Narrow Results

We report on theoretical investigation of interactions of different mechanisms and their influence onto DNA cooperativity of helix–coil transition (melting). Using the modified version of microscopic Potts-like one-dimensional model we showed that increased stacking results in decreased correlation length. The decrease in cooperativity is explained as a result of combined hydrogen bonding and stacking.

The secondary amide unit is a subject of particular interest, because of its occurrence in peptides and proteins. Molecular interaction between N-benzylformamide (NBF) with 1-alcohols (1-propanol, 1-butanol, 1-pentanol) has been studied in carbon tetrachloride by using X-band microwave bench at 936 GHz. Dielectric constant (ε') and dielectric loss (ε″) of alcohol and NBF and their binary mixture for different mole fractions of NBF have been determined. Dielectric relaxation time (τ) of the binary system is obtained by both Higasi's method and the Gopalakrishna single-frequency concentration variational method. The results show that the most likely interaction between alcohols and NBF is 1:1 complex for binary mixture through the free hydroxyl group of the alcohol and the carbonyl group of NBF. The alkyl chain-length of both alcohol and amide plays an important role in the determination of the strength of hydrogen bond (O–H: C=O) formed. The variation of relaxation time of NBF+1-alcohol mixtures in CCl₄ indicates a weak solute-solvent type of molecular association. The result shows that as the relaxation time of the proton acceptor increases, the donating ability of the solute environment increase.

Hydrolysis is an important component of the aging of cellulose, and it severely affects the insulating performance of cellulosic materials. The diffusion behavior of water molecules in amorphous cellulose and their destructive effect on the hydrogen bonding structure of cellulose were investigated by molecular dynamics. The change in the hydrogen bonding structure indicates that water molecules have a considerable effect on the hydrogen bonding structure within cellulose: both intermolecular and intramolecular hydrogen bonds decreased with an increase in ingressive water molecules. Moreover, the stabilities of the cellulose molecules were disrupted when the number of intermolecular hydrogen bonds declined to a certain degree. Both the free volumes of amorphous cells and water molecule-cellulose interaction affect the diffusion of water molecules. The latter, especially the hydrogen bonding interaction between water molecules and cellulose, plays a predominant role in the diffusion behavior of water molecules in the models of which the free volume rarely varies. The diffusion coefficient of water molecules has an excellent correlation with water molecule-cellulose interaction and the average hydrogen bonds between each water molecule and cellulose; however, this relationship was not apparent between the diffusion coefficient and free volume.

In order to develop a new DNA sequencing method by using chemical force microscopy (CFM), we have investigated the interaction of the hydrogen bonding between surfaces of nucleobase self-assembled monolayers (SAMs) and AFM-tips modified with the nucleobases. The two different adhesion forces, the jump-in force and pull-off force, between the AFM-tip modified with cytosine-SAM and the surfaces of four kinds of nucleobase SAMs were measured in water (20°C) by CFM. The adsorption of poly (C) onto a nucleobase-SAM on a gold electrode of quartz crystal microbalance (QCM) was measured as resonance frequency changes. The relative relation among four bases showed similar tendency in the adhesion force measured by the cytosine AFM-tip and in the adsorption amount of poly (C) on the QCM electrode as well as in the theoretically calculated interaction energies between two nucleobases.

The effect of gelation and the modulation of their properties with the variation of aliphatic hydrocarbon solvents, e.g., n-decane and n-dodecane have been presented for a homologous series of amides of L-alanine with fatty acids. The gelation properties of these compounds were studied by a number of physical methods including scanning electron microscopy, X-ray diffraction, differential scanning calorimetry, rheology etc. It was found that the gelation properties vary with the chain length of the host aliphatic hydrocarbons. Scanning electron microscopic images showed modulation of the fiber diameters upon changing the solvent from n-decane to n-dodecane and this has been confirmed by the results obtained from small angle X-ray scattering studies independently. Thermal properties were observed under the differential scanning calorimetric studies which showed an increase in the sol–gel transition temperatures upon increase in the chain length of the hydrocarbon solvent. The mechanical behavior of such assemblies has been observed under rheological experiments which showed a more viscoelastic response for the gels in n-decane compared to n-dodecane.

