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1.
The hydrogen bonding interactions of the HNO dimer have been investigated using ab initio molecular orbital and density functional theory (DFT) with the 6-311++G(2d,2p) basis set. The natural bond orbital (NBO) analysis and atom in molecules (AIM) theory were applied to understand the nature of the interactions. The interrelationship between one N-H...O hydrogen bond and the other N-H...O hydrogen bond has been established by performing partial optimizations. The dimer is stabilized by the N-H...O hydrogen bonding interactions, which lead to the contractions of N-H bonds as well as the characteristic blue-shifts of the stretching vibrational frequencies nu(N-H). The NBO analysis shows that both rehybridization and electron density redistribution contribute to the large blue-shifts of the N-H stretching frequencies. A quantitative correlations of the intermolecular distance H...O (r(H...O)) with the parameters: rho at bond critical points (BCPs), s-characters of N atoms in N-H bonds, electron densities in the sigma*(N-H), the blue-shift degrees of nu(N-H) are presented. The relationship between the difference of rho (|Deltarho|) for the one hydrogen bond compared with the other one and the difference of interaction energy (DeltaE) are also illustrated. It indicates that for r(H...O) ranging from 2.05 to 2.3528 A, with increasing r(H...O), there is the descending tendency for one rho(H...O) and the ascending tendency for the other rho(H...O). r(H...O) ranging from 2.3528 to 2.85 A, there are descending tendencies for the two rho(H...O) with increasing r(H...O). On the potential energy surface of the dimer, the smaller the difference between one rho(H...O) and the other rho(H...O) is, the more stable the structure is. As r(H...O) increases, the blue-shift degrees of nu(N-H) decrease. The cooperative descending tendencies in s-characters of two N atoms with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H). Ranging from 2.05 to 2.55 A, the increase of the electron density in one sigma*(N-H) with elongating r(H...O) weakens the blue-shift degrees of nu(N-H), simultaneously, the decrease of the electron density in the other sigma*(N-H) with elongating r(H...O) strengthens the blue-shift degrees of nu(N-H). Ranging from 2.55 to 2.85 A, the cooperative ascending tendencies of the electron densities in two sigma*(N-H) with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H). 相似文献
2.
The cooperativity between the O-H...O and C-H...O hydrogen bonds has been studied by quantum chemical calculations at the MP2/6-311++G(d,p) level in gaseous phase and at the B3LYP/6-311++G(d,p) level in solution. The interaction energies of the O-H...O and C-H...O H-bonds are increased by 53 and 58%, respectively, demonstrating that there is a large cooperativity. Analysis of hydrogen-bonding lengths, OH bond lengths, and OH stretching frequencies also supports such a conclusion. By NBO analysis, it is found that orbital interaction plays a great role in enhancing their cooperativity. The strength increase of the C-H...O H-bond is larger than that of the O-H...O H-bond due to the cooperativity. The solvent has a weakening effect on the cooperativity. 相似文献
3.
Alonso JL Antolínez S Blanco S Lesarri A López JC Caminati W 《Journal of the American Chemical Society》2004,126(10):3244-3249
The oxirane-trifluoromethane dimer generated in a supersonic expansion has been characterized by Fourier transform microwave spectroscopy. The rotational spectra of the parent species and of its two (13)C isotopomers in combination with ab initio calculations have been used to establish a C(s)() geometry for the dimer with the two monomers bound by one C-H.O and two C-H.F-C hydrogen bonds. An overall bonding energy of about 6.7 kJ/mol has been derived from the centrifugal distortion analysis. The lengths of the C-H.O and C-H.F hydrogen bonds, r(O.H) and r(F.H), are 2.37 and 2.68 A, respectively. The C-H.F-C interactions give rise to the HCF(3) internal rotation motion barrier of 0.55(1) kJ/mol, which causes the A-E splittings observed in the rotational spectra. The analysis of the structural and energetic features of the C-H.O and C-H.F-C interactions allows us to classify them as weak hydrogen bonds. Ab initio calculations predict these weak interactions to produce blue shifts in the C-H vibrational frequencies and shortenings of the C-H lengths. 相似文献
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5.
