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In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

A new series of thermotropic polyurethanes containing biphenyl units was synthesized by polyaddition reaction of diisocyanates such as 2,6-tolylene diisocyanate, 2,5-tolylene diisocyanate, 2,4-tolylene diisocyanate, and 1,4-phenylene diisocyanate, with 4,4□-bis(9-hydroxynonoxy)biphenyl (BP9). Structures of the monomer and the corresponding polymers were identified using FT-IR and ¹H NMR spectroscopic methods. BP9 exhibited a smectic type mesophase, however, nematic phase was found for all synthesized liquid crystalline polyurethanes except for 1,4-phenylene diisocyanate/BP9 based polyurethane. Their phase transition temperatures and thermal stability were investigated by differential scanning calorimetry (DSC), optical polarizing microscopy, and X-ray scattering. The infrared study indicated that the hydrogen bonding among urethane linkages attributed to the mesomorphism. Thermal gravimetric analysis (TGA) of synthesized polyurethanes showed that no weight loss of the polymers observed up to 280°C.

The effects of structure nonuniformity and thermal perturbation on properties of proton conductivity in hydrogen-bonded systems with damping exposed in an externally applied electric-field have been numerically studied by fourth order Runge–Kutta method in our soliton model. The results obtained show that the proton-soliton is very robust against the structure disorder including the fluctuation of the force constant and disorder in the sequence of masses and thermal perturbation and damping effect of medium, its velocity of conductivity increases with increasing externally applied electric-field and with decreasing damping coefficient of medium, but the proton-soliton disperses at quite great fluctuations of force constant and damping coefficient. In the meantime, the proton-soliton in ice crystals is thermally stable in the region of temperature of T ≤ 273 K. From the numerical simulation, we find out that the mobility (or velocity) of proton conduction in ice is a nonmonotonic function of temperature in the temperature region of 170–273 K, i.e., it increases initially, reaches a maximum at about 191.4 K, subsequently decreases to a minimum at about 211.6 K, and then increases again. This changed rule of mobility obtained consists qualitatively with its experimental datum in ice in the same temperature region. Thus these results provide an evidence for the soliton excited in the hydrogen-bonded systems.

The degree of polymerization (DP) has been regarded as an important symbol of mechanical strength, reflecting the aging condition of transformer insulation paper. In this article, a new concept called fracture degree is proposed on the basis of DP. First, nine cellulose I_β crystal models with different fracture degrees were built. Then relevant mechanical parameters and hydrogen bond numbers were calculated by molecular dynamics (MD) simulation. Results showed that during the aging process of insulation paper with fracture of cellulose chain, the elastic constant C₃₃ produces appreciable impact on the Young's modulus (E). With the decrease of DP and increase of fracture degree, the Young's modulus step decreases. To the 50% and 100% fracture degree models respectively, the relationship between their different degrees of polymerization and Young's modulus is subjected to similar exponential distributions. With the increase of the fracture degree, the average hydrogen bond number drops, and the change rules apply to the Young's modulus. Since hydrogen bond is the main factor of mechanical strength, it can be inferred that the fracture degree influences mechanical strength seriously.

The Debye relaxation of dielectric spectroscopy exists extensively in monohydroxy alcohols, and the existing theory of the dielectric strength is obviously inconsistent with the experimental results. In this paper, we propose an Ising model of infinite free-rotating pseudospin chains and get the exact solution of the dielectric strength versus temperature. The model predictions are qualitatively consistent with the experimental results, especially the crossover from the low to the high-temperature Curie–Weiss law. The quantitative comparisons indicate that the model predictions can agree well with the experimental data below 250 K.

We studied the morphology of yarns obtained from Manila hemp (also known as Abacá) fiber bundles to find a possible correlation with the enhancement in mechanical properties of yarns relative to the original natural fiber bundle. Long Manila hemp fiber bundles had lignin and hemicelluloses removed, twisted and dried to form yarns. Scanning electron micrography revealed that the collapse of lumens inside the fibers leads to densification and consequent increase of tensile properties of the yarns. The densification occurs after the chemical removal of noncellulosic substances from the interstices of cellulose fibrils. These cellulosic elements are then bridged by hydrogen bonds during the drying step of yarn fabrication.

The original length d₀ of N—H and H⋯O bonds in various inorganic systems was comprehensively studied from a chemical bond viewpoint. Two linear relationships between d₀ and the average bond lengths of each system, d_{0, N-H}, versus and d_{0, H⋯O} versus were respectively established. It is indicated that d₀ is affected by the crystalline environment evidently, therefore, the valence electron distribution of hydrogen atom which depends on the lengthening degree of the original bond length is strongly affected by the chemical environment of hydrogen atoms. The obtained valence electron distributions of hydrogen are in a good agreement with the bond valence sum rule, and their overall applicability to ammonium ion interactions was discussed.

