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Oliveira BG, Araújo RCMU. Bonding topology, hydrogen bond strength, and vibrational chemical shifts on hetero-ring hydrogen-bonded complexes — Theoretical insights revisited. CAN J CHEM 2012. [DOI: 10.1139/v2012-009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This work presents a theoretical study about the interaction strength of the hydrogen-bonded complexes C2H4O···HF, C3H6O···HF, C2H4O···HCF3, and C3H6O···HCF3 at the B3LYP/6–311++G(d,p) level. The structures, hydrogen bond energies, charge transfers, and dipole moments of these complexes were analyzed in accordance with routine spectroscopy events, such as the red- and blue-shifts on the stretch frequencies of the proton donors (HF and HCF3). The ChelpG atomic charges were used to quantify the charge-transfer fluxes from electron donor (O) towards to acceptors (HF or HCF3). Moreover, the topological calculations on the basis of the quantum theory of atoms in molecules (QTAIM) approach were also used to unveil the hydrogen bond strength (O···H), mainly in the determination of their electronic densities and Laplacian shapes.
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Affiliation(s)
- Boaz G. Oliveira
- Instituto de Ciências Ambientais e Desenvolvimento Sustentável, Universidade Federal da Bahia, 47801-100, Barreiras – BA, Brazil
| | - Regiane C. M. U. Araújo
- Departamento de Química, Universidade Federal da Paraíba. 58059-900, João Pessoa, PB – Brazil
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52
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McDowell SAC, Volney GS. A comparative computational study of FKrCCH...Y, FCCKrH...Y, and FCCH...Y complexes (Y = BF, CO, N2, OH2, OH(CH3), O(CH3)2). J Chem Phys 2012; 136:124306. [PMID: 22462856 DOI: 10.1063/1.3696966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structural and spectroscopic changes in complexes of FCCKrH...Y and FKrCCH...Y (Y = BF, CO, N(2), OH(2), OH(CH(3)), O(CH(3))(2)) were computed at the MP2∕6-31++G(d,p) level of theory and compared with the corresponding properties for FCCH...Y. The computed bond length changes and frequency shifts on complexation were rationalized by comparing with a perturbation model, which gives quantitative agreement with the standard ab initio results. A recently proposed model also gives a reasonable qualitative account of the observed trends in these complexes.
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Affiliation(s)
- Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Barbados.
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53
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McDowell SAC, St Hill JAS. A theoretical study of hydrogen- and lithium-bonded complexes of F-H∕Li and Cl-H∕Li with NF3, NH3, and NH2(CH3). J Chem Phys 2012; 135:164303. [PMID: 22047235 DOI: 10.1063/1.3653476] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Hydrogen- and lithium-bonded complexes of A-H∕Li (A = F, Cl) with the amine analogues NF(3), NH(3), and NH(2)(CH(3)) were studied at the MP2∕6-311++G(d,p) level of theory. Bond extensions and redshifts were obtained for the H-bonded complexes, while bond extensions and blueshifts were obtained for the Li-bonded species. The variation of these and other properties with the basicity of the amines was investigated and rationalized by comparing the ab initio results with predictions from a model derived from perturbation theory.
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Affiliation(s)
- Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Barbados, West Indies.
