Interplay Between Hydrogen Bond Formation and Multicenter π-Electron Delocalization: Intermolecular Hydrogen Bonds

2008 ◽  
Vol 112 (34) ◽  
pp. 7898-7904 ◽  
Author(s):  
Pieterjan Lenain ◽  
Marcos Mandado ◽  
Ricardo A. Mosquera ◽  
Patrick Bultinck
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Bond Formation ◽  
Electron Delocalization ◽  
Intermolecular Hydrogen Bonds ◽  
Hydrogen Bond Formation

A 2′-deoxycytidine long-linker click adduct forming two conformers in the asymmetric unit

2012 ◽  
Vol 68 (4) ◽  
pp. o174-o178 ◽  
Author(s):  
Frank Seela ◽  
Hai Xiong ◽  
Simone Budow ◽  
Henning Eickmeier ◽  
Hans Reuter
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystalline State ◽  
Bond Formation ◽  
Three Dimensional ◽  
Sugar Residue ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds ◽  
Hydrogen Bond Formation

The title compound {systematic name: 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-[6-(1-benzyl-1H-1,2,3-triazol-4-yl)hex-1-ynyl]pyrimidin-2(1H)-one}, C24H28N6O4, shows two conformations in the crystalline state,viz.(I-1) and (I-2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N-glycosylic bonds of both conformers adopt similaranticonformations, with χ = −168.02 (12)° for conformer (I-1) and χ = −159.08 (12)° for conformer (I-2). The sugar residue of (I-1) shows anN-type (C3′-endo) conformation, withP= 33.1 (2)° and τm= 29.5 (1)°, while the conformation of the 2′-deoxyribofuranosyl group of (I-2) isS-type (C3′-exo), withP = 204.5 (2)° and τm= 33.8 (1)°. Both conformers participate in hydrogen-bond formation and exhibit identical patterns resulting in three-dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N—H...N, N—H... O, O—H...N and O—H...O).

1H -NMRInvestigations on the Hydrogen Bond Formation between the Tranquilizers Diazepam and Nitrazepam and Some Nucleobases

1978 ◽  
Vol 33 (11-12) ◽  
pp. 870-875 ◽  
Author(s):  
Hans-Helmut Paul ◽  
Helmut Sapper ◽  
Wolfgang Lohmann
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binding Sites ◽  
Spectroscopic Data ◽  
Proton Magnetic Resonance ◽  
Proton Magnetic Resonance Spectroscopy ◽  
Bond Formation ◽  
Resonance Spectroscopy ◽  
Hydrogen Bond Formation ◽  
Dimer Model

The formation of hydrogen bonds between the minor tranquilizers diazepam and nitrazepam and a few nucleobases was studied in deuterochloroform solution by means of proton magnetic resonance spectroscopy. The thermodynamic and spectroscopic data of the associations were evaluated on the basis of a dimer model, using the concentration dependent shifts of the protons involved in hydrogen bonds. The interactions of nitrazepam (ΔH0= -10 to -21 k J/mol; ΔG250 - 0.2 to -7.4 kJ/mol) were found to be stronger than those of diazepam (ΔH0 = - 10 to - 13 kJ/mol; ΔG250 = 6.0 to 6.4 k j/mol). The various binding sites of the benzodiazepines for hydrogen bonds are discussed.

scholarly journals Polarisable Hydrogen Bond Formation and Ionic Interactions in Model Phospholipid Polar Head Molecules

1973 ◽  
Vol 28 (5-6) ◽  
pp. 323-330 ◽  
Author(s):  
Georg Papakostidis ◽  
Georg Zundel
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Phosphoric Acid ◽  
Bond Formation ◽  
Ion Pairs ◽  
Water Soluble ◽  
Ionic Interactions ◽  
Hydrogen Bond Formation ◽  
Continuous Absorption ◽  
Phosphate Groups

The serine phosphoric acid P-methylester (SPM) and the ethanol-amine phosphoric acid P-methylester (EPM) were synthesized as water soluble models for the functional groups of the corresponding phospholipids. Investigations were made of the aqueous solutions of these molecules as a function of deprotonation and protonation. An intramolecular, easily polarisable hydrogen bond occurs in the zwitterion of the SPM. The solutions of different salts of SPM were studied as well as the influence of counter ion pairs. Counterion pairs hardly influence these bonds. At about 50% deprotonation extremely easily polarisable intermolecular bonds form. At about 100% deprotonation of the zwitterion the hydrogen bonds observed are affected by the presence of CO2. The above is indicated by changes of the bands of the carboxylic and phosphate groups, and in particular by a continuous absorption in the infrared spectrum. During protonation of the EPM easily polarisable intermolecular POH+ ... OP hydrogen bonds form at first, but as protonation increases the solutions become acidic, that is, H5O2+ groupings form.

scholarly journals Microscopic Structural Features of Water in Aqueous-Reline Mixture of Varying Composition

