Solution and solid-state models of peptide CH...O hydrogen bonds

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.     

几种二醇与非质子溶剂相互作用的红外光谱研究

测定了1，2-乙二醇、1，2-丙二醇、1，4-丁二醇和1，6-己二醇在CCl4中分别与十几种非质子溶剂相互作用的红外光谱，通过考察频率位移的变化，定量地研究了二醇分子内氢键与分子间氢键的协同效应．在四氯化碳介质中，乙二醇、1，2-丙二醇和1，4-丁二醇体系中存在明显的氢键协同效应。利用红外光谱数据，估算了常温下二醇分子内缔体与非质子溶剂的交叉缔合常数，其数值大于一元正链醇与相应溶剂的交叉缔合常数．     

Hydrogen-bonding effects in calix

The synthesis and spectroscopic characterization of self-assembling calix[4]arene based capsules 1a.1a and 1b.1b are described. These compounds feature four urea substituents at the upper rims and four secondary amide fragments at the lower rims that can participate in inter- and intramolecular hydrogen bonding in apolar solution. Communication between the calixarene rims in 1a, b influences the self-assembled cavity's size and shape. Specifically. dimerization results in a perfect cone conformation of the calixarene skeleton in 1a, b and stabilizes a seam of intramolecular amide C=O...H-N hydrogen bonds at the lower rim. This seam is cycloenantiomeric, with either clockwise or counterclockwise arrangements of the head-to-tail amides. Complexation of Na+-cation breaks hydrogen bonds at the lower rim but maintains the capsular assembly. Encapsulation properties of 1a.1a and 1b.1b were studied in nonpolar solvents and their binary mixtures as well as through heterodimerization experiments. The presence of amide groups at the lower rim causes notable differences in the capsule's binding affinities when compared to the corresponding tetraester capsules 1c.1c and 1d.1d. In the monomeric state calixarenes 1a, b are in a pinched cone conformation. The solid state X-ray crystallographic studies with monomeric 1a reveal only two intramolecular C=O...H-N hydrogen bonds between the adjacent amides at the lower rim, and an extensive network of intermolecular hydrogen bonds between urea groups at the upper rim.     

Intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides: an atoms in molecules study

The molecular structure and relative stability of different conformers of isolated canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (pdT), 2-deoxycytidine-5'-phosphate (pdC), 2-deoxyadenosine-5'-phosphate (pdA), and 2'-deoxyguanosine-5'-phosphate (pdG) were calculated using the B3LYP/6-31++G(d,p) level of theory. The results of the calculations reveal that, for all nucleotides except pdG, conformers with a syn orientation of the base do not correspond to a minimum on the potential energy surface. In the case of pdA and pdC, conformers with an orthogonal orientation of the nucleobase are located instead, north/syn conformers. These conformers as well as syn conformers of pdG are stabilized by intramolecular N-H...O hydrogen bonds. Analysis of the electron density distribution within the atoms in molecules theory reveals the presence of numerous C-H...O hydrogen bonds in the nucleotides. However, a more detailed consideration of the properties of these bonds demonstrates that many of them should be considered as strong attractive electrostatic interactions rather than true hydrogen bonds. True hydrogen bonds are represented mainly by C6/ C8-H...O5'/O-P in anti conformers and the N-H...O-P bonds in syn conformers. It is demonstrated that the values of ellipticity of the electron density at the bond critical point (BCP) and the distance between BCP and ring critical point are the most reliable indicators for determining the true intramolecular hydrogen bonds.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: strengthening and weakening

Time-dependent density functional theory (TD-DFT) method was used to study the excited-state hydrogen bonding of three esculetin complexes formed with aprotic solvents. The geometric structures, molecular orbitals (MOs), electronic spectra and the infrared (IR) spectra of the three doubly hydrogen-bonded complexes formed by esculetin and aprotic solvents dimethylsulfoxide (DMSO), tetrahyrofuran (THF) and acetonitrile (ACN) in both ground state S(0) and the first singlet excited state S(1) were calculated by the combined DFT and TD-DFT methods with the COSMO solvation model. Two intermolecular hydrogen bonds can be formed between esculetin and the aprotic solvent in each hydrogen-bonded complex. Based on the calculated bond lengths of the hydrogen bonds and the groups involved in the formation of the intermolecular hydrogen bonds in different electronic states, it is demonstrated that one of the two hydrogen bonds formed in each hydrogen-bonded complex is strengthened while the other one is weakened upon photoexcitation. Furthermore, it is found that the strength of the intermolecular hydrogen bonds formed in the three complexes becomes weaker as the solvents change from DMSO, via THF, to ACN, which is suggested to be due to the decrease of the hydrogen bond accepting (HBA) ability of the solvents. The spectral shifts of the calculated IR spectra further confirm the strengthening and weakening of the intermolecular hydrogen bonds upon the electronic excitation. The variations of the intermolecular hydrogen bond strengths in both S(0) and S(1) states are proposed to be the main reasons for the gradual spectral shifts in the absorption and fluorescence spectra both theoretically and experimentally.     