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54
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Inagaki S, Murai H, Takeuchi T. Theory of electron localization and its application to blue-shifting hydrogen bonds. Phys Chem Chem Phys 2012; 14:2008-14. [DOI: 10.1039/c2cp23047j] [Citation(s) in RCA: 10] [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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55
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McDowell SAC, Yarde HK. Cooperative effects of hydrogen, lithium and halogen bonding on F–H/Li⋯OH2 complexes. Phys Chem Chem Phys 2012; 14:6883-8. [DOI: 10.1039/c2cp40203c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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56
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Oliveira BG, Araújo RCMU. Theoretical aspects of binary and ternary complexes of aziridine···ammonia ruled by hydrogen bond strength. J Mol Model 2011; 18:2845-54. [PMID: 22127607 DOI: 10.1007/s00894-011-1300-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/02/2011] [Indexed: 11/27/2022]
Abstract
B3LYP calculations, ChelpG atomic charges, and quantum theory of atoms in molecules (QTAIM) integrations were used to investigate the binary (1:1) and ternary (1:2) hydrogen-bonded complexes formed by aziridine (1) and ammonia (2). In a series of analysis, geometry data, electronic parameters, vibrational oscillators, and topological descriptors were used to evaluate hydrogen bond strength, and additionally to determine the more prominent molecular deformations upon the formation of C(2)H(5)N···NH(3) (1:1) and C(2)H(5)N···2NH(3) (1:2) systems. Taking a spectroscopic viewpoint, results obtained from analysis of the harmonic infrared spectrum were examined. From these, new vibrational modes and red- and blue-shifts related to the stretch frequencies of either donors or acceptors of protons were identified. Furthermore, the molecular topology of the electronic density modeled in accord with QTAIM was absolutely critical in defining bond critical points (BCP) and ring critical points (RCP) on the heterocyclic structures. Taking all the results together allowed us to identify and characterize all the N···H hydrogen bonds, as well as the strain ring of the aziridine and its stability.
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Affiliation(s)
- Boaz G Oliveira
- Instituto de Ciências Ambientais e Desenvolvimento Sustentável, Universidade Federal da Bahia, Barreiras, Brazil.
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57
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58
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Zierkiewicz W, Czarnik-Matusewicz B, Michalska D. Blue Shifts and Unusual Intensity Changes in the Infrared Spectra of the Enflurane···Acetone Complexes: Spectroscopic and Theoretical Studies. J Phys Chem A 2011; 115:11362-8. [PMID: 21913646 DOI: 10.1021/jp205081r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | | | - Danuta Michalska
- Faculty of Chemistry, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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59
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60
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McDowell SAC, Buckingham AD. Cooperative hydrogen bonding in trimers involving HCN and HBO. Phys Chem Chem Phys 2011; 13:14097-100. [DOI: 10.1039/c1cp20660e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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61
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Liu X, Xu Y. Infrared and microwave spectra of the acetylene–ammonia and carbonyl sulfide–ammonia complexes: a comparative study of a weak C–H⋯N hydrogen bond and an S⋯N bond. Phys Chem Chem Phys 2011; 13:14235-42. [DOI: 10.1039/c1cp21554j] [Citation(s) in RCA: 15] [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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62
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Karpfen A. Blue-shifted A–H stretching frequencies in complexes with methanol: the decisive role of intramolecular coupling. Phys Chem Chem Phys 2011; 13:14194-201. [DOI: 10.1039/c1cp20607a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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63
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Keefe CD, Istvankova Z. Computational study of proper and improper hydrogen bonding in methanol complexes. CAN J CHEM 2011. [DOI: 10.1139/v10-155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The bulk properties of alcohols, like those of aqueous solutions, are governed mostly by hydrogen bonding; however, in contrast with water molecules, the chemical structure of a simple alcohol such as methanol offers an opportunity to explore the effects of both proper and improper hydrogen bonding on a single hydrogen donor. The presence of the hydroxyl group generally gives rise to a strong proper hydrogen bond, while the methyl group of methanol is likely involved in the weaker improper hydrogen bond, among other weak non-covalent interactions. The effects of the two types of hydrogen bonds on the stability, geometric parameters, and properties of electron density of methanol complexes are examined while considering different geometrical arrangements of the methanol dimer and the binary complexes of methanol with water, acetonitrile, and chloromethane. Subsequently, potential conclusions about the nature of improper hydrogen bonding and the origin of the C–H bond contraction that results upon complex formation are discussed. Quantum theory of atoms in molecules and natural bond orbital methods were used in the analysis; all calculations were performed at the MP2(full)/6-311++G(d,p) level of theory.
