Association of mono- and dimethyl ethers of chlorine 6 in ethanol-water solutions

The association of γ-mono- and 6,γ-dimethyl ethers of chlorin e₆ (I and II) in mixtures of a phosphate buffer and ethanol is studied. The number of molecules in associates and the dimerization constants are determined. The formation of the dimers of compound I and dimers and associates of a higher order for II is established. It is found that, unlike I, the shift of the Q absorption band of the dimer toward larger wavelengths is rather great as compared to the monomer band for II; it exceeds 30 nm, which is uncommon for porphyrins. This difference of spectral changes in association of I and II is attributed to the dissimilar character of interaction of their molecules with each other and with the molecules of the surroundings, and also to the structural features of the dimers. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 67, No. 4, pp. 440–444, July–August, 2000.     

Multiscale modelling strategies and experimental insights for the solvation of cellulose and hemicellulose in ionic liquids

ABSTRACT

The present study investigates the dissolution behaviour of cellulose and hemicellulose in potential ionic liquids (ILs) using both the quantum chemical and experimental validation. For converging upon the recommended IL, 1428 ILs consisting of 42 cations and 34 anions were studied with the conductor like screening model for real solvents (COSMO-RS) model. Based on the infinite dilution activity coefficient of the components in IL, the selected anions and cations were visualised by observing their interactions with cellulose and hemicellulose using interaction energies, natural bonding orbital analysis and molecular dynamics simulations. The dissolution order of cellulose and hemicellulose in ILs was primarily determined by the evaluation of hydrogen bonds between the oxygen atom of anion and hydroxyl proton of cellulose/hemicellulose. From this discernible fact, the anion of the IL was observed to play a leading role in the solvation process as compared to the cation. Eventually, acetate [OAc]^– anion and 1-ethyl-3-methylimidazolium [EMIM]⁺ cation were found to be good candidates for the dissolution of cellulose and hemicellulose. This was further confirmed by the measurement of solid-liquid equilibria with cellulose and hemicellulose. The regenerated cellulose powder was then characterised by Fourier transform spectroscopy(FTIR), X-ray diffraction (XRD) and Thermal gravimetric analysis (TGA).     

Molecular interaction of silybin with hyaluronidase: A spectroscopic and molecular docking study

In this study, the molecular interaction of silybin with hyaluronidase was investigated by spectroscopic methods and molecular docking. It was found that silybin had strong ability to quench the intrinsic fluorescence of hyaluronidase by a static quenching procedure. The binding constants were obtained at three temperatures (293, 298, and 310 K). The results of synchronous fluorescence and three-dimensional fluorescence and molecular docking showed that silybin bound into the hyaluronidase cavity site and the binding of silybin to hyaluronidase could induce micro-environmental and conformational changes in hyaluronidase, which resulted in the reduced hyaluronidase activity. The thermodynamic parameter analysis and molecular docking experiments revealed that all types of non-covalent interaction, including hydrogen bonding interaction, van der Waals forces, hydrophobic interaction, and electrostatic interaction were present in the binding process of silybin with hyaluronidase. The results obtained here will provide direct evidence at a molecular level to understand the mechanism of the inhibitory effect of silybin against hyaluronidase.     

气体-表面相互作用中动量和能量分量间转化机制的分子动力学研究

气体分子与壁面之间的相互作用是影响稀薄气体流动状态的主要因素,但是由于其物理上的复杂性和微观性,这一过程的机理并没有得到充分揭示.本文利用分子束法对Ar分子在金属Pt表面的碰撞过程进行了分子动力学模拟,并探究了入射速度、角度和壁面粗糙度对动量、能量转化机制的影响.结果表明,当气体分子以5°的极角入射时,分子的法向速度分...     

Analysis of the binding mechanism between o-phenylenediamine and bovine hemoglobin by molecular spectroscopy and molecular modeling methods

Abstract

This study was aimed to reveal the binding mechanism between bovine hemoglobin and o-phenylenediamine by using molecular spectroscopy techniques and molecular modeling methods. The experimental results revealed that the fluorescence quenching mechanism was a combined dynamic and static quenching. The binding constant was (1.17?±?0.02)×10⁴ L/mol, and only a single binding site exists. The binding distance was 2.46?nm. The binding process was a spontaneous reaction, dominated by hydrophobic forces. The molecular docking simulations have also confirmed the results of the spectroscopic methods. The results reported here may significantly help understanding the interaction mechanism of o-phenylenediamine and hemoglobin.     

