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Tsyrenova BD, Tarasevich BN, Khrustalev VN, Gloriozov IP, Nenajdenko VG. Hydrogen bonding in acetylene containing dichlorodiazaalkadienes. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Jones LO, Mosquera MA, Schatz GC, Ratner MA. Molecular Junctions Inspired by Nature: Electrical Conduction through Noncovalent Nanobelts. J Phys Chem B 2019; 123:8096-8102. [PMID: 31525929 DOI: 10.1021/acs.jpcb.9b06255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Charge transport occurs in a range of biomolecular systems, whose structures have covalent and noncovalent bonds. Understanding from these systems have yet to translate into molecular junction devices. We design junctions which have hydrogen-bonds between the edges of a series of prototype noncovalent nanobelts (NCNs) and vary the number of donor-acceptors to study their electrical properties. From frontier molecular orbitals (FMOs) and projected density of state (DOS) calculations, we found these NCN dimer junctions to have low HOMO-LUMO gaps and states at the Fermi level, suggesting these are metallic-like systems. Their conductance properties were studied with nonequilibrium Green's functions density functional theory (NEGF-DFT) and was found to decrease with cooperative H-bonding, that is, the conductance decreased as the alternating donor-acceptors around the nanobelts attenuates to a uniform distribution in the H-bonding arrays. The latter gave the highest conductance of 51.3 × 10-6 S and the Seebeck coefficient showed n-type (-36 to -39 μV K-1) behavior, while the lower conductors with alternating H-bonds are p-type (49.7 to 204 μV K-1). In addition, the NCNs have appreciable binding energies (19.8 to 46.1 kcal mol-1), implying they could form self-assembled monolayer (SAM) heterojunctions leading to a polymeric network for long-range charge transport.
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Affiliation(s)
- Leighton O Jones
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martín A Mosquera
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - George C Schatz
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - Mark A Ratner
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
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3
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Haack R, Schulz S, Jansen G. Dispersion interactions between neighboring Bi atoms in (BiH 3 ) 2 and Te(BiR 2 ) 2. J Comput Chem 2018. [PMID: 29533472 DOI: 10.1002/jcc.25209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR2 )2 molecules (R = H, Me, Et) and in (BiH3 )2 were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component-scaled second-order Møller-Plesset theory (SCS-MP2) agree well with coupled-cluster singles and doubles theory including perturbative triples (CCSD(T)). Density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) was used to study the anisotropy of the interplay of dispersion attraction and steric repulsion between the Bi atoms. Finally, geometries and relative stabilities of syn-syn and syn-anti conformers of Te(BiR2 )2 (R = H, Me, Et) and interconversion barriers between them were computed. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Rebekka Haack
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, Essen, 45117, Germany
| | - Stephan Schulz
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, Essen, 45117, Germany
| | - Georg Jansen
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, Essen, 45117, Germany
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4
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Gopi R, Ramanathan N, Sundararajan K. Probing C-H⋯N interaction in acetylene-benzonitrile complex using matrix isolation infrared spectroscopy and DFT computations. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Samanta AK, Wang Y, Mancini JS, Bowman JM, Reisler H. Energetics and Predissociation Dynamics of Small Water, HCl, and Mixed HCl–Water Clusters. Chem Rev 2016; 116:4913-36. [DOI: 10.1021/acs.chemrev.5b00506] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amit K. Samanta
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Yimin Wang
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - John S. Mancini
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Hanna Reisler
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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6
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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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7
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Matena M, Stöhr M, Riehm T, Björk J, Martens S, Dyer M, Persson M, Lobo-Checa J, Müller K, Enache M, Wadepohl H, Zegenhagen J, Jung T, Gade L. Aggregation and Contingent Metal/Surface Reactivity of 1,3,8,10-Tetraazaperopyrene (TAPP) on Cu(111). Chemistry 2010; 16:2079-91. [DOI: 10.1002/chem.200902596] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Intermolecular Hydrogen Bonding and Vibrational Analysis of N,N-Dimethylformamide Hexamer Cluster. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.11.2595] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Abstract
Photofragment spectroscopy is combined with imaging techniques and time-resolved measurements of photoions and photoelectrons to explore the predissociation dynamics of weakly bound molecules. Recent experimental advances include measurements of pair-correlated distributions, in which energy disposal in one cofragment is correlated with a state-selected level of the other fragment, and femtosecond pump-probe experiments, in some cases with coincidence detection. An application in which coincident measurements are carried out in the molecular frame is also described. To illustrate these state-selective and time-resolved techniques, we review two recent applications: (a) the photoinitiated dissociation of the covalently bound NO dimer on the ground and excited electronic states and the role of state couplings and (b) the state-selected vibrational predissociation of hydrogen-bonded acetylene dimers with HCl (acid) and ammonia (base) and the importance of angular momentum constraints. We highlight the crucial role of theoretical models in interpreting results.