We report a computational study for the 17O NMR tensors (electric field gradient and chemical shielding tensors) in crystalline uracil. We found that N-H...O and C-H...O hydrogen bonds around the uracil molecule in the crystal lattice have quite different influences on the 17O NMR tensors for the two C=O groups. The computed 17O NMR tensors on O4, which is involved in two strong N-H...O hydrogen bonds, show remarkable sensitivity toward the choice of cluster model, whereas the 17O NMR tensors on O2, which is involved in two weak C-H...O hydrogen bonds, show much smaller improvement when the cluster model includes the C-H...O hydrogen bonds. Our results demonstrate that it is important to have accurate hydrogen atom positions in the molecular models used for 17O NMR tensor calculations. In the absence of low-temperature neutron diffraction data, an effective way to generate reliable hydrogen atom positions in the molecular cluster model is to employ partial geometry optimization for hydrogen atom positions using a cluster model that includes all neighboring hydrogen-bonded molecules. Using an optimized seven-molecule model (a total of 84 atoms), we were able to reproduce the experimental 17O NMR tensors to a reasonably good degree of accuracy. However, we also found that the accuracy for the calculated 17O NMR tensors at O2 is not as good as that found for the corresponding tensors at O4. In particular, at the B3LYP/6-311++G(d,p) level of theory, the individual 17O chemical shielding tensor components differ by less than 10 and 30 ppm from the experimental values for O4 and O2, respectively. For the 17O quadrupole coupling constant, the calculated values differ by 0.30 and 0.87 MHz from the experimental values for O4 and O2, respectively. 相似文献
6.
Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted. 相似文献
7.
Scheiner S 《The journal of physical chemistry. B》2006,110(37):18670-18679
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. 相似文献
8.
9.
10.
A large number of Calpha-H...O contacts are present in transmembrane protein structures, but contribution of such interactions to protein stability is still not well understood. According to previous ab initio quantum calculations, the stabilization energy of a Calpha-H...O contact is about 2-3 kcal/mol. However, experimental studies on two different Calpha-H...O hydrogen bonds present in transmembrane proteins lead to conclusions that one contact is only weakly stabilizing and the other is not even stabilizing. We note that most previous computational studies were on optimized geometries of isolated molecules, but the experimental measurements were on those in the structural context of transmembrane proteins. In the present study, 263 Calpha-H...O=C contacts in alpha-helical transmembrane proteins were extracted from X-ray crystal structures, and interaction energies were calculated with quantum mechanical methods. The average stabilization energy of a Calpha-H...O=C interaction was computed to be 1.4 kcal/mol. About 13% of contacts were stabilizing by more than 3 kcal/mol, and about 11% were destabilizing. Analysis of the relationships between energy and structure revealed four interaction patterns: three types of attractive cases in which additional Calpha-H...O or N-H...O contact is present and a type of repulsive case in which repulsion between two carbonyl oxygen atoms occur. Contribution of Calpha-H...O=C contacts to protein stability is roughly estimated to be greater than 5 kcal/mol per helix pair for about 16% of transmembrane helices but for only 3% of soluble protein helices. The contribution would be larger if Calpha-H...O contacts involving side chain oxygen were also considered. 相似文献
11.
A. Bende . Vibk G. J. Halsz S. Suhai 《International journal of quantum chemistry》2005,101(2):186-200
The equilibrium structures, the binding energies, and the second‐order energy components of a series of hydrogen‐bonded complexes involving acetylene are studied. The strength of the binding energy of the selected systems (HF … HCCH, HCl … HCCH, HCN … HCCH, and HCCH … HCCH) was different, ranging from a very weak interaction to a strong interaction. Calculations have been carried out at both the Hartree–Fock and correlated (second‐order Møller–Plesset perturbation theory) levels of theory, using several different basis sets [6‐31G(d,p), 6‐311G(d,p), 6‐31G++(d,p), 6‐311G++(d,p), 6‐31++G(2d,2p) and 6‐311++G(2d,2p)]. The widely used a posteriori Boys–Bernardi counterpoise (CP) correction scheme has been compared with the a priori CHA/CE, CHA–MP2, and CHA–PT2 methods, using the chemical Hamiltonian approach (CHA). The results show that at both levels the CP and the appropriate CHA results are very close to each other. Only the monomer‐based CHA‐PT2 theory gives slightly overcorrected results, reflecting that the charge transfer and polarization effects are not taken into account in this method up to second order. We have also applied our earlier developed energy decomposition scheme in order to decompose the second‐order energy contribution into different physically meaningful components. The results show that at large and intermediate intermolecular distances, the second‐order intermolecular contribution is almost equal to the sum of different physically meaningful components (e.g., polarization, charge transfer, dispersion), while at shorter distances the slightly strong overlap effects fairly disturb this simple additivity. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 相似文献
12.
Baures PW Beatty AM Dhanasekaran M Helfrich BA Pérez-Segarra W Desper J 《Journal of the American Chemical Society》2002,124(38):11315-11323
Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures. 相似文献
13.