二静电体系相互作用力与相互作用能一般关系的正确表达式

指出二静电体系的相互作用力的普遍表达式F=-↓△w1=-↓△w并不恰当。正确的表达式应当是Fj=δW1/δqj=-δW1/δqj,其中Fj是沿广义坐标qj方向的广义力,W1是静电场总能量,W1是二静电体系的相互作用能,qj为表征二静电体系相对位移的某一广义坐标。     

Localized self-trapping in the two-dimensional discrete molecular lattice with the interaction between Frenkel excitons and phonons

We investigate the interactions of lattice phonons with Frenkel exciton, which has a small radius in a two-dimensional discrete molecular lattice, by the virtue of the quasi-discreteness approximation and the method of multiple-scale, and obtain that the self-trapping can also appear in the two-dimensional discrete molecular lattice with harmonic and nonlinear potential. The excitons' effect on the molecular lattice does not distort it but only causes it to localize which enables it to react again through phonon coupling to trap the energy and prevent its dispersion.     

光学二次谐波法研究乙醇与吸附于银表面的分子态氧的相互作用

本文报道了在超高真空环境下,首次利用光学二次谐波法研究乙醇与预吸附分子态氧的多晶银表面相互作用的过程,发现乙醇与分子态氧的相互作用是由两个过程组成:一个是乙醇在表面因分子态氧的存在而导致的吸附增强过程;另一个是乙醇与分子态氧的反应过程。从测量这一体系的二次谐波信号升温谱,还可以得到乙醇与分子态氧作用强弱的信息。     

The electronic spectrum of the SiC radical: A theoretical study

Electronic structure and spectroscopic properties of the low-lying electronic states of the SiC radical have been determined from the ab initio based configuration interaction calculations. Potential energy curves of 32 Λ-S states of singlet, triplet, and quintet spin multiplicities have been constructed. Spectroscopic constants (r_e, T_e, and ω_e) of 23 states within 6 eV are reported and compared with the existing data. The dipole moments (μ_e) of most of these states at their respective equilibrium bond lengths have been computed. Effects of the spin-orbit coupling on the spectroscopic properties of SiC have been studied. The E³Π state is found to be an important one which has not been studied before. A transition of the type E³Π-X³Π is predicted to take place in the range 25 000-26 000 cm⁻¹. The partial radiative lifetimes for several electric dipole allowed transitions such as A³Σ⁺-X³Π, B³Σ⁺-X³Π, C³Π-X³Π, D³Δ-X³Π, E³Π-X³Π etc. have been reported.     

A link between the second-order Jahn-Teller effect and the highest occupied molecular orbital postulate for molecular shapes

For a closed-shell molecule, a connection is drawn between two recent models for molecular shapes, namely, those based on the second-order Jahn-Teller (SOJT) effect and the highest occupied molecular orbital (HOMO) postulate respectively. Two necessary and sufficient conditions are derived within the molecular orbital framework for the approximation inherent in the SOJT model to be valid. One of these conditions is akin to the HOMO postulate.     

Diffusion activation energy versus the favourable energy in two-order-parameter model:A molecular dynamics study of liquid Al

In the present work, we find that both diffusion activation energy E_a(D) and E_a(S^ex) increase linearly with pressure and have the same slope (0.022±0.001 eV/GPa) for liquid Al. The temperature and pressure dependence of excess entropy is well fitted by the expression -S^ex(T,P)/k_B=a(P)+b(P)T+c(P)exp(E_f/k_BT), which together with the small ratio of E_f/k_BT leads to the relationship of excess entropy to temperature and pressure, i.e. S^ex≈-cE_f/T, where c is about 12 and E_f (=Δ E-PΔV) is the favourable energy. Therefore, there exists a simple relation between E_a(S^ex) and E_f, i.e. E_a(S^ex)≈cE_f.     

Combined experimental and theoretical DFT study of molecular nanowires negative differential resistance and interaction with gold clusters

Electric-field-assisted assembly has been used to place rod-shaped metal nanowires containing 4-[[2-nitro-4-(phenylethynyl) phenyl] ethynyl] benzenthiol molecules onto lithographically defined metal pads. These junctions exhibited negative differential resistance. The quantum chemical approach was used to compare the properties of Au-bonded 4-[[2-nitro-4-(phenylethynyl) phenyl] ethynyl] benzenthiol molecule and a molecule that does not exhibit the negative differential resistance, Au-bonded 4-[[4-(phenylethynyl) phenyl] ethynyl] benzenthiol. The influence of the static electric field and charge variation were modelled for both systems.     