Methyl substituents are introduced into solvated ammonium perchlorate (AP) systems to explicate the effects of methylation on localized hydrogen-bonding. Methylation systems are modeled using density functional theory (DFT) B3LYP type with 4-31G(d, p), 6-311+(2d, p) basis set methods, indicating that whichever methyl group is substituted at the proton site in an ammonium ion or solvent, both methyl groups cease to H-bond, as evidence by elongation of the neighboring bond and characteristic red-shifts in the frequency of vibration. The energy barriers to the conversion from reactants to products in solvated AP systems are also discussed herein to help to elucidate the relationship solubility and H-bonding.

The intramolecular hydrogen bonding formation in ortho-substituted compounds of Acetanilide, ortho-hydroxy Acetanilide and ortho-nitro Acetanilide, was investigated using Density Functional Theory (DFT), Møller-Plesset second-order (MP2) method and "Atoms in Molecules (AIM)" theory. It was found that in each case, the cis isomer is more stable than the trans isomer and ortho-nitro Acetanilide forms a stronger hydrogen bond than ortho-hydroxy Acetanilide. The effects of hydrogen bonding on structural parameters of the considered systems were studied using Becke's functional (B3LYP) and at the ab initio MP2 level in conjunction with different basis sets and suitable structural factors. The results are in agreement with the results of AIM theory.

Hydrogen bonding interactions between trimethylamine (TMA) and a series of para substituted phenols (X–C₆H₄OH, X = H, CH₃, NH₂, Cl, CN, and NO₂) are studied by using density functional theory with the hybrid B3LYP functional and the 6-31++G(d,p) basis set. Both electron donor and acceptor substituents (X) are chosen to study systematically the relation between the proton donor ability of the phenols and the strength of the OH…N hydrogen bond. The effect of hydrogen bonding on spectral and structural parameters and their inter relation are discussed. The natural bond orbital (NBO) analysis (occupation of σ* orbitals, hyperconjugative energies and atomic charges) is also carried out to elucidate the reason behind the spectral and structural changes due to hydrogen bond formation. Several correlations between hydrogen bond strength and bond properties are discussed.

A modified semiempirical model named RM1_BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1_BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1_BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1_BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

We report ReaxFF molecular dynamic simulations of structure change of crystalline nitromethane and the formation of hydrogen bond under high pressure. Under high pressure, the angles between C–N bonds and X, Y and Z axes have changed. Through the calculation of g(r) of O and H atoms, we found a new peak near 1.6 Å, which indicates the formation of the hydrogen bond between O and H atoms. We calculated the distribution of the angles of the C–N bonds orientations, the distribution of the dihedral angle of CNOO, and the charge distribution of nitromethane molecules under various pressures, and made a comparison between low and high pressures. The effects of hydrogen bonding in high explosive materials are discussed.

The time-dependent density functional theory (TDDFT) method has been carried out to investigate the hydrogen-bonding dynamics of methyl acetate (CH₃ CO₂CH₃) in hydrogen-donating water solvent. The ground-state geometry optimizations, electronic transition energies and corresponding oscillation strengths of the low-lying electronically-excited states for the isolated CH₃CO₂CH₃ and H₂O monomers, the hydrogen-bonded CH₃CO₂CH₃-(H₂O)_{1, 2} complexes have been calculated using DFT and TDDFT methods respectively. One intermolecular hydrogen bond C=O⋯H–O is formed between CH₃CO₂CH₃ and one water molecule in CH₃CO₂CH₃-H₂O dimer. Meanwhile, in CH₃CO₂CH₃-(H₂O)₂ trimer, two intermolecular hydrogen bonds C=O⋯H–O are formed between CH₃CO₂CH₃ and two water molecules. By theoretically monitoring the excitation energy changes among the CH₃CO₂CH₃ monomer, the CH₃CO₂CH₃-H₂O dimer, and the CH₃CO₂CH₃-(H₂O)₂ trimer, we have demonstrated interestingly that in some electronically-excited states, the intermolecular hydrogen bonds are strengthened inducing electronic spectral redshifts, while in others weakened with electronic spectral blueshifts. The phenomenon that hydrogen bonds are strengthened in some electronic states while weakened in others can arouse further probe into CH₃CO₂CH₃-(H₂O)_{1, 2} complexes.

Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.

