The nature of hydrogen bonding in R22(8) crystal motifs – a computational exploration

R²₂(8), a commonly occurring motif in organic crystals, has been examined here through ab initio and density functional theory (DFT) methods. The 11 R²₂(8) motifs reported by Allen et al. have been classified into five types; their structural features, hydrogen-bonding patterns and the kind of interactions stabilising these motifs have been studied. Results reveal that the electronegativity of donor atoms plays a major role in directing the hydrogen bonds, whereas their positions in the motif have been found to be less important. Quantum theory of atoms in molecules (QTAIM) and reduced density gradient-based non-covalent-interaction analyses have been used to understand the weak interactions between monomers. Homonuclear interactions within the motifs have been found to be stronger with higher covalent character at the bond critical points than heteronuclear interactions. In addition, a localised molecular orbital energy decomposition analysis (LMOEDA) has been accomplished to provide useful insight into various long- and short-range interactions that contribute to the total stabilisation energies. The stabilising n → σ* interactions have been explained using natural bond orbital (NBO) analysis. Overall, this study provides the essential criteria for an organic crystal to be in an R²₂(8) motif and further discusses the different combinations of hydrogen-bonding features within the R²₂(8) motifs.     

Exciton eigenstates and biexciton interaction energies in a spherical core/shell semiconductor hetero-nano structure

The exciton eigenstates and biexciton interaction energies in a spherical core–shell hetero-nano structure in the type II and the quasi-type II carrier localization regimes have been analyzed. For the analysis, we have evaluated the electron–hole overlap integral, the binding energy of exciton ground state, and the interaction energy of bi-exciton ground state in the structure. In the evaluation, the first order perturbation approach has been employed, where the direct Coulomb interaction energy, the surface polarization energy and the dielectric solvation energy are included. Our results show that the exciton eigenenergies and exciton–exciton interaction energy strongly depend on the choice of materials on which both the dielectric constants and the electron and hole effective masses rely.     

单壁碳纳米管能带及其电子特性研究

从能带理论出发,采用电子紧束缚能量色散关系,推导锯齿,扶手椅和手性单壁碳纳米管(SWCNT)的电子能带结构表达式,指出单壁碳纳米管或为金属或为半导体的判据。结果表示:单壁碳纳米管的电子结构与其几何结构密切相关,如扶手椅型单壁碳纳米管是金属性的,而对其它类型的单壁碳纳米管是与碳纳米管的手性指数有关,只有手性指数n和m的差别等于3的倍数时,单壁碳纳米管是金属性的,否则会显出有带隙的半导体特性。这意味着单壁碳纳米管是由特殊的电子传输和光学性质,在纳米电子学领域具有巨大的潜在应用价值。     

光谱法研究ZnO量子点与头孢哌酮钠的相互作用

本文采用均匀沉淀法,在室温条件下,合成了较为稳定的ZnO量子点。用荧光光谱法、紫外可见分光光度法分析了ZnO量子点与头孢哌酮的相互作用,用Stern-Volmer方程研究了头孢哌酮对ZnO量子点的荧光猝灭作用,结果表明属于静态荧光猝灭,计算了不同温度时的猝灭常数(292K:9.550×103 L·mol-1、303K:5.980×103 L·mol-1、313K:4.412×103 L·mol-1)和热力学参数,证明二者主要以范德华作用和氢键作用力结合。根据Forster的偶极-偶极非辐射能量转移原理计算出结合位置距离色氨酸残基2.47nm,发生分子内的非辐射能量转移。为探讨纳米颗粒与此类药物分子之间相互作用的化学机理提供了重要的信息。     

Molecular dynamics study of DNA binding by INT‐DBD under a polarized force field

The DNA binding domain of transposon Tn916 integrase (INT‐DBD) binds to DNA target site by positioning the face of a three‐stranded antiparallel β‐sheet within the major groove. As the negatively charged DNA directly interacts with the positively charged residues (such as Arg and Lys) of INT‐DBD, the electrostatic interaction is expected to play an important role in the dynamical stability of the protein–DNA binding complex. In the current work, the combined use of quantum‐based polarized protein‐specific charge (PPC) for protein and polarized nucleic acid‐specific charge (PNC) for DNA were employed in molecular dynamics simulation to study the interaction dynamics between INT‐DBD and DNA. Our study shows that the protein–DNA structure is stabilized by polarization and the calculated protein–DNA binding free energy is in good agreement with the experimental data. Furthermore, our study revealed a positive correlation between the measured binding energy difference in alanine mutation and the occupancy of the corresponding residue's hydrogen bond. This correlation relation directly relates the contribution of a specific residue to protein–DNA binding energy to the strength of the hydrogen bond formed between the specific residue and DNA. © 2013 Wiley Periodicals, Inc.     