Peculiar features of the interaction potential between hydrogen and antihydrogen at intermediate separations

This paper evaluates the interaction potential between a hydrogen and an antihydrogen using the second-order perturbation theory within the framework of the four-body system in a separable two-body basis. It finds that the H-H interaction potential possesses the peculiar features of a shallow local minimum located around interatomic separations of r ～ 6a.u. and a barrier rising at τ ≤5a.u.     

A molecular dynamics study of the swelling patterns of Na/Cs-montmorillonites and the hydration of interlayer cations

We report on a molecular dynamics study of the swelling patterns of an Na-rich/Cs-poor montomorillonite and a Csmontomorillonite.The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer.The simulations reproduce the swelling patterns of the Na and Cs-montomorillonite,suggesting a mechanism of its hydration different from that of the montomorillonite.In addition,we find that the differences in size and hydration energy of Na and Cs ions have strong implications for the structure and the internal energy of interlayer water.In particular,our results indicate that the hydrate difference in the presence of coexistent Na and Cs has a larger influence on the behavior of a clay-water system.For Na-rich/Cs-poor montomorillonite,the hydration energy values of Na ions and water molecules each have a dramatic increase compared with those in Na-montomorillonite on the interlayer spacing,and the hydration energy values of Cs ions and water molecules decrease somewhat compared with those in Cs-montomorillonite.     

Investigation of structure interaction to nutrient properties and utilization in co-products after pellet processing at various conditions using advanced molecular spectroscopy

The molecular infrared (micro)spectroscopy, developed as a rapid, non-destructive and non-invasive analytical technique, is able to reveal structure features at a molecular level and provide tissue structure and chemistry information simultaneously. However, to date, this analytical technique is seldomly used in study processing induced structure change in relation to nutrient properties, utilization, and delivery in livestock. The objective of this article was to review the inter-relationship between molecular structures with nutritive properties and nutrient delivery in co-products from bioenergy production after pelleted processing using vibrational molecular spectroscopy. First, this article reviews recent progress in pelleting process research, related to physical quality of pellets, utilization for animals, processing quality, and current nutrition evaluation methodologies for pelleting. The emphasis of this study focused on the effect of conditioning temperature and time of the pellet processing on molecular structure changes and nutrient properties and nutrient delivery. The methods for nutritive properties and nutrient delivery were reviewed, which included various in vitro, in situ, in vivo, and nutrient modeling techniques. The molecular spectroscopic techniques included globar-sourced and synchrotron-sourced molecular spectroscopic techniques. The molecular spectra analysis included univariate and multivariate molecular spectral analyses. The relationship between molecular structural changes and truly absorbed nutrient supply was quantified. The research provides an insight how inherent structure changes induced by pellet processing on a molecular basis affected nutrient properties, utilization, and availability.     

Fluid structure and molecular interaction of acetophenone derivatives

Dielectric constants of the binary mixtures of acetophenone,p-chloroaceto-phenone,p-methylacetophenone ando-hydroxyacetophenone in dilute solutions of benzene and 1,4-dioxane were measured at 303 K and at frequency 100 kHz. The low frequency molecular dynamics of acetophenone and its derivatives have been studied by evaluating the Kirkwood correlation factorg, molar polarizationP ₂, excess correlation factor δg and excess free energy ΔG. The dipolar contribution to excess free energy of mixing arising from long-range electrostatic interaction and short-range interaction between identical molecules has been assessed separately. The presence of α- and β-multimers in the above systems was identified. The results have been used to interpret the fluid structure in such mixtures.     

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

ABSTRACT

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.     

A theoretical investigation of radiative effects and microphysical processes involved in the interaction of aerosol particulates in the atmosphere and validation of the theoretical results with the INDOEX observations

A theoretical approach, which is based on certain physical assumptions and quantum physical concepts, has been extended to investigate the radiative effects and the microphysical properties involved in the interaction of aerosol particulates in the atmosphere which may have important climatic effect. The theoretical findings are used to validate some of the observations of Indian Ocean Experiment (INDOEX) during its First Field Phase-98 (FFP-98) and Intense Field Phase-99 (IFP-99). The aerosol optical depth and the radiative forcing of the surface and the top of the atmosphere are computed and the results are found to have a good correspondence with the INDOEX results.