2020 ◽  
Author(s):  
Soham Sarkar ◽  
Atanu Maity ◽  
Rajarshi Chakrabarti
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Choline Chloride ◽  
Bond Formation ◽  
Orientational Order ◽  
Water Structure ◽  
Structural Features ◽  
Water Molecules ◽  
Hydrogen Bond Formation ◽  
Hydrogen Bonded

Reline, a mixture of urea and choline chloride in 2:1 molar ratio, is one of the most frequently used deep eutectic solvents. Pure reline and its aqueous solution have large scale industrial use. Owing to the presence of active hydrogen bond formation sites, urea and choline cation can disrupt the hydrogen-bonded network in water. However, a quantitative understanding of the microscopic structural features of water in the presence of reline is still lacking. We use extensive all-atom molecular dynamics simulations to elucidate the effect of the gradual addition of co-solvents on microscopic arrangements of water molecules. We consider four aqueous solutions of reline, between the wt% 26.3 to 91.4. A disruption of the local hydrogen-bonded water structure is observed on inclusion of urea and choline chloride. The extent of deviation of water structure from tetrahedrality is quantified using the orientational order parameter. Our analyses show a monotonic increase in structural disorder as the co-solvents are added. Increment in the values are observed when highly electro-negative hetero-atoms like Nitrogen, Oxygen of urea and choline cations are counted as the partners of the central water molecules. Further insights are drawn from the characterization of the hydrogen-bonded network of the water and we observe gradual rupturing of water-water hydrogen bonds and its subsequent replacement by the water-urea hydrogen bonds. A negligible contribution from the hydrogen bonds between water and bulky choline cation has also been found. Considering all the constituents as the hydrogen bond partner we calculate the possibility of successful hydrogen bond formation with a central water molecule. This gives a clear picture of the underlying mechanism of water replacement by urea.

scholarly journals A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα–H hydrogen bonds

2014 ◽  
Vol 111 (10) ◽  
pp. E888-E895 ◽  
Author(s):  
Benjamin K. Mueller ◽  
Sabareesh Subramaniam ◽  
Alessandro Senes
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Bond Formation ◽  
Geometric Analysis ◽  
Prediction Method ◽  
Causal Link ◽  
Conformational Space ◽  
Hydrogen Bond Formation ◽  
Frequent Motif ◽  
Single Region

Carbon hydrogen bonds between Cα–H donors and carbonyl acceptors are frequently observed between transmembrane helices (Cα–H···O=C). Networks of these interactions occur often at helix−helix interfaces mediated by GxxxG and similar patterns. Cα–H hydrogen bonds have been hypothesized to be important in membrane protein folding and association, but evidence that they are major determinants of helix association is still lacking. Here we present a comprehensive geometric analysis of homodimeric helices that demonstrates the existence of a single region in conformational space with high propensity for Cα–H···O=C hydrogen bond formation. This region corresponds to the most frequent motif for parallel dimers, GASright, whose best-known example is glycophorin A. The finding suggests a causal link between the high frequency of occurrence of GASright and its propensity for carbon hydrogen bond formation. Investigation of the sequence dependency of the motif determined that Gly residues are required at specific positions where only Gly can act as a donor with its “side chain” Hα. Gly also reduces the steric barrier for non-Gly amino acids at other positions to act as Cα donors, promoting the formation of cooperative hydrogen bonding networks. These findings offer a structural rationale for the occurrence of GxxxG patterns at the GASright interface. The analysis identified the conformational space and the sequence requirement of Cα–H···O=C mediated motifs; we took advantage of these results to develop a structural prediction method. The resulting program, CATM, predicts ab initio the known high-resolution structures of homodimeric GASright motifs at near-atomic level.

scholarly journals Polymorphism, Hydrogen Bond Properties, and Vibrational Structure of 1H-Pyrrolo[3,2-h]Quinoline Dimers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Alexandr Gorski ◽  
Sylwester Gawinkowski ◽  
Roman Luboradzki ◽  
Marek Tkacz ◽  
Randolph P. Thummel ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Raman Spectra ◽  
Bond Formation ◽  
Vibrational Structure ◽  
Hydrogen Bond Donor ◽  
Intermolecular Hydrogen Bonds ◽  
Hydrogen Bond Formation ◽  
Bifunctional Molecule ◽  
Donor And Acceptor ◽  
Ir And Raman

Two forms of cyclic, doubly hydrogen-bonded dimers are discovered for crystalline 1H-pyrrolo[3,2-h]quinoline, a bifunctional molecule possessing both hydrogen bond donor and acceptor groups. One of the forms is planar, the other is twisted. Analysis of IR and Raman spectra, combined with DFT calculations, allows one to assign the observed vibrations and to single out vibrational transitions which can serve as markers of hydrogen bond formation and dimer structure. Raman spectra measured for samples submitted to high pressure indicate a transition from the planar towards the twisted structure. Formation of intermolecular hydrogen bonds leads to a large increase of the Raman intensity of the NH stretching band: it can be readily observed for the dimer, but is absent in the monomer spectrum.