From the chemical bond viewpoint, the microscopic characterstatics of hydrogen bonds in M_i—OH₂⋯O (M is the metal cation coordinated to water molecule and i is the number of M) systems were comprehensively studied. It is shown that the original O—OH and H⋯O bond lengths of each hydrogen bonding system are evidently influenced by the crystalline environment and strongly dependent on the corresponding average bond lengths of each system, and . Furthermore, the hydrogen bonding capability of water molecules coordinated to various metal cations was properly estimated and found to be related to the ionic electronegativities of these metal cations. The current work provides a useful route to calculating hydrogen bond valences within reasonable accuracy and sheds light on the rational utilization of hydrogen bonds in crystal design.

The crystals of a new molecular complex, i.e. p-nitroaniline with L-tartaric acid were obtained by slow evaporation of an aqueous solution at room temperature. Room temperature powder infrared measurements were carried out. Tentative assignment for most bands was done. Very strong and broad absorption in the region of 3200–1800 cm^-1 of infrared spectrum is observed. This notable vibrational effect suggests the presence of intense hydrogen-bonded network in the crystal structure of the complex. Second harmonic generation (SHG) efficiency d_eff = 3.85 d_eff(KDP). Some spectral features of this new crystal are referred to corresponding one for two other crystals comprising p-nitroaniline molecule i.e. p-nitroanilinium perchlorate and p-nitroanilinium-p-toluene-sulphonate.

Experimental studies of the Raman scattering of the band of C = O vibrations of acetone (1710 cm^–1) showed that the parallel and perpendicular polarized components have a large half-width (respectively, 11.6 and 18 cm^–1) and also the bands' maxima of these components are shifted by ~5 cm^–1. In the neutral solvent (heptane), the difference of the maxima position of the bands decreases. Calculations showed that the molecules of acetone can aggregate to form a dimer with the energy gain of 10.1 kJ/mole. In the dimer several hydrogen bonds are formed between the oxygen atom of one molecule and the hydrogen atoms of CH₃-group of another molecule. In an aqueous mixture of acetone, according to calculations, there is a possibility for formation of dimers and closed trimer aggregates with the energy gain, respectively, 19.1 and 45.8 kJ/mole. Calculation showed that symmetric and antisymmetric O–H vibrations of water are displaced in the interaction with acetone to lower frequencies, respectively, to 3808.4 and to 3931.8 ^–1.

A new inorganic molecule [Co(Hbim)(C₆H₄O₂)(NH₃)₂]₂ that can be used as a new optically durable molecular switch was theoretically designed in the framework of density functional theory. Three stable minima, belonging to ¹A_g, ⁵A₁, and ⁹A_g states, were found in the complex. Theoretically predicted infrared spectra of the complexes showed that a strong peak of NH stretching vibration is observed at 2690, 2120, and 2770 cm^-1 in the ¹A_g, ⁵A₁, and ⁹A_g states, respectively. The apparent red shift of the NH stretching vibration band in the ⁵A₁ state make it possible to distinguish the electronic state from others (¹A_g and ⁹A_g). This means that the complex can be used as a molecular level switch whose memory can be stably read by IR light without any photoreaction process; namely, without memory degradation.

A theoretical investigation about the cooperative effect on (HCN)_n homo and (HCN)_n ⋯ HF heterochains was performed in terms of structural parameters and topological properties obtained in concordance with the protocol of Bader's atoms in molecules theory. Initially, the hydrogen bonding distances, electronic densities, and Laplacian descriptors were used to characterize small (HCN)_n and (HCN)_n ⋯ HF chains formed by n = 2–4 units of HCN. Hydrogen bond distances and distribution of charge density have revealed that the cooperative effect on (HCN)_n ⋯ HF heterochains is ruled by the polarity of the extreme hydrofluoric acid species. Furthermore, we investigated larger homo and heterochain systems formed by n = 2–8 molecules of HCN. In this insight, the drastic polarized effect caused by HF molecule which was considered very substantial at prior, in fact is seriously limited by an excessive number of HCN molecules connected to the heterochain. This leads to a stabilization of the (N ⋯ HF) hydrogen bonds with invariable electronic density in the range of . In this stage and henceforth, the cooperative effect is re-established with n = 4 molecules of HCN. Thereby, the electronic density of the hydrogen bonds become unaltered within the (HCN)_n ⋯ HF heterochains.

Ab initio and density functional calculations are used to analyze the interaction between a molecule of fulminic acid with one, two, three, and four molecules of ammonia along with a 2:2 complex at B3LYP/6-311++G(d, p) and MP2/6-311++G(d, p) computational levels. Cooperative effect (CE) in terms of stabilization energy of clusters is calculated and discussed as well. For the studied clusters, the CE is increased with increasing cluster size. Red shifts of H–C stretching frequency for complexes involving HCNO as H-donor are predicted. Atom in molecules is used to analyze the cooperative effect on topological parameters.