New deuterium isotope effects on C and F chemical shifts across intramolecular hydrogen bonds of non-resonance assisted systems

A series of thioanilides and corresponding anilides, some of which contain fluorinated phenyl rings, have been synthesized as model compounds. They all contain rather strong intramolecular hydrogen bonds, the strength of which varies. Deuterium isotope effects on ¹⁹F and ¹³C chemical shifts due to deuteriation at the NH proton show interesting new long-range isotope effects on chemical shifts that may be related to the existence of an intramolecular hydrogen bond and to transmission of the isotope effect due to an electric field effect. Deuterium isotope effects on chemical shifts report on variations in hydrogen bonding, for example, as a function of changes in substituents or temperature. Deuteriation leads to a strengthening of the hydrogen bond.     

“Crystal” conformations of 2-methyl-2,4-pentanediol: Dipole moment calculations and molecular structure optimizations

The structures of eight symmetrically independent molecules of 2-methyl-2,4-pentanediol (MPD) in six crystal substances are studied based on the data retrieved from the Cambridge Structural Database (CSD). Coordinates of the most part of hydrogen atoms in MPD molecules were not determined experimentally or not presented in CSD, however, O...O distances provide the conclusion about the formation of intramolecular hydrogen bonds in four molecules. To perform quantum chemical calculations the absent hydrogen atoms were added. The choice of H atomic positions in hydroxyl groups are based on the analysis of possible formation of intra- and intermolecular hydrogen bonds by MPD molecules in the respective crystals. The DFT method with the B3PW91 functional and the 6-31G(d,p) basis set is used to carry out for the first time: 1) the calculation of dipole moments and energies for MPD molecules in “crystal” conformations; 2) the optimization of the structure of these molecules with the calculation of dipole moments for the conformations corresponding to the local energy minima. It is found that among the molecules with the experimental geometric parameters one of the conformations without intramolecular hydrogen bonds is most favorable (μ = 0.56 D). As a result of the energy minimization of eight “crystal” conformations in vacuum, five energetically different conformers are obtained. Among them the conformer with the intramolecular hydrogen bond has the lowest energy (μ = 3.53 D). Four variants of the molecular structure correspond to it in the considered crystals, out of which two are R-enantiomers and two S-enantiomers.     

Molecular interpretation of water structuring and destructuring effects: hydration of alkanediols

Molecular electrostatic potential (MESP) guidelines are employed for understanding the reactivity and hydration patterns in alkanediol molecules. The deeper oxygen lone pair MESP minima indicate stronger basicity of 1,n-diols and 2,4-pentanediol (2,4-PeD) as compared to that of vicinal diols. The existence and strength of the intramolecular hydrogen bond in diols are gauged in terms of the electron density at the bond saddle points. A model named electrostatic potential for intermolecular complexation (EPIC) is used for generating the structures of hydrated complexes, which are subsequently subjected to ab initio calculations at M?ller-Plesset second-order perturbation level of theory. Further, the nature of water...water as well as diol...water interactions is appraised employing many-body energy decomposition analysis. It is seen that water...water interactions are more favorable in vicinal diol...6H(2)O than those in 1,n-diol...6H(2)O (n=3, 4, 5,...) complexes. Exactly opposite trends are shown by diol...water interaction energies. Thus vicinal diols, being more effective at strengthening water...water network, are expected to act as water structuring agents, whereas the non-vicinal diols are expected to be water destructuring agents.     