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Affiliation(s)
- C. Dale Keefe
- Department of Chemistry, Cape Breton University, Sydney, NS B1P 6L2, Canada
| | - Zuzana Istvankova
- Department of Chemistry, Cape Breton University, Sydney, NS B1P 6L2, Canada
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64
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Iuga C, Alvarez-Idaboy JR, Vivier-Bunge A. Single water-molecule catalysis in the glyoxal+OH reaction under tropospheric conditions: Fact or fiction? A quantum chemistry and pseudo-second order computational kinetic study. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.043] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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65
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Selvam L, Chen F, Wang F. Solvent effects on blue shifted improper hydrogen bond of C–H⋯O in deoxycytidine isomers. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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66
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Cao LJ, Li AY, Ji HB, Xu L, Zhang Y. Theoretical study on the ring stretching modes of pyridine in the hydrogen bonding with H2O, HCONH2 and CH3COOH. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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67
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McDowell SAC, Marcellin RC. A comparative computational study of hydrogen and lithium-bonded complexes. J Chem Phys 2010; 133:144307. [DOI: 10.1063/1.3494601] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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68
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Ramasami P, Ford TA. Ab initio studies of the vibrational spectra of some hydrogen-bonded complexes of fluoroacetylene. CAN J CHEM 2010. [DOI: 10.1139/v10-028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio molecular orbital theory has been used to compute the properties of a number of hydrogen-bonded complexes between fluoroacetylene as proton donor and ammonia, water, hydrogen fluoride, phosphine, hydrogen sulfide, and hydrogen chloride as proton acceptors. The properties considered were the vibrational spectra, the molecular structures, the hydrogen-bond energies, and the electron densities, and one of the aims of the study was to ascertain whether there was any evidence of blue-shifting hydrogen-bond character in the complexes formed. The adducts with NH3, H2O, PH3, and H2S were of the conventional CH···X kind (X = N, O, P, S), with hydrogen-bond energies decreasing in the order NH3 > H2O > PH3 ≈ H2S. Those formed with HF and HCl showed the presence of three alternative structures; in addition to the CH···F(Cl) complexes, adducts of the F(Cl)H···F and F(Cl)H···π type were also found to be stationary points on the potential energy surfaces, with stabilities in the order F(Cl)H···π > CH···F(Cl) > F(Cl)H···F. The hydrogen-bond energies of the CH···X series correlated with the gas-phase basicities of the proton acceptors; moreover, the CH bond-length changes, the wavenumber shifts, the complex–monomer infrared intensity ratios of the CH stretching modes, and the amounts of charge transferred on complex formation were all found to track with the hydrogen-bond energies. All those properties considered here are consistent with the formation of red-shifting hydrogen bonds, to the exclusion of the blue-shifting alternatives.
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Affiliation(s)
- Ponnadurai Ramasami
- Department of Chemistry, University of Mauritius, Réduit, Mauritius
- Centre for Theoretical and Computational Chemistry, School of Chemistry, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
| | - Thomas A. Ford
- Department of Chemistry, University of Mauritius, Réduit, Mauritius
- Centre for Theoretical and Computational Chemistry, School of Chemistry, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
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69
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van der Veken B, Delanoye S, Michielsen B, Herrebout W. A cryospectroscopic study of the blue-shifting C–H⋯O bonded complexes of pentafluoroethane with dimethyl ether-d6, acetone-d6 and oxirane-d4. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.02.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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70
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Cooperativity of multiple H-bonds in influencing structural and spectroscopic features of the peptide unit of proteins. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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71
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Chen F, Selvam L, Wang F. Blue shifted intramolecular C−H···O improper hydrogen bonds in conformers of zidovudine. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.05.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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72
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Ravinder P, Subramanian V. Substitution Effects of Diborane on the Interaction with Borazine (Inorganic Benzene). J Phys Chem A 2010; 114:5565-72. [DOI: 10.1021/jp910717j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- P. Ravinder
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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73
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Karpfen A, Kryachko ES. The dimers of glyoxal and acrolein with H2O and HF: Negative intramolecular coupling and blue-shifted C–H stretch. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.02.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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74
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Mukhopadhyay A, Pandey P, Chakraborty T. Blue- and Red-Shifting CH···O Hydrogen Bonded Complexes between Haloforms and Ethers: Correlation of Donor νC−H Spectral Shifts with C−O−C Angular Strain of the Acceptors. J Phys Chem A 2010; 114:5026-33. [PMID: 20334425 DOI: 10.1021/jp100524q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anamika Mukhopadhyay
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prasenjit Pandey
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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75
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Crystal structure, energy band and optical properties of benzoic acid —2-amino-4,6-dimethylpyrimidine (1:1) co-crystals. J STRUCT CHEM+ 2010. [DOI: 10.1007/s10947-010-0008-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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76
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McDowell SAC, Buckingham AD. Cooperative and diminutive hydrogen bonding in Y⋯HCN⋯HCN and NCH⋯Y⋯HCN trimers (Y=BF,CO,N2). J Chem Phys 2010; 132:064303. [PMID: 20151739 DOI: 10.1063/1.3297894] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, P.O. Box 64, Bridgetown, Barbados.
