039/b613346k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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397
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Rozas I. On the nature of hydrogen bonds: an overview on computational studies and a word about patterns. Phys Chem Chem Phys 2007; 9:2782-90. [PMID: 17538725 DOI: 10.1039/b618225a] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of hydrogen bond interactions (HB) is still today the subject of many discussions. We present an overview of computational methods and parameters (interaction energy, HB distance and radii, electron density topological parameters or orbital energies) required for an accurate description of HB systems. As well, we present the different correlations that have been found between these descriptors providing a global view of HB interactions. A synopsis of the different HBs reported in terms of their strength was presented. Considering the definitions of covalent and ionic bonds, HB interactions could occur between these two extremes. Thus, we look into some of the very strong HBs (LBHB, CAHB, RAHB) and some of the weak HBs (weak donors: C-H or weak acceptors: pi systems). Subsequently, aspects such as cooperativity or solvation are examined. Finally, we present a study on multiple "parallel" and "bifurcated" HB systems. Our results indicate that HB pattern and electron density determine the strength of the interaction and that "parallel" HB interactions are more stable than the "bifurcated" ones.
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Affiliation(s)
- Isabel Rozas
- Centre for Synthesis and Chemical Biology, School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
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398
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Despotović I, Kovačević B, Maksić ZB. Pyridine and s-triazine as building blocks of nonionic organic superbases—a density functional theory B3LYP study. NEW J CHEM 2007. [DOI: 10.1039/b617914b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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399
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Lankau T, Yu CH. The relationship between the bond length and the difference in proton affinities for the observation of heteronuclear low barrier hydrogen bonds. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.11.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Derossi S, Farrell DT, Harding CJ, McKee V, Nelson J. N-methylation of macrobicycles reduces encapsulation ability. Dalton Trans 2007:1762-72. [PMID: 17471371 DOI: 10.1039/b617907j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-methylation alters the conformation of octa-azacryptands leaving them unable to use all potential N-donors to coordinate copper(II) and anionic guests. This restriction, in the presence of other donors, normally results in exogenous coordination, with the exception of carbonate complexes, where two O-donors from the bridging anion along with three N-donors from the cryptand serve, in this series uniquely, to retain a pair of copper(II) ions within the "basket-shaped" cavity.
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Affiliation(s)
- Sofia Derossi
- Chemistry Department, Loughborough University, Loughborough, UKLE11 3TU
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