A quantum chemical investigation has been performed to spotlight the structure–property relationship among methoxybenzeylidene-based humidity sensor and water molecules. The chemical interactions among (E)-2-(4-(2-(3,4-dimethoxybenzeylidene)hydrazinyl)phenyl) ethane-1,1,2-tricarbonitrile (DMBHPET) sensor and water molecules have been studied using density functional theory (DFT) methods. The molecular structural parameters, binding energies and Infrared (IR) spectroscopic analyses have been performed to assess the nature of intermolecular interactions. Three different positions have been identified for possible attachments of H₂O molecules through hydrogen bonding interactions. These positions include NH (complex 1a), p-OCH₃ (complex 1b) and N=N (complex 1c) group in sensor molecule (1) for the chemical adsorption of water molecules. While, the complex 1abc includes all three sites with simultaneously three H₂O molecules attached to it through hydrogen bonding. The binding energies calculated for complex 1a(NH…H₂O), complex 1b(CH₃O…H₂O), complex 1c(N=N…H₂O) and complex 1abc are -30.97, -18.41, -13.80 and -65.36 kcal/mol, respectively. The counterpoise (CP) scheme has been used to correct the basis set superposition error (BSSE) in calculation of binding energies of sensor and H₂O complexes. The higher binding energy of -65.36 kcal/mol for complex 1abc represents that the present methoxybenzeylidene-based sensor has significant potential through hydrogen bonding formation for sensing humidity as indicated in our previous experimental investigation. The evidence of hydrogen bonding interactions between sensor 1 and H₂O molecules has been traced through structural parameters, red shift in IR spectra as well as molecular electrostatic maps. Thus the present investigation highlights the first computational framework for a molecular level structure-binding activity of a methoxybenzeylidene-based sensor and water molecules.

The hydrogen bonding interactions between letrozole (Let) anticancer drug and three copolymers of methacrylic acid-trimethylolpropane trimethacrylate (M1–M3 as molecular imprinted polymers) were studied using density functional theory (DFT) at both B3LYP and B3PW91 levels. The binding energies were corrected for the basis set superposition error (BSSE) and zero-point vibrational energies (ZPVE) so that the most negative $\mathrm{\Delta }{E}_{\mathrm{\text{binding}}}$ were measured for compounds 7 and 8 formed between M1 copolymer and endocyclic N1 and N2 atoms of drug, respectively. Also, among complexes 13–15 in which two copolymers were contributed in the formation of O–H$\dots$N bonds with the drug, compound 13 (containing two M1 copolymers) showed the highest $\mathrm{\Delta }{E}_{\mathrm{\text{binding}}}$ value. The interactions of all copolymers with drug were exergonic (spontaneous interaction) and exothermic. The QTAIM data supported the covalent character of the C–N, C–H, N–N, C–O, O–H and O–H$\dots$N bonds, the intermediate nature of C$\equiv$N and C$=$O bonds while the electrostatic character of C–H$\dots$O, HC$\dots$HC and CH$\dots$N interactions. According to the $\mathrm{\Delta }{E}_{\mathrm{\text{binding}}}$, $\mathrm{\Delta }{G}_{\mathrm{\text{interaction}}}$ and $\mathrm{\Delta }{H}_{\mathrm{\text{interaction}}}$ values, it was suggested that t complexes 7 and 8 (among two particles systems) as well as complex 13 (among three particles systems) can be the most promising drug delivery systems.

The genome sequence of Plasmodium falciparum reveals that many metabolic pathways are unique as compared to its human host. Metabolic Network Analysis was carried out to find the essential enzymes critical for the survival of the pathogen. In the present study, choke point and load point analysis was used to locate putative targets. The identified targets were further checked to confirm that no alternate pathway or human homolog exists. Among the top 15 enzymes obtained from this analysis, we have selected P. falciparum orotidine-5'-monophosphate decarboxylase (PfODCase) enzyme as it is sequentially and structurally different from that of humans, for searching novel inhibitors. A five-point 3D pharmacophore was generated for the crystal structure of PfODCase complexes with uridine-5'-monophosphate (U5P). The binding site environment shows three H-bond acceptors, one H-bond donor and one negative ionizable feature. This pharmacophore model was used as a 3D query to perform virtual screening experiments against 2,664,779 standard lead compounds obtained from the freely available ZINC database. Top 10 hits obtained from virtual screening were selected for molecular docking experiments against PfODCase in order to verify their results and to have a better insight into their binding modes. Here, docking of U5P with PfODCase is used as a control. We have identified six compounds, among them, few are U5P analogs and others are novel ones with diverse scaffolds. The key residues: Lys42, Asp20, Lys72, Ser127, Ala184, Gln185 and Arg203 at the main binding pocket of PfODCase are responsible for better stability of diverse ligands. These compounds according to their free energy of binding could serve as potent leads for designing novel inhibitors against malarial ODCase enzyme.