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Affiliation(s)
- Hanna Reisler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
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10
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Boese R, Bläser D, Jansen G. Synthesis and Theoretical Characterization of an Acetylene-Ammonia Cocrystal. J Am Chem Soc 2009; 131:2104-6. [DOI: 10.1021/ja8059705] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Roland Boese
- Fachbereich Chemie, Universität Duisburg-Essen, Campus Essen, Universitätsstr. 5, D-45117 Essen, Germany
| | - Dieter Bläser
- Fachbereich Chemie, Universität Duisburg-Essen, Campus Essen, Universitätsstr. 5, D-45117 Essen, Germany
| | - Georg Jansen
- Fachbereich Chemie, Universität Duisburg-Essen, Campus Essen, Universitätsstr. 5, D-45117 Essen, Germany
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11
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Vibrational Analysis and Intermolecular Hydrogen Bonding of Azodicarbonamide in the Pentamer Cluster. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.10.1951] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Kryachko ES, Scheiner S. Bonding rearrangements of hydrogen-bonded complexes involving alkynes. J Phys Chem A 2008; 112:1940-5. [PMID: 18266343 DOI: 10.1021/jp076795e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecules containing a C-C triple bond, such as HC[triple bond]CH, FC[triple bond]CF, and the C[triple bond]CH radical, are allowed to interact with a partner molecule of H2O, NH3, or HF. Quantum chemical calculations show that these C[triple bond]CH...X H-bonded complexes are bound by up to 4 kcal x mol(-1). More importantly, they can rearrange in such a way that the partner molecule adds to the triple bond so as to form a double C=C bond. Whereas this process is strongly exoergic, there is a high-energy barrier to this rearrangement process. On the other hand, when a second water molecule is added to the complex, it can shuttle protons from the donor part of the complex to the acceptor, and thereby greatly reduce the rearrangement energy barrier. In the case of CCH + 2H2O, this barrier is computed to be less than 4 kcal x mol(-1).
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Affiliation(s)
- Eugene S Kryachko
- Department of Chemistry, Bat. B6c, University of Liege, Sart-Tilman, B-4000 Liege 1, Belgium.
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13
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Scheiner S. Contributions of NH...O and CH...O hydrogen bonds to the stability of beta-sheets in proteins. J Phys Chem B 2007; 110:18670-9. [PMID: 16970498 DOI: 10.1021/jp063225q] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ab initio quantum calculations are applied to both the parallel and the antiparallel arrangements of the beta-sheets of proteins. The energies of the NH...O and CH...O hydrogen bonds present in the beta-sheet are evaluated separately from one another by appropriate modifications of the model systems. The bond energies of these two sorts of hydrogen bonds are found to be very nearly equal in the parallel beta-sheet. The NH...O bonds are stronger than CH...O in the antiparallel geometry but only by a relatively small margin. Moreover, the former NH...O bonds are weakened when placed next to one another, as occurs in the antiparallel beta-sheet. As a result, there is little energetic distinction between the NH...O and CH...O bonds in the full antiparallel beta-sheet, just as in the parallel structure.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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Parr JA, Li G, Fedorov I, McCaffery AJ, Reisler H. Imaging the State-Specific Vibrational Predissociation of the C2H2−NH3Hydrogen-Bonded Dimer. J Phys Chem A 2007; 111:7589-98. [PMID: 17542567 DOI: 10.1021/jp070838+] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The state-to-state vibrational predissociation (VP) dynamics of the hydrogen-bonded ammonia-acetylene dimer were studied following excitation in the asymmetric CH stretch. Velocity map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Following vibrational excitation of the asymmetric CH stretch