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77
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McDowell SAC. Halogen and hydrogen bonding to the Br atom in complexes of FBr. J Chem Phys 2010; 132:044312. [DOI: 10.1063/1.3300099] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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78
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DFT prediction of anomalously large blue shift of the C–H stretching frequency in 2-vinyloxypyridine and -quinoline due to the intramolecular C–H···N hydrogen bonding. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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79
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Shirhatti PR, Wategaonkar S. Blue shifted hydrogen bond in 3-methylindole·CHX3 complexes (X = Cl, F). Phys Chem Chem Phys 2010; 12:6650-9. [DOI: 10.1039/b924288k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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80
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Samanta AK, Pandey P, Bandyopadhyay B, Chakraborty T. Cooperative Strengthening of an Intramolecular O—H···O Hydrogen Bond by a Weak C—H···O Counterpart: Matrix-Isolation Infrared Spectroscopy and Quantum Chemical Studies on 3-Methyl-1,2-cyclohexanedione. J Phys Chem A 2009; 114:1650-6. [DOI: 10.1021/jp907881b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amit K. Samanta
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prasenjit Pandey
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Bandyopadhyay
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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81
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Jabłoński M, Palusiak M. Divalent carbon atom as the proton acceptor in hydrogen bonding. Phys Chem Chem Phys 2009; 11:5711-9. [PMID: 19842489 DOI: 10.1039/b901968e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proton-accepting properties of the divalent carbon atom in carbodiphosphoranes and their simple derivatives as well as in carbenes have been investigated. Both these groups of chemical compounds may be characterized by the formula CL2, where L is a sigma electron donor. Therefore, the carbon atom within both these systems, being in its atomic state, can have one or two lone electron pairs and, as a result, it may form hydrogen bonds of the type D-H...CL2, where C acts as a proton acceptor. Complexes of C(NH3)2, C(PH3)2, C[P(CH3)3]2, CF2, CCl2, and imidazol-2-ylidene with such proton donors as H2O, HCF3, HCN and HCCH have been analyzed by means of high-level quantum chemical methods. Density functional theory (DFT) and second-order Møller-Plesset (MP2) approaches have been applied in conjunction with the aug-cc-pVTZ basis set. The electron density distribution calculated by means of the atoms in the molecules procedure has also been analyzed. Proton-accepting properties of the carbon atom are discussed in detail. It is shown that the divalent carbon atom in the group of chemical systems investigated should be treated as a normal proton acceptor, similar to the much more electronegative O or N atoms. Moreover, hydrogen bonds of the type D-H...CL2 within the complexes investigated have been found to be rather strong. The highest proton accepting ability of the carbon(0) atom found for the (NH3)2C derivative of carbodiphosphorane is explained on the basis of the Leffler-Hammond postulate. Within the group of carbenes, the strongest hydrogen bonds are formed by imidazol-2-ylidene. This is attributed to the significant aromatic character of the imidazol-2-ylidene ring that increases the proton-accepting properties of the carbene carbon atom.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Toruń, Poland.