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000‐fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end‐state free energy method to calculate the binding free energies of biotin to wild type streptavidin and its F130L mutant. The absolute binding affinities based on AMBER charge are repulsive, and the mutation induced binding loss is underestimated. When using the polarized protein‐specific charge, the absolute binding affinities are significantly enhanced. In particular, both the absolute and relative binding affinities are in line with the experimental measurements. Further investigation indicates that polarization effect is indispensable in both the generation of structural ensembles and the calculation of interaction energies. This work verifies Baugh's conjecture that electrostatic polarization effect plays an essential role in modulating the binding affinity of biotin to the streptavidin through F130L mutation. © 2013 Wiley Periodicals, Inc.     

Spectral Studies on the Binding Behavior of Cationic Dyes and Surfactants with Bacterial Polysaccharide of Klebsiella K43

The binding behavior of acidic capsular polysaccharide (SPS), isolated from Klebsiella serotype K43, with oppositely charged dyes and surfactants have been studied by way of absorbance and emission spectroscopic measurements. Each repeating unit of the SPS consists of three D-mannose, one D-galactose, and one D-glucuronic acid residue. The anionic polysaccharide exhibited chromotropic character and induced strong metachromasy in the cationic dye, pinacyanol chloride (PCYN) through the formation of a 1:1 stoichiometric complex. Evaluation of thermodynamic parameters, viz., changes in free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), for the formation of dye-polymer complex and studies on the effect of different cosolvents were also evaluated to shed light on the binding nature as well as the extent of stability of the dye-polymer complex. Fluorescence of the cationic dye acridine orange (AO) was quenched with the progressive addition of SPS, which was found to be of Stern-Volmer type. Cationic surfactants in their pure form as well as in the mixed state with nonionic surfactant (Tween-20), replaced the dye bound to the polymer matrices; thus the original band intensities of the dyes could be reverted. Such studies revealed the involvement of both electrostatic as well as hydrophobic interactions between the dye-polymer as well as surfactant-polymer aggregates.     

Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

Synthesis,Characterization, Solution Stability Studies,Electrochemistry, and DNA‐Binding Behavior of Cu(II) Complexes of D‐Gluconic Acid

The chemistry of saccharides has emerged as a new subarea of pharmaceuticals. Condensation reactions of D‐gluconic acid with [M(en)₂]Cl₂/[M(ea)₂]Cl₂ where M=Cu, Ni, en=ethylenediamine, and ea=ethanolamine were carried out and a new series of chiral complexes have been isolated and characterized. Molar conductance measurements show that the complexes are ionic, and the spectral data are indicative of octahedral geometry of the complexes [Cu(D‐GlcCO₂H en*)₂ (H₂O)₂] · Cl₂ (1b), [Cu(D‐GlcCO₂H ea*) (H₂O)₂] · Cl₂ (3b) and [Ni(D‐GlcCO₂H ea*) (H₂O)₂] · Cl₂ (4), and the square planar geometry of complex [Ni(D‐GlcCO₂H en*)₂] · Cl₂ (2b). Polarimetric data along with CD spectra establish the chiral nature of complexes. Solution stabilities of these complexes were evaluated by cyclic voltammetric techniques as a function of pH. Electrochemical behavior of the complexes was studied in aqueous solution and showed an irreversible Cu^II/Cu^I couple. Kinetic studies of complex 1b and 3b with calf thymus DNA have been investigated spectrophotometrically under pseudo‐first order conditions, and k _obs values have been evaluated. Circular dichroism, cyclic voltammetry determinations, and viscosity measurements have also been carried out to authenticate the binding of DNA with metal complexes. Complexes 1b and 3b bind to DNA by covalent bond formation.