Two bis(mu-methoxo)dichromium(III) complexes, [L(Se)(2)Cr(2)(mu-OCH(3))(2)(CH(3)OH)(2)] 1 and [L(Se)(2)Cr(2)(mu-OCH(3))(2)(CH(3)OH)(CH(3)O)](-) 2, where L(Se) represents the dianion of 2,2'-selenobis(4,6-di-tert-butylphenol), have been reported to demonstrate the effect of hydrogen bonding on the exchange coupling interactions between the chromium(III) centers. The corresponding sulfur analogue of the ligand, i.e., 2,2'-thiobis(4,6-di-tert-butylphenol), also yields the analogous [L(S)(2)Cr(2)(mu-OCH(3))(2)(CH(3)OH)(2)] 3 and [L(S)(2)Cr(2)(mu-OCH(3))(2)(CH(3)O)(CH(3)OH)](-) 4, which exhibit similar exchange coupling parameters. An acid-base dependent equilibrium between 1 and 2 or 3 and 4 has been established by electronic spectral measurements. 相似文献
14.
The N-H...O hydrogen bonds are analyzed for formamide dimer and its simple fluorine derivatives representing a wide spectrum of more or less covalent interactions. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. To explain the nature of such interactions, the Bader theory was also applied, and the characteristics of the bond critical points (BCPs) were analyzed: the electron density at BCP and its Laplacian, the electron energy density at BCP and its components, the potential electron energy density, and the kinetic electron energy density. These parameters are used to justify the statement that some of the interactions analyzed are partly covalent in nature. An analysis of the interaction energy components for the systems considered indicates that the covalent character of the hydrogen bond is manifested by a markedly increased contribution of the delocalization term relative to the electrostatic interaction energy. Moreover, the ratio of stabilizing the delocalization/electrostatic contributions grows linearly with the decreasing lengths of the hydrogen bond. 相似文献
15.
Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted. 相似文献
16.
Summary From a survey of spectroscopic and structural data of six corresponding 2-hydroxybenzamides and 2-hydroxythiobenzamides (amide, N-methylamide, N,N-dimethylamide, piperidide, morpholide, 2,6-dimethylpiperidide) remarkable similarities between O(N)-H ... O and O(N)-H ... S hydrogen-bonds are obtained, concerning both, hydrogen-bond patterns and hydrogen-bond strengths. In dilute solution the OH groups of all compounds are intramolecularly associated to the (thio)carbonyl O (S) atoms with distinctly larger hydrogen-bond strengths for primary and secondary amides [
(O-H)=2950–3020 cm–1, (OH)=12.16–11.99 ppm] and thioamides [
(O-H)=2960–3000 cm–1, (OH)=11.65–11.13 ppm], than for tertiary amides [
(O-H)=3200–3250 cm–1, (OH)=9.95–8.95 ppm] and thioamides [
(O-H)=3245–3330 cm–1, (OH)=8.09–7.06 ppm]. In the solid state, the OH groups of the primary and secondary (thio)amides are also engaged in rather strong intramolecular O-H ... O=C [O ... O=2.51 Å,
(O-H)=2700–2750 cm–1] and O-H ... S=C [O ... S=2.90–2.94 Å,
(O-H)=2700–2840 cm–1] hydrogen-bonds; thetrans-NH groups of the primary (thio)amides and the NH groups of the secondary (thio)amides connect the molecules to N-H ... O-H [N ... O=2.93–3.10 Å,
(N-H)=3319–3407 cm–1] hydrogen-bonded chains; the remainingcis-NH groups of the primary (thio)amides give rise to eight-membered cyclic dimers via N-H ... O=C [N ... O=2.93 Å,
(N-H)=3226 cm–1] and N-H ... S=C [N ... S=3.46–3.47 Å,
(N-H)=3233–3277 cm–1] hydrogen-bonds. Contrary, the OH groups of the tertiary (thio)amides are intermolecular associated in the solid state and link the molecules to O-H ... O=C [O ... O=2.63–2.75 Å,
(O-H)=3075–3135 cm–1] and O-H ... S=C [O ... S=3.18–3.26 Å,
(O-H)=3130–3190 cm–1] hydrogen-bonded chains.