fundamental, ammonia fragments were detected by 2 + 1 REMPI via the B1E'' <-- X1A1' and C'1A1' <-- X1A1' transitions. The fragments' center-of-mass (c.m.) translational energy distributions were determined from images of selected rotational levels of ammonia with one or two quanta in the symmetric bend (nu2 umbrella mode) and were converted to rotational-state distributions of the acetylene co-fragment. The latter is always generated with one or two quanta of bending excitation. All the distributions could be fit well when using a dimer dissociation energy of D0 = 900 +/- 10 cm(-1). Only channels with maximum translational energy <150 cm(-1) are observed. The rotational excitation in the ammonia fragments is modest and can be fit by temperatures of 150 +/- 50 and 50 +/- 20 K for 1nu2 and 2nu2, respectively. The rotational distributions in the acetylene co-fragment pair-correlated with specific rovibrational states of ammonia appear statistical as well. The vibrational-state distributions, however, show distinct state specificity among channels with low translational energy release. The predominant channel is NH3(1nu2) + C2H2(2nu4 or 1nu4 + 1nu5), where nu4 and nu5 are the trans- and cis-bend vibrations of acetylene, respectively. A second observed channel, with much lower population, is NH3(2nu2) + C2H2(1nu4). No products are generated in which the ammonia is in the vibrational ground state or the asymmetric bend (1nu4) state, nor is acetylene ever generated in the ground vibrational state or with CC stretch excitation. The angular momentum (AM) model of McCaffery and Marsh is used to estimate impact parameters in the internal collisions that give rise to the observed rotational distributions. These calculations show that dissociation takes place from bent geometries, which can also explain the propensity to excite fragment bending levels. The low recoil velocities associated with the observed channels facilitate energy exchange in the exit channel, which results in statistical-like fragment rotational distributions.
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Affiliation(s)
- Jessica A Parr
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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15
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MP2/6-311++G(d,p) study on galactose–aromatic residue analog complexes in different position-orientations of the saccharide relative to aromatic residue. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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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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17
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Hunter KC, Millen AL, Wetmore SD. Effects of Hydrogen-Bonding and Stacking Interactions with Amino Acids on the Acidity of Uracil. J Phys Chem B 2007; 111:1858-71. [PMID: 17256895 DOI: 10.1021/jp066902p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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18
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Baker AB, Samet C, Lyon JT, Andrews L. Pentachlorocyclopropane/Base Complexes: Matrix Isolation Infrared Spectroscopic and Density Functional Study of C−H- - -N Hydrogen Bonds. J Phys Chem A 2005; 109:8280-9. [PMID: 16834216 DOI: 10.1021/jp0581781] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-bonded complexes of pentachlorocyclopropane with the bases acetonitrile, ammonia, monomethylamine, and dimethylamine have been isolated and characterized for the first time in argon matrices at 16 K. Coordination of the proton of pentachlorocyclopropane (Pccp) to the electron donor (N) of the base was evidenced by red shifts of the CH stretching mode. These shifts, which range from 22 to 170 cm(-1), increase in the order CH3CN, NH3, (CH3)NH2, and (CH3)2NH. Density functional theory (DFT) calculations at the B3LYP level agree well with experiment and support the formation of 1:1 complexes of Pccp/base. Distinct changes were observed in ring modes as well as CCl and CCl2 modes. The hydrogen bond energy of the complexes varies from 2.95 to 4.22 kcal/mol and is stronger than our previously studied bromocyclopropane-ammonia complex (2.35 kcal/mol, MP2).