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82
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Scheiner S. Identification of spectroscopic patterns of CH...O H-bonds in proteins. J Phys Chem B 2009; 113:10421-7. [PMID: 19575539 DOI: 10.1021/jp9035138] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ab initio calculations are used to identify characteristics of vibrational and NMR spectra that signal the involvement of a protein backbone in a CH...O H-bond and that distinguish this sort of interaction from other H-bonds in which a protein might participate. Glycine and alanine dipeptides, in both their C7 and C5 minimum-energy structures, are paired with formamide in a number of different H-bonding arrangements. The CH...O H-bond is characterized by a small contraction of the C-H bond length, along with a blue shift in its stretching frequency, accompanied by an intensification of this vibrational band. In the context of NMR spectra, the bridging CH proton's chemical shift is moved downfield by 1-2 ppm. The aforementioned features are not produced by other H-bonds in which the protein backbone might participate, such as NH proton donation or accepting a proton via the peptide C=O.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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83
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Golubev NS, Denisov GS, Macholl S, Smirnov SN, Shenderovich IG, Tolstoy PM. NMR Study of Blue-Shifting Hydrogen Bonds Formed by Fluoroform in Solution. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.2008.5385] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Low-temperature (193 K) 1H, 13C and 15N NMR spectra of blue- and red-shifting H-bonded complexes formed by fluoroform with various proton acceptors were measured. Experimental NMR parameters were plotted versus the ab initio calculated H-bond strength (MP2/6–31+G(d, p); interaction energy varies from ~5 up to 25 kJ · mol−1 in the series). We show that experimental 1H and 15N shieldings, as well as the H/D isotope effect on 13C shielding change monotonously with the calculated H-bond strengthening. The 13C chemical shift and the CH scalar coupling change non-monotonously and the extremum points are situated approximately in the region of transformation from blue- to red-shifting H-bonds. The most informative NMR feature is the H/D isotope effect on 15N shielding which changes its sign upon transformation from blue- to red-shifting H-bonds.
To rationalize these observations, ab initio calculations of 13C and 15N shieldings as functions of C···H and C···N distances were performed for complexes of CHF3 with acetonitrile (blue-shifting) and pyridine (red-shifting). The coupling of the vibrations of the covalent and hydrogen bonds has been accounted for by direct computation of the distance C···N = f(C···H) dependence. We demonstrate that the unusual sign of the H/D isotope effect on 15N chemical shift across a blue-shifting H-bond can be explained as a result of the inversion of the dynamic coupling of two vibrations.
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Affiliation(s)
- Nicolai S. Golubev
- St. Petersburg State University, Inst. of Physics, St. Petersburg, Russische Föderation
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84
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Mirkin NG, Krimm S. Conformation dependence of the C(alpha)D(alpha) stretch mode in peptides. II. explicitly hydrated alanine peptide structures. Biopolymers 2009; 91:791-800. [PMID: 19425050 DOI: 10.1002/bip.21250] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Our previous studies of the potential utility of the C(alpha)D(alpha) stretch frequency, nu(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923-10924; 2007, 111, 5300-5303) dealt with the spectroscopic characteristics of isolated alanine peptides with alpha(R), beta, and polyproline II structures. We have now extended these ab initio calculations to include various explicit-water environments interacting with such conformers. We find that the structure-discriminating feature of this technique is in fact enhanced as a result of the conformation-specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C(alpha)--D(alpha)...O(water) hydrogen bonds can be present in addition to those expected between water and the CO and NH of the peptide groups. In fact, nu(CD) is hardly affected by the latter bonding but can be shifted by up to 70 cm(-1) by the former hydrogen bonds. We also discuss the factors that will have to be considered in developing the molecular dynamics (MD) treatment needed to satisfactorily take account of the influence of outer water layers on the structure of the first-layer water molecules that hydrogen bond to the peptide backbone.