Investigation of self-association of the selected glycols on cellulose sorbents

A comparison was performed of the selected glycols, i.e., 1,2-ethanediol, 1,3-propanediol, 1,4-butanediol, and 1,5-pentanediol, in respect of their ability to form intramolecular hydrogen bonds. The following analytical techniques were employed: ir absorption spectroscopy and a new method taking advantage of chromatographic paper.     

Interplay of intramolecular hydrogen bonds,OH orientations,and symmetry factors in the stabilization of polyhydroxybenzenes

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     

Dimerization of the keto tautomer of acetohydroxamic acid-infrared matrix isolation and theoretical study

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO...HON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO...HN hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular NH...O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies (DeltaE(ZPE)(CP)I, II=-7.02, -6.34 kcal mol-1) being less stable than calculated structures III and IV (DeltaE(ZPE)(CP)III, IV=-9.50, -8.87 kcal mol-1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO...HON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA)2 dimers in the studied matrixes indicates that the formation of (AHA)2 is kinetically and not thermodynamically controlled.     

CP/MAS 13C NMR analyses of hydrogen bonding and the chain conformation in the crystalline and noncrystalline regions for poly(vinyl alcohol) films

The chain conformation and hydrogen bonding in the crystalline and noncrystalline regions have been characterized for atactic poly(vinyl alcohol) (PVA) films prepared under different conditions by CP/MAS ¹³C NMR analyses developed recently. The CH resonance lines of the crystalline and noncrystalline components split in different ways, depending significantly on casting solvents and annealing. These lines are found to be successfully resolved into 3–7 constituent lines by the least‐squares curve fitting. In this analysis, nine lines with different chemical shifts are prepared as elementary lines for the curve fitting by assuming the upfield shifts due to the γ‐gauche effect and the downfield shifts due to the formation of the intramolecular hydrogen bonds. The integrated intensities of the constituent lines thus obtained are also interpreted in terms of statistical calculations, assuming the random distribution of the trans and gauche conformations along PVA chains and the statistical distribution of the intramolecular and intermolecular hydrogen bonds between appropriate adjacent OH groups. On the basis of probabilities f_t and f_a for the trans conformation and the intramolecular hydrogen bond obtained through these analyses, the effects of casting solvents and annealing are discussed for both crystalline and noncrystalline components. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1–9, 2000     

The effect of the solvents on the specific intramolecular C-H...N interactions studied by1H NMR spectroscopy

The analysis of the effect of the solvents on the proton chemical shifts in¹H NMR spectra of 2-vinyloxypyridine indicates that the C—H...N interaction of weak intramolecular hydrogen bond type hinders the formation of intermolecular hydrogen C—H...X and C-H... bonds. The protonating solvents reduce the intramolecular C—H...N interaction due to association with the N atom of the pyridine cycle.Translated fromIzvestiya Akademii Nauk. Seriya Khimieheskaya, No. S, pp. 1202–1204, May, 1996.     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

Chiral discrimination in hydrogen‐bonded complexes of 2‐methylol oxirane with hydrogen peroxide

A systematic quantum chemical study reveals the effects of chirality on the intermolecular interactions between two chiral molecules bound by hydrogen bonds. The methods used are second‐order Møller–Plesset perturbation theory (MP2) with the 6‐311++g(d,p) basis set. Complexes via the O? H···O hydrogen bond formed between the chiral 2‐methylol oxirane (S) and chiral HOOH (P and M) molecules have been investigated, which lead to four diastereomeric complexes. The nomenclature of the complexes used in this article is enantiomeric configuration sign corresponding to English letters. Such as: sm, sp. The relative positions of the methylol group and the hydrogen peroxide are designated as syn (same side) and anti (opposite side). The largest chirodiastaltic energy was ΔE_chir = ?1.329 kcal mol^?1 [9% of the counterpoise correct average binding energy D_e(corr)] between the sm‐syn and sp‐anti in favor of sm‐syn. The largest diastereofacial energy was ?1.428 kcal mol^?1 between sm‐syn and sm‐anti in favor of sm‐syn. To take into account solvents effect, the polarizable continuum model (PCM) method has been used to evaluate the chirodiastaltic energies, and diastereofacial energies of the 2‐methylol oxirane···HOOH complexes. The chiral 2,3‐dimethylol oxirane (S, S) is C₂ symmetry which offers two identical faces. Hence, the chirodiastaltic energy is identical to the diastereomeric energy, and is ΔE_chir = 0.563 kcal mol^?1 or 5.3% of the D_e(corr) in favor of s,s‐p. The optimized structures, interaction energies, and chirodiastaltic energies for various isomers were estimated. The harmonic frequencies, IR intensities, rotational constants, and dipole moments were also reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Spectroscopic studies on intra- and inter-molecular hydrogen bonding in 2,4-dinitrophenol and 3,5-dinitrosalicylic acid