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Affiliation(s)
- Alexander B Baker
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania 17013, USA
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19
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Shi T, Ge J, Guo J, Zhu Q. The ionization and dissociation mechanisms of pyridine–ammonia hydrogen bonding complex. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.08.098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Whittleton SR, Hunter KC, Wetmore SD. Effects of Hydrogen Bonding on the Acidity of Uracil Derivatives. J Phys Chem A 2004. [DOI: 10.1021/jp048318r] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah R. Whittleton
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8 Canada
| | - Ken C. Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8 Canada
| | - Stacey D. Wetmore
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8 Canada
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21
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Larsen RW, Hegelund F, Nelander B. Observation and Rovibrational Analysis of the Intermolecular HCl Libration Band in OC−HCl. Modeling of the Intermolecular Potential Energy Surface. J Phys Chem A 2004. [DOI: 10.1021/jp036935u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. Wugt Larsen
- Chemical Center, Department of Chemical Physics, Lund University, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - F. Hegelund
- Chemical Center, Department of Chemical Physics, Lund University, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - B. Nelander
- Chemical Center, Department of Chemical Physics, Lund University, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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22
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C–H⋯X interactions of fluoroform with ammonia, water, hydrogen cyanide, and hydrogen fluoride: conventional and improper hydrogen bonds. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2003.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Liu Y, Suhm MA, Botschwina P. Supersonic jet FTIR and quantum chemical investigations of ammonia/acetylene clusters. Phys Chem Chem Phys 2004. [DOI: 10.1039/b408919g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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24
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Kawaki H. The Interaction of Monosubstituted Benzenes with the Stationary Liquid in Gas Liquid Chromatography. Chem Pharm Bull (Tokyo) 2004; 52:221-5. [PMID: 14758007 DOI: 10.1248/cpb.52.221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In gas liquid chromatography (GLC), the relative retention values log gamma was mainly expressed by van der Waals energy (the sum of the dispersion E(dis) and repulsive E(rep) energies) to the interactions between monosubstituted benzene derivatives and the nonpolar stationary liquid as squalane. The single exception was that of anilines, and it was corrected by the electrostatic energy (E(ES)) due to C-H/pi hydrogen bond. When the stationary liquid changed from the nonpolar to polar, log gamma was estimated by the inductive interaction energy (included in E(ES)) in addition to the sum of E(dis) and E(rep). In the benzene solution, the relative equilibrium values log K/K(o) introduced from the interactions between phenol and substituted benzene derivatives were estimated by E(ES). The E(ES) of COCH(3), CO(2)C(2)H(5) groups is especially originated in the excited dipole moments micro(e). The relative frequency values log nu/nu(o) derived from O-H or O-D stretching vibration of phenol or methanol-D gave the correlation to E(ES) as well as log K/K(o). That of anilines-methanol-D however had been out of a linear relation to E(ES). The cause is concluded that the aniline-methanol-D is making the proton transfer structure from the discussion about the proton affinity (PA) of the base.
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Affiliation(s)
- Hideko Kawaki
- Pharmaceutical Research and Technology Institute, Kinki University, Higashi-Osaka, Japan.
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25
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Di Laudo M, Whittleton SR, Wetmore SD. Effects of Hydrogen Bonding on the Acidity of Uracil. J Phys Chem A 2003. [DOI: 10.1021/jp035496w] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Mariana Di Laudo
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Sarah R. Whittleton
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Stacey D. Wetmore
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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Cheng J, Kang C, Zhu W, Luo X, Puah CM, Chen K, Shen J, Jiang H. N-methylformamide-benzene complex as a prototypical peptide N-H...pi hydrogen-bonded system: density functional theory and MP2 studies. J Org Chem 2003; 68:7490-5. [PMID: 12968905 DOI: 10.1021/jo026910b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the existence of peptide N-H...pi hydrogen bonds recently has been reported in protein structures, little is known about their strength and binding nature and, therefore, the relative importance of the interaction. To shed light on this binding, the N-methylformamide-benzene complex, as a model of the peptide N-H...pi hydrogen bonding, was studied by using density functional theory and Møller-Plesset second-order perturbation (MP2) methods. The geometry of the complex was fully optimized at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels. The optimized interaction distances are about 3.6 and 3.2 A, respectively, at the two levels. The binding energy corrected by basis set superposition error with the MP2/cc-pVTZ method based on the MP2/6-31G geometry is -4.37 kcal/mol, which is as strong as the conventional hydrogen bonding. The calculated results suggest that the peptide N-H...pi hydrogen bonding is of sufficient strength to play an important role in the stabilization of protein structures. These results are helpful to better understand the characteristics and nature of the peptide N-H...pi interaction as well as to modify current force fields to better represent this special interaction.