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Affiliation(s)
- Noemi G Mirkin
- LSA Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA
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85
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Solimannejad M, Massahi S, Alkorta I. A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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86
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A theoretical study of red-shifting and blue-shifting hydrogen bonds occurring between imidazolidine derivatives and PEG/PVP polymers. J Mol Model 2009; 16:119-27. [PMID: 19517145 DOI: 10.1007/s00894-009-0525-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
A theoretical study is presented with the aim to investigate the molecular properties of intermolecular complexes formed by the monomeric units of polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) polymers and a set of four imidazolidine (hydantoine) derivatives. The substitution of the carbonyl groups for thiocarbonyl in the hydantoin scaffold was taken into account when analyzing the effect of the hydrogen bonds on imidazolidine derivatives. B3LYP/6-31G(d,p) calculations and topological integrations derived from the quantum theory of atoms in molecules (QTAIM) were applied with the purpose of examining the N-H···O hydrogen bond strengths formed between the amide group of the hydantoine ring and the oxygen atoms of PVP and PEG polymers. The effects caused by the N-H···O interaction fit the typical evidence for hydrogen bonds, which includes a variation in the stretch frequencies of the N-H bonds. These frequencies were identified as being vibrational red-shifts because their values decreased. Although the values of such calculated interaction energies are between 12 and 33 kJ mol(-1), secondary intermolecular interactions were also identified. One of these secondary interactions is formed through the interaction of the benzyl hydrogen atoms with the oxygen atoms of the PVP and PEG structures. As such, we have analyzed the stretch frequencies on the C-H bonds of the benzyl groups, and blue-shifts were identified on these bonds. In this sense, the intermolecular systems formed by hydantoine derivatives and PVP/PEG monomers were characterized as a mix of red-shifting and blue-shifting hydrogen-bonded complexes.
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87
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Chen C, Li W, Song Y, Yang J. Molecular dynamics simulation studies of cryoprotective agent solutions: the relation between melting temperature and the ratio of hydrogen bonding acceptor to donor number. Mol Phys 2009. [DOI: 10.1080/00268970902852632] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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88
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Karpfen A, Kryachko ES. On the Intramolecular Origin of the Blue Shift of A−H Stretching Frequencies: Triatomic Hydrides HAX. J Phys Chem A 2009; 113:5217-23. [DOI: 10.1021/jp9005923] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alfred Karpfen
- Institute for Theoretical Chemistry, University of Vienna, Währinger Straβe 17, A-1090 Vienna, Austria, and Bogolyubov Institute for Theoretical Physics, Kiev-143, 03680 Ukraine
| | - Eugene S. Kryachko
- Institute for Theoretical Chemistry, University of Vienna, Währinger Straβe 17, A-1090 Vienna, Austria, and Bogolyubov Institute for Theoretical Physics, Kiev-143, 03680 Ukraine
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89
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Mirkin NG, Krimm S. Peptide C(alpha)D(alpha) stretch frequencies in a hydrated conformation are perturbed mainly by C(alpha)-D(alpha)...O hydrogen bonding. J Phys Chem B 2009; 112:15267-8. [PMID: 18975891 DOI: 10.1021/jp808515t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have shown (J. Phys. Chem. A 2004, 108, 10923; 2007, 111, 5300) that the C(alpha)D(alpha) stretch frequency, nu(CD), can discriminate between uniform alpha(R), beta, and polyproline II conformations of isolated peptides. Similar results for such peptides to which explicit waters are hydrogen bonded exhibit shifts in nu(CD) from those of the isolated structures. We demonstrate that the main source of these frequency shifts is the formation of C(alpha)-D(alpha)...O hydrogen bonds to water. Taking into account C-H...O(water) hydrogen bonding, together with the traditional bonding of peptide groups to water, can be expected to increase our understanding of the interaction of proteins with their aqueous environment.