Large perturbations of long-range nJ(1H,1H) and nJ(1H,19F) by the intramolecular hydrogen bonds in 2-mercaptobenzaldehyde, salicylaldehyde, and some derivatives. Reference structures for intramolecular hydrogen bonds

1993 ◽  
Vol 71 (7) ◽  
pp. 960-967 ◽  
Author(s):  
Ted Schaefer ◽  
Rudy Sebastian ◽  
David M. McKinnon ◽  
Perry W. Spevack ◽  
Kerry J. Cox ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Long Range ◽  
Bond Formation ◽  
Coupling Constants ◽  
Hydrogen Bond Formation ◽  
Intramolecular Hydrogen Bonds ◽  
Large Perturbation ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

Precise 1H nuclear magnetic resonance spectral parameters are reported for salicyladehyde and its 3-fluoro and 5-fluoro derivatives in nonpolar solutions. Such data are also given for the 2-mercapto, 2-methylthio, and 2-methoxy derivatives of benzaldehyde. Comparison of the long-range coupling constants in the various compounds and their conformers shows a large perturbation of their magnitudes by hydrogen bond formation. For the salicylaldehyde system, the perturbation is particularly large for couplings involving the aldehyde proton and protons or fluorine nuclei placed ortho to the hydroxyl group. For example, 5Jt (F, CHO) is reduced by about 50%. The perturbation, as expected, is much smaller for coupling constants of nuclei remote from the site of the hydrogen bond. In 2-mercaptobenzaldehyde the long-range coupling constants are also sensitive to hydrogen bond formation, those involving the sulfhydryl proton markedly so compared to the hydroxyl proton in salicylaldehyde. The strength of the [Formula: see text] bond is discussed. It is argued that the reference conformer for the mercapto compound in such a discussion is less easily defined than for salicylaldehyde because [Formula: see text] are similar to [Formula: see text] energies. The experimental data for the CCl4 solutions imply a free energy of formation of the [Formula: see text] bond of 4.8(5) kJ/mol at 300 K. Molecular orbital computations on the four planar conformers of each salicylaldehyde and 2-mercaptobenzaldehyde with the 6-31 G**(5D) basis are reported. For salicylaldehyde, the [Formula: see text] arrangement is taken as the reference conformer, with a computed energy of 25.7 kJ/mol relative to the hydrogen-bonded structure. For 2-mercaptobenzaldehyde, the [Formula: see text] and [Formula: see text] conformers are calculated to be isoenergetic, at 5.1 kJ/mol relative to the hydrogen-bonded conformer. Hence either arrangement serves as a reference structure in computations of the strength of the hydrogen bond. The computations are consistent with the experimental results for solutions of the molecules under discussion. An appendix gives the computed geometries of the eight planar conformers, as well as some atomic charges, allowing a rationalization of the relative energies of the conformers.

Resonance-Induced Hydrogen Bonding at Sulfur Acceptors in R 1 R 2C=S and R 1CS2 − Systems

1997 ◽  
Vol 53 (4) ◽  
pp. 680-695 ◽  
Author(s):  
F. H. Allen ◽  
C. M. Bird ◽  
R. S. Rowland ◽  
P. R. Raithby
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Bond Formation ◽  
Lone Pair ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Coordination Numbers ◽  
Wide Range

The hydrogen-bond acceptor ability of sulfur in C=S systems has been investigated using crystallographic data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. The R1R2C=S bond lengths span a wide range, from 1.58 Å in pure thiones (R 1 = R 2 = Csp 3) to 1.75 Å in thioureido species (R 1 = R 2 = N) and in dithioates —CS^{-}_2. The frequency of hydrogen-bond formation at =S increases from 4.8% for C=S > 1.63 Å to more than 70% for C=S > 1.70 Å in uncharged species. The effective electronegativity of S is increased by conjugative interactions between C=S and the lone pairs of one or more N substituents (R 1 R 2): a clear example of resonance-induced hydrogen bonding. More than 80% of S in —CS^{-}_2 accept hydrogen bonds. C=S...H—N,O bonds are shown to be significantly weaker than their C=O...H—N,O analogues by (a) comparing mean S...H and O...H distances (taking account of the differing non-bonded sizes of S and O and using neutron-normalized H positions) and (b) comparing frequencies of hydrogen-bond formation in `competitive' environments, i.e. in structures containing both C=S and C=O acceptors. The directional properties and hydrogen-bond coordination numbers of C=S and C=O acceptors have also been compared. There is evidence for lone-pair directionality in both systems, but =S is more likely (17% of cases) than =O (4%) to accept more than two hydrogen bonds. Ab initio calculations of residual atomic charges and electrostatic potentials reinforce the crystallographic observations.

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