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Affiliation(s)
- Jiagao Cheng
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
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Galabov B, Bobadova-Parvanova P, Ilieva S, Dimitrova V. The electrostatic potential at atomic sites as a reactivity index in the hydrogen bond formation. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00149-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Dimitrova V, Ilieva S, Galabov B. Electrostatic Potential at Atomic Sites as a Reactivity Descriptor for Hydrogen Bonding. Complexes of Monosubstituted Acetylenes and Ammonia. J Phys Chem A 2002. [DOI: 10.1021/jp026203m] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valia Dimitrova
- Department of Chemistry, University of Sofia, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
| | - Sonia Ilieva
- Department of Chemistry, University of Sofia, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
| | - Boris Galabov
- Department of Chemistry, University of Sofia, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
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29
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Kryachko ES, Zeegers-Huyskens T. Theoretical study of the interaction of fluoroform and chloroform with the hydroxide ion. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(02)00226-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Wetmore SD, Schofield R, Smith DM, Radom L. A Theoretical Investigation of the Effects of Electronegative Substitution on the Strength of C−H···N Hydrogen Bonds. J Phys Chem A 2001. [DOI: 10.1021/jp011087t] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stacey D. Wetmore
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Robyn Schofield
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - David M. Smith
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Leo Radom
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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31
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Mó O, Yáñez M, González L, Elguero J. Spontaneous Self-Ionization in the Gas Phase: A Theoretical Prediction. Chemphyschem 2001; 2:465-7. [DOI: 10.1002/1439-7641(20010716)2:7<465::aid-cphc465>3.0.co;2-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2001] [Indexed: 11/07/2022]
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32
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Longarte A, Fernández JA, Unamuno I, Basterrechea F, Castaño F. Experimental determination of phenol (CH3F)1 complex binding energies in the S0, S1, and I0 states and comparison with ab initio calculations. J Chem Phys 2001. [DOI: 10.1063/1.1375027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Hartmann M, Wetmore SD, Radom L. C−H···X Hydrogen Bonds of Acetylene, Ethylene, and Ethane with First- and Second-Row Hydrides. J Phys Chem A 2001. [DOI: 10.1021/jp001672e] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Hartmann
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Stacey D. Wetmore
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Leo Radom
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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34
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Abstract
Although the peptide C(alpha)H group has historically not been thought to form hydrogen bonds within proteins, ab initio quantum calculations show it to be a potent proton donor. Its binding energy to a water molecule lies in the range between 1.9 and 2.5 kcal/mol for nonpolar and polar amino acids; the hydrogen bond (H-bond) involving the charged lysine residue is even stronger than a conventional OH..O interaction. The preferred H-bond lengths are quite uniform, about 3.32 A. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the C(alpha)H stretching frequency, potential diagnostics of the presence of such an H-bond within a protein.
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Affiliation(s)
- S Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan 84322-0300, USA.
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35
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Hilfiker MA, Mysak ER, Samet C, Maynard A. Matrix Isolation Infrared and ab Initio Study of the 1:1 Complexes of Cyclopentadiene with Nitrogen and Oxygen Bases: C−H···N(O) Hydrogen Bonding Involving an sp3-Hybridized Carbon. J Phys Chem A 2001. [DOI: 10.1021/jp004464v] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark A. Hilfiker
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania 17013
| | - Erin R. Mysak
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania 17013
| | - Cindy Samet
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania 17013
| | - Andy Maynard
- Laboratory of Experimental and Computational Biology, IRSP, SAIC−Frederick, National Cancer Institute−FCRDC, Frederick, Maryland 21702
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36
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Vishveshwara S, Madhusudhan MS, Maizel JV. Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study. Biophys Chem 2001; 89:105-17. [PMID: 11254205 DOI: 10.1016/s0301-4622(00)00221-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is growing evidence that some enzymes catalyze reactions through the formation of short-strong hydrogen bonds as first suggested by Gerlt and Gassman. Support comes from several experimental and quantum chemical studies that include correlation energies on model systems. In the present study, the process of proton transfer between hydroxyl and imidazole groups, a model of the crucial step in the hydrolysis of RNA by the enzymes of the RNase A family, is investigated at the quantum mechanical level of density functional theory and perturbation theory at the MP2 level. The model focuses on the nature of the formation of a complex between the important residues of the protein and the hydroxyl group of the substrate. We have also investigated different configurations of the ground state that are important in the proton transfer reaction. The nature of bonding between the catalytic unit of the enzyme and the substrate in the model is investigated by Bader's atoms in molecule theory. The contributions of solvation and vibrational energies corresponding to the reactant, the transition state and the product configurations are also evaluated. Furthermore, the effect of protein environment is investigated by considering the catalytic unit surrounded by complete proteins--RNase A and Angiogenin. The results, in general, indicate the formation of a short-strong hydrogen bond and the formation of a low barrier transition state for the proton transfer model of the enzyme.
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Affiliation(s)
- S Vishveshwara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
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