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Affiliation(s)
- Noemi G Mirkin
- LSA Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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90
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Mukhopadhyay A, Mukherjee M, Pandey P, Samanta AK, Bandyopadhyay B, Chakraborty T. Blue Shifting C−H···O Hydrogen Bonded Complexes between Chloroform and Small Cyclic Ketones: Ring-Size Effects on Stability and Spectral Shifts. J Phys Chem A 2009; 113:3078-87. [DOI: 10.1021/jp900473w] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anamika Mukhopadhyay
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Moitrayee Mukherjee
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prasenjit Pandey
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Amit K. Samanta
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Bandyopadhyay
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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91
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Keefe CD, Gillis EAL, MacDonald L. Improper Hydrogen-Bonding CH·Y Interactions in Binary Methanol Systems As Studied by FTIR and Raman Spectroscopy. J Phys Chem A 2009; 113:2544-50. [DOI: 10.1021/jp8092034] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- C. Dale Keefe
- Department of Chemistry, Cape Breton University, Sydney, Nova Scotia, Canada, B1Y 6L2
| | | | - Lisa MacDonald
- Department of Chemistry, Cape Breton University, Sydney, Nova Scotia, Canada, B1Y 6L2
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92
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Sánchez-González I, Rodríguez-Casado A, Careche M, Carmona P. Raman analysis of surimi gelation by addition of wheat dietary fibre. Food Chem 2009. [DOI: 10.1016/j.foodchem.2008.05.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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93
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Rutkowski KS, Herrebout WA, Melikova SM, van der Veken BJ, Koll A. A cryosolution FTIR and ab initio study of the blue shifting C–H···F hydrogen bonded complexes F2ClCH·FCD3 and Cl2FCH·FCD3. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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94
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Gutberlet A, Birer O, Poerschke T, Havenith M. High resolution infrared spectroscopy of the asymmetric C-H stretch of 1,2,4,5-tetracyanobenzene (TCNB) and (TCNB)(2) in superfluid helium nanodroplets. J Chem Phys 2008; 129:174311. [PMID: 19045351 DOI: 10.1063/1.2996356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the observation of the C-H stretch vibration of 1,2,4,5-tetracyanobenzene (TCNB) and (TCNB)(2) embedded in superfluid helium droplets. The asymmetric C-H stretch of TCNB was observed at 3053.488(3) cm(-1). The corresponding band of the (TCNB)(2) is slightly blueshifted and was observed at 3054.651(2) cm(-1). The intensity of the IR band is increased compared to the monomer absorption. Based on a comparison of our experimental results with predicted IR bands, we conclude that (TCNB)(2) is formed in a C(2h) structure in the droplet.
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Affiliation(s)
- Anna Gutberlet
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
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95
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Scheiner S, Kar T. Spectroscopic and Structural Signature of the CH−O Hydrogen Bond. J Phys Chem A 2008; 112:11854-60. [DOI: 10.1021/jp806984g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Tapas Kar
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
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96
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Jabłoński M, Sadlej AJ. Influence of the external pressure on improper character of intramolecular C–H⋯O interactions. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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97
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Lignell A, Khriachtchev L. Intermolecular interactions involving noble-gas hydrides: Where the blue shift of vibrational frequency is a normal effect. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.07.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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98
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Zeegers-Huyskens T. Vibrational frequencies in hydrogen-bonded and non-hydrogen-bonded CH groups. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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99
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100
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Lignell A, Lundell J, Khriachtchev L, Räsänen M. Experimental and Computational Study of HXeY···HX Complexes (X, Y = Cl and Br): An Example of Exceptionally Large Complexation Effect. J Phys Chem A 2008; 112:5486-94. [DOI: 10.1021/jp801363u] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Antti Lignell
- Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 35, FIN-40014 University of Jyväskylä, Finland
| | - Jan Lundell
- Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 35, FIN-40014 University of Jyväskylä, Finland
| | - Leonid Khriachtchev
- Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 35, FIN-40014 University of Jyväskylä, Finland
| | - Markku Räsänen
- Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 35, FIN-40014 University of Jyväskylä, Finland
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