O-H ... O(S)-Wasserstoffbrückenbindungen in 2-Hydroxy(thio)benzamiden. Ein Überblick über spektroskopische und strukturelle Daten
Zusammenfassung Aus einer Zusammenstellung von spektroskopischen und strukturellen Daten von sechs entsprechenden 2-Hydroxybenzamiden und 2-Hydroxythiobenzamiden (Amid, N-Methylamid, N,N-Dimethylamid, Piperidid, Morpholid, 2,6-Dimethylpiperidid) ergeben sich bemerkenswerte Analogien zwischen O(N)-H ... O und O(N)-H ... S H-Brücken, die sowohl die H-Brücken-Muster als auch die H-Brücken-Stärken betreffen. In verdünnter Lösung sind die OH-Gruppen aller Verbindungen intramolekular mit den O(S)-Atomen der (Thio)Carbonylgruppen assoziiert, wobei die H-Brücken bei den primären und sekundären Amiden [ (O-H)=2950–3020 cm–1, (OH)=12.16–11.99 ppm] und Thioamiden [ (O-H)=2960–3060 cm–1, (OH)=11.65–11.13 ppm] deutlich stärker sind, als bei den tertiären Amiden [ (O-H)=3200–3250 cm–1, (OH)=9.95–8.95 ppm] und Thioamiden [ (O-H)=3245–3330 cm–1, (OH)=8.09–7.06 ppm]. Im Festkörper weisen die primären und sekundären (Thio)Amide ebenfalls sehr starke intramolekulare O-H ... O=C [O ... O=2.51 Å, (O-H)=2700–2750 cm–1] und O-H ... S=C [O ... S=2.90–2.94 Å, (O-H)=2700–2840 cm–1] H-Brücken auf; dietrans-NH-Gruppen der primären (Thio)Amide und die NH-Gruppen der sekundären (Thio)Amide verknüpfen die Moleküle über N-H ... O-H H-Brücken [N ... O=2.93–3.10 Å, (N-H)=3318–3407 cm–1] zu Ketten; die verbleibendencis-NH-Gruppen der primären (Thio)Amide bilden zyklische, über N-H ... O=C [N ... O=2.93 Å, (N-H)=3226 cm–1] und N-H ... S=C [N ... S=3.46–3.47 Å, (N-H)=3233–3277 cm–1] H-Brücken gebundene, 8-Ring-Dimere. Im Gegensatz dazu sind die OH-Gruppen der tertiären (Thio)Amide im Festkörper intermolekular assoziiert und verknüpfen die Moleküle über O-H ... O=C [O ... O=2.63–2.75 Å, (O-H)=3075–3135 cm–1] und O-H ... S=C [O ... S=3.18–3.26 Å, (O-H)=3130–3190 cm–1] H-Brücken zu Ketten.相似文献
17.
Liliana Mammino Mwadham M. Kabanda 《International journal of quantum chemistry》2011,111(14):3701-3716
Polyhydroxybenzenes are the parent compounds of large classes of derivatives, many of which exhibit biological activities. The study of derivatives highlights the importance of the conformation stabilizing factors of the parent compounds. To identify these factors, a systematic comparative study of polyhydroxybenzenes was carried out through a computational study of all possible structures and conformers in vacuo and in three solvents differing by their polarities and by the types of interactions with the solute molecule (water, chloroform, and acetonitrile); the results in solution are complemented by the study of adducts with explicit water molecules and, for the simpler structures, also with explicit acetonitrile molecules. The greatest conformation stabilizing effect pertains to intramolecular hydrogen bonds, with preference for consecutive H‐bonds. Uniform orientation of the phenol OH is a stabilizing factor for structures with meta OH groups. Preference for structures with meta OH and with greater symmetry increases as the medium polarity increases. The coexistence of intramolecular H‐bonds and solute–solvent intermolecular H‐bonds in water and acetonitrile solution narrows the solvent‐effect difference between conformers with and without intramolecular H‐bonds. Comparison of results from different calculation methods (HF, MP2, and DFT/B3LYP, with 6‐31G(d,p) and 6‐31++G(d,p) basis sets) shows consistency of the identified trends. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011 相似文献
18.
A three-residue trans-cyclopropane gamma-peptide adopts an infinite parallel sheet structure in the solid state stabilized by intermolecular C-H...O hydrogen bonds, as demonstrated by single crystal X-ray diffraction. 相似文献
19.
A specific assembly process, driven by coexisting X-H...O hydrogen bonding and X...O short intermolecular contacts (X = C, N, O) is described, in which the pseudo-Keggin polyoxoanion and two types of molecule...cation pairs (with C1 and Ci symmetries) were assembled to the programmed supramolecular architecture. Cooperation of the positive-charge, resonance effect and the O=C...Oterminal intermolecular contact led to the short and strong symmetrical [O...H...O]+ hydrogen bond (O...O = 2.449(13) Å) in one of the molecule...cation pairs [C4H9NO...H...ONC4H9]+ with the H-bonded proton in the center of inversion. The other [C4H9NOH...ONC4H9]+ molecule...cation pair (non-centrosymmetric) was formed through a very strong asymmetric [O.H.O]+ hydrogen bond of 2.431(13) Å in length which was created via the synergistic effect between the minor N-H...O secondary interaction, +CAHB (positive-charge-assisted hydrogen bond) and RAHB (resonance assisted hydrogen bond) mechanisms. 相似文献
20.
The comparison of the values of the chemical shifts of the pyridinium protons in the ylides of -dicarbonyl compounds and in betainealdehydes of thiazole and imidazole established the presence of the intramolecular C-H...O and C-H...N hydrogen bond between the -protons of the pyridinium and the oxygen atoms of the formyl group and the nitrogen of the amide fragment in the anionoid part of the betaine. The conclusion was confirmed by the varying influence of the effects of protonation on the character of the deshielding of the - and -protons.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 626–628, May, 1989. 相似文献