The effects of hydrogen bond interactions upon ionization potentials (IPs) and electron affinities (EAs) of adenine–formamide (AF) complexes have been investigated employing the density functional theory B3LYP. It is found that the hydrogen bond interactions between adenine and formamide play a more important role in the process of electron attachment than in the process of electron detachment. Meanwhile, the hydrogen bond interactions facilitate the adiabatical electron detachment and attachment but have different effects on the vertical electron detachment and attachment with different positions of formamide. Furthermore, when the complexes were dissociated to the free monomers, the processes AF^- → A^- + F and AF⁺ → A⁺ + F are energetically preferable for AF^- and AF⁺, respectively.

A DFT/B3LYP study was performed to calculate ¹⁵N chemical shielding tensors in (benzamide)_{n = 1-6} clusters. We found that N–H⋯O hydrogen bonds around the benzamide molecule in crystalline lattice have significant influences on the ¹⁵N chemical shielding tensors. For (benzamide)_n clusters, the n-dependent trend in ¹⁵N chemical shielding appears to be correlated with cooperative effects in R_[N–H⋯O] bond distance. Natural bonding orbital (NBO) analysis was used to rationalize the chemical shielding results in terms of charge delocalization effects in the benzamide clusters. This suggests that ¹⁵N chemical shielding measurements can provide a useful probe of electron delocalization phenomena in both gaseous and condensed media.

The micro-structure, and IR spectrum of water molecules in 1-butyl-3-methylimi- dazolium tetrafluoroborate([Bmim]BF₄)/water mixture with different concentrations (x₁ = 25.0%, 50.0%, 75.0%, and 90.0%) were studied with molecular dynamics simulation at room temperature. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in pure water. With the increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift from 566.2 to 651.4 cm^-1 and from 1638.4 to 1683.2 cm^-1 respectively, whereas the O–H stretch bands show blue shift from 3519.8 to 3452 cm^-1, which agree well with the experimental results. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the inter- or intra-molecular modes of water molecules.

The hydrogen-bonding characters between FNO and HO₂ radical are studied systematically with the MPWB1K method and 6-311++G(d, p), aug-cc-PVDZ as well as aug-cc-PVTZ basis sets. The relevant geometrical characteristics, energy properties, and the characters of the intramolecular hydrogen bonds have been reported in this work. In addition, the changes of electrostatic potential density are presented for further understanding the nature of hydrogen bonds and the preference of F atom as the hydrogen-bonding site.

It is important to understand how ionic liquids interact with aromatic sulfur compounds in view of ionic liquids application in desulfurization from fuels. Ion pairs of N, N-dialkylimidazolium dialkylphosphate ionic liquids were optimized at the Becke3LYP level of density functional theory. The most stable geometries were obtained. The stable ion pairs indicate there exist hydrogen bonding interactions between them. The calculated interaction energies of ion pairs were found to increase in magnitude with decreasing alkyl chain length, and with decreasing anionic radius. Furthermore, the interactions between the IL and aromatic sulfur compound, and benzene molecule were investigated. The results indicate that there exist hydrogen bonds between them. The calculated interaction energy between IL and sulfur compound is larger than that between IL and benzene. The aromatic ring π - π interaction and hydrogen bonding interaction may be the dominant factors to influence the trend of interaction between ILs and aromatic sulfur compounds.

Compared with para-substitution, substituent effects (R = NH₂, OH, CH₃, F, Cl, H, SiH₃, CHO, CN, NO₂) of meta-position effects on hydrogen-bonded complex of aniline with one water molecule are studied at B3LYP/6-311++G(d,p) level of theory. The differences in hydrogen bonding and some properties associated with the H-bond (such as bond length, vibrational frequency, binding energies, pK_a values of aniline derivatives) are discussed between meta and para substitutions. Natural bond orbital (NBO) and atoms in molecules (AIM) analysis are applied to investigate the physical origin of the differences. The results show that the differences are mainly attributed to the variations in electron delocalization from amino group to phenyl ring (reflected by interaction) induced by substituents.

Quantum chemical calculations at the MP2 level with the aug-cc-pVTZ basis set were used to investigate the HX⋯(BrCl)_n (X = F, Cl, Br and n = 1, 2) complexes. They are connected via hydrogen bond or halogen bond in dimers and together in trimers. Molecular geometries, interaction energies, cooperative energies and atomic charge of dyads and triads have been studied at the Mp2/aug-cc-pVTZ computational level. All studied trimers show cooperativity with the simultaneous presence of a hydrogen and one or two halogen bond. The molecular electrostatic potential has been employed to explore the formation mechanisms of these molecular complexes. The AIM analysis has been performed at the Mp2/aug-cc-pVTZ level to examine the topological characteristics, confirming the coexistence of hydrogen bonds and one or two halogen bond for each complex.