Effect of solvent on the electronic spectral behaviour of 2,4-dinitrophenol (I) and 3,5-dinitrosalicylic acid (II) is examined and discussed. It is deduced that in case of (I) the intramolecular hydrogen bond to nitro breaks to form an intermolecular hydrogen bond depending upon the nature of solvent used whereas (II) remains intramolecularly hydrogen bonded to carbonyl group in solvents as strongly basic as DMF.     

Structures of N—（2,3,4,6—Tetra—O—acetyl—β—D—glycosyl） thiocarbamic Benzoyl Hydrazine

The crystal structure of N-(2,3,4,6-tetra-O-acetyl-β-D-gly-cosyl)-thiocarbamic benzoyl hydrazine(C22H27N3O9S) was determined by X-ray diffracton method.The hexopyranosyl ring adopts a chair conformation.All the ring substituents are in the equatorial positions.The acetoxyl-methyl group is in synclinal conformation.The S atom is in synperiplanar conformation while the benzoyl hydrazine moiety is anti-periplanar.The thiocarbamic moiety is almost companar with the benzoyl hydrazine group.There are two intramolecular hydrogen bonds and one intermolecular hydrogen bond for each molecule in the crystal structure.The molecules form a network structure through intermolecular hydrogen bonds.     

Effects of sugar ring puckering, anti-syn interconversion and intramolecular interactions on N-glycosidic bond cleavage in 3-methyl-2��-deoxyadenosine and 2��-deoxyadenosine

The effects of structural parameters and intramolecular interactions on N-glycosidic bond length in 3-methyl-2??- deoxyadenosine (3MDA) and 2??-deoxyadenosine (DA) were investigated employing quantum mechanical methods. All calculations were performed at B3LYP/6-311++G** level in the gas phase. The N-glycosidic bond length strongly depends on sugar configuration; it is shorter in syn conformation relative to anti in many cases where they have the same sugar ring configuration. The sugar conformation can influence the N-glycosidic bond through interaction with the O4?? atom. The impact of intramolecular improper hydrogen bonds and H-H bonding interactions on N-glycosidic bond length was investigated in DA and 3MDA and their modeled structures. Improper hydrogen bonds decrease N-glycosidic bond length while H-H bonding interactions increase it.     

Critical effects of alkyl chain length on fibril structures in benzene-trans(RR)- or (SS)-N,N'-alkanoyl-1,2-diaminocyclohexane gels

Vibrational circular dichroism (VCD) spectra were recorded on benzene-d(6) gels formed by chiral low molecular mass gelators (LMGs), trans(RR)- or trans(SS)-N,N'-alkanoyl-1,2-diaminocyclohexane (denoted by RR-C(n) or SS-C(n), respectively; n = the number of carbon atoms in an introduced alkanoyl group). Attention was focused on the effects of alkyl chain length on the structures of the gels. When n was changed from 6 to 12, the signs of the coupled peaks around 1550 cm(-1) in the VCD spectra, which were assigned to the symmetric and asymmetric C=O stretching vibrations from the higher to lower wavenumber, respectively, critically depended on the alkyl chain length. In the case of RR-C(n), for example, the signs of the couplet were plus and minus for n = 8, 9, 10 and 12, while the signs of the same couplet were reversed for n = 6 and 7. The conformations of LMGs in fibrils were determined by comparing the observed IR and VCD spectra with those calculated for a monomeric molecule. The observed reversal of signs in the C=O couplet was rationalized in terms of the different modes of hydrogen bonding. In the case of C(8), C(9), C(10) and C(12), gelator molecules were stacked with their cyclohexyl rings in parallel, forming double anti-parallel chains of intermolecular hydrogen bonds using two pairs of >NH and >C=O groups. In case of C(6) and C(7), gelator molecules were stacked through a single chain of intermolecular hydrogen bonds using a pair of >NH and >C=O groups. The remaining pair of >NH and >C=O groups formed an intramolecular hydrogen bond.