The adsorption behavior of pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) in aqueous solution has been investigated using a hypercrosslinked polystyrene adsorbent (NDA-99) modified by dimethylamine group as well as a nonionic macroporous adsorbent (XAD-4). The Langmuir and Freundlich isotherm models were employed to fit the experimental data to describe adsorption mechanism. It shows that NDA-99 resin exhibits an adsorption affinity for 2,4-D higher than XAD-4 resin owing to its exceptional micropore structure and the amine group of the hypercrosslinked matrix. Further studies indicate that the hydrogen bonding interaction and the stronger π-π conjugation play a significant role in the course of the adsorption of 2,4-D on NDA-99 resin, which is in agreement with the IR spectroscopic results and the ΔE values of HOMO (the highest occupied molecular orbit) of adsorbent and LUMO (the lowest unoccupied molecular orbit) of adsorbate calculated from the MINDO/3 model.

Divinylbenzene-80 (DVB-80) and polar monomer acrylic acid (AA) having hydrogen bonding at a total monomer loading of 5 vol% were precipitated-copolymerized in a variety of organic solvents with 2,2′-azobis(isobutyronitrile) (AIBN) as initiator. The experiments were investigated from a two-dimensional matrix, i.e., the actual crosslinking degree of DVB varying from 0 to 80% and the solvent composition varying from 0 to 100% of toluene mixture with acetonitrile, when the mixture of acetonitrile and toluene was used as the reaction solvent. Under various reaction conditions, six distinct morphologies including soluble polymers, swellable microgels, coagulum, irregular microparticles, and nano-/micrometer microspheres were formed and the structures of these polymer architectures were described. A morphological map was utilized to discuss the effects of both crosslinking degree of DVB and composition of solvent on the transitions between morphology domains. The results demonstrated that the microspheres are formed by an internal contraction due to the marginal solvency of the continuous phase and the crosslinking of the polymer network through the covalent bonding from DVB as well as the interchain hydrogen-bonding between the carboxylic acid units.

The intrinsic viscosity [η], Huggins constant (K_H), [η]₀, α³ and flow activation energy values of nylon 6 have been measured in water/m-cresol (0/100–20/80) systems at different temperatures (20–60°C). It has been found that the intrinsic viscosity, [η]₀ and α³ increase with the increase in water contents in m-cresol up to 15% and then decrease. They increase with the increase in temperature irrespective of solvent composition. It has been noted that the percent increase of α³ is the highest at 60°C and the lowest at 20°C for a particular solvent system. The intrinsic viscosity data obey Arrhenius equation over the considered conditions. The activation energy and the K_H values decrease very sharply with the addition of water, giving a minimum value at 15% of water and then increase slowly. The variation of all the parameters has been explained in terms of variation in thermodynamic quality of solvent with the addition of water to m-cresol and change in temperature, resulting in the change of conformational and orientational properties of polymer molecules. This change of solvent quality also results in variation of selective sorption of solvent over the polymer, such as hydrogen bonding, etc.

Monodisperse poly(poly(ethyleneglycol) methyl ether acrylate-co-acrylic acid) (poly(PEGMA-co-AA)) microspheres were prepared by distillation-precipitation polymerization with divinylbenzene (DVB) as crosslinker with 2,2′-azobisisobutyronitrile (AIBN) as initiator in neat acetonitrile without stirring. Under various reaction conditions, four distinct morphologies including the sol, microemulsion, microgels and microspheres were formed during the distillation of the solvent from the reaction system. A 2D morphological map was established as a function of crosslinker concentration and the polar monomer AA concentration, in comonomer feed in the transition between the morphology domains. The effect of the covalent crosslinker DVB on the morphology of the polymer network was investigated in detail at AA fraction of 40 vol%. The ratios of acid to ethylene oxide units presenting in the comonomers dramatically affected the polymer-polymer interaction and hence the morphology of the resultant polymer network. The covalent crosslinking by DVB and the hydrogen bonding crosslinking between two acid units as well as between the acid and ethylene oxide unit played key roles in the formation of monodisperse polymer microspheres.

A ternary self-assembling system consisting of two Zn(II)carboxyphenylporphyrins and an aliphatic diamine linker was constructed via hydrogen bonding and Coulombic interactions between the porphyrin carboxylic moieties and the amino groups of the spacer. The properties of the resulting structures, in terms of binding of several aromatic diamine guests are described. The stability and geometry of the final host-guest supramolecular architecture (i.e. cyclic or linear array) can be modulated by the nature of the spacer.