H2S在五边形BCN上的吸附与解离的第一性原理计算研究

基于密度泛函理论的第一性原理计算方法,研究了H2S分子在五边形BCN上的吸附与解离过程. 研究结果表明,五边形BCN结构的B原子是H2S分子的最稳定的活性吸附位点. H2S分子在该活性位点极易解离,其初步解离过程为放热反应且分解势垒仅为0.208 eV,并形成稳定的HS/H产物. 深入研究发现,H2S分子初步解离后的五边形BCN表面,可直接分解后续吸附的H2S分子. 该研究结果为五边形BCN对H2S分子的吸附解离机制提供理论借鉴,并且首次提出五边形BCN可作为功能性材料净化有害气体H2S的理想候选者.     

H2O分子在五边形BCN上的吸附与解离特性研究

基于密度泛函理论的第一性原理计算方法,研究了H₂O分子在五边形BCN上的吸附与解离过程.研究结果表明,五边形BCN结构的B原子是H₂O分子的最稳定的活性吸附位点. H₂O分子在该活性位点极易解离,其初步解离过程为放热反应且分解势垒仅为0.191 eV,并形成稳定的OH/H产物.深入研究发现,H₂O分子初步解离后的五边形BCN表面,可直接分解后续吸附的H₂O分子.该研究结果为五边形BCN对H₂O分子的吸附解离机制提供理论借鉴.     

Sigma trans promotion effect in transition metal complexes: a manifestation of the composite nature of binding energy

It is well known that intra-fragment electronic reorganization is one among several important components of the binding energy (bond dissociation energy) for two fragments forming an adduct. An interesting manifestation of this notion is proposed: a counterintuitive trend in binding energies that shall be commonly observed for a series of particular open shell transition metal containing complexes binding a small molecule at an empty coordination site. The prediction is that stronger σ interaction between the metal and the ligand trans to the empty site will result in a larger magnitude of binding energy and, possibly, a lower substrate coordination barrier. This trend, which we call the ‘trans promotion effect’ (TPE), is exemplified with a case study of dinitrogen binding by tri- and four-coordinated Mo(III) complexes. It is demonstrated that a trans amine ligand significantly increases the magnitude of dinitrogen binding energy. Orbital analysis and decomposition of the binding energy show that substrate coordination is favoured by stronger interaction of Mo with the trans ligand due to the d_z2 orbital of Mo that is occupied in the complex but vacant in the dinitrogen adduct.     

Exact analytical expressions for diatomic rotational and centrifugal distortion constants for a Kratzer-Fues oscillator

The exact closed-form expression for the vibrational-rotational eigenvalues of the Kratzer-Fues oscillator served as the starting point for a derivation of exact analytical expressions for the rotational constant B_υ, and the set D_υ to S_υ of centrifugal distortion constants up to 11th-order. The derivations employed the MAPLE symbolic algebra coprocessor. The expressions for B_υ to S_υ were then employed in the calculation of a set of constants for a Kratzer-Fues potential with specified dissociation energy and equilibrium internuclear separation for a hypothetical diatomic molecule with a reduced mass of unity. The tabulated constants serve as a benchmark against which the reliability of various existing or future numerical methods for the determination of rotational and centrifugal distortion constants may be assessed. The near-dissociation behaviour of the calculated constants was also examined and is useful in predicting the behaviour of such constants for real electronic states having pure ionic long-range form.     

Soluble Spin-Label as a NMR Relaxation Probe in the Study of the Enzyme-Substrate Complexes

Abstract

The paramagnetic contributions induced by TEMPOL soluble spin-label on gentiobiose carbon spin-lattice relaxation rates are analyzed. Selective effects in the β(1–6) glycosidic bond region were observed. The possibility of using soluble spin-label to determine the stereochemistry of the substrate-enzyme interaction was then explored.

The results obtained with different diamagnetic and paramagnetic systems enabled us to distinguish the region of gentiobiose most involved in interaction with the enzyme, and the region of the disaccharide molecule located on the surface of the enzyme and most exposed to the nitroxide.

The results obtained could be used to model the enzyme surface of the gentiobiose binding site.

Soluble spin-labels have been widely used in the investigation of the conformational and dynamical properties of biomolecules in solution (1–4). The main effects of nit oxide spin-labels, like TEMPO or TEMPOL, is the increase in NMR spin-lattice relaxation rates of solvent exposed nuclei. In small molecules like the disaccharide gentiobiose, the spin-label can be used to discriminate molecular regions with a different solvent accessibility and to investigate interaction with the enzyme are the C1s, C2s and C4s carbons (where s refers to α and β and to the reducing and most reducing moiety). It is interesting to observe that although the results come from four independent systems, complementary and self consistent information was obtained on the substrate region involved in the interaction with the enzyme and on the region of the substrate in contact with the surface of the enzyme and exposed to the solvent and nitroxide molecules.

This method proved useful for investigating the surface and the conformation of the enzyme interacting with the substrate molecule, and is a new application of soluble spin label in structural studies.     

Complexation of fluoroquinolone antibiotics with human serum albumin: A fluorescence quenching study

Mechanism of interaction and detailed physico-chemical characterization of the binding of four fluoroquinolones: levofloxacin, sparfloxacin, ciprofloxacin HCl and enrofloxacin with human serum albumin has been studied at physiological pH (7.4) using fluorescence spectroscopic technique. The stoichiometry of interaction was found to be 1:1 for all the drugs used. The association constants for the interaction were of the order of 10⁴ in most cases. At low drug:protein ratios, a significant fraction of the added drug was bound. The predominant interactions involved are hydrogen bonding and Van der Waal’s interactions in the case of levofloxacin, hydrophobic interactions in the case of ciprofloxacin hydrochloride and enrofloxacin and hydrogen bonding, hydrophobic and electrostatic interactions in the case of sparfloxacin.The drug binding region did not coincide with that of the hydrophobic probe, 1-anilinonaphthalene-8-sulfonate (ANS). From the displacement of site-specific probes and site-marker drugs, it was concluded that ciprofloxacin hydrochloride is site II-specific while enrofloxacin is a site I-specific drug. Levofloxacin binds at both site I and site II with equal affinity. Sparfloxacin had higher affinity for site II than site I. It is also possible that sparfloxacin binds at the interface between site I and site II. Stern-Volmer analysis of the data showed that the quenching mechanism is predominantly collisional for the binding of ciprofloxacin HCl and enrofloxacin while both static and collisional quenching mechanisms are operative in the case of levofloxacin and sparfloxacin. High magnitude of the rate constant for quenching showed that the process is not entirely diffusion controlled. Circular dichroism (CD) spectroscopic studies showed that the presence of drugs did not cause any major changes in the secondary structure of HSA.     

MCR-ALS结合分子对接研究隐色孔雀石绿与BSA的作用过程

孔雀石绿(LMG)在治理鱼卵中霉菌和杀灭鱼体寄生虫等方面的效果显著, 广泛应用于水产运输和养殖。孔雀石绿进入动物机体后, 通过生物转化代谢为脂溶性的隐色孔雀石绿(LMG), LMG的毒性超过MG; LMG能快速在组织中蓄积, 具有致癌、致畸、致突变等毒副作用。白蛋白可与多种内源和外源化合物结合, 是血浆中含量最丰富的载体蛋白, 也是药物发挥作用的重要载体和靶标。模拟pH 7.4的生理条件, 通过荧光光谱和圆二色谱法(CD)采集两种不同滴加方式的LMG与牛血清白蛋白(BSA)动态作用过程中的多维数据, 并应用化学计量学多元曲线分辨-交替最小二乘法(MCR-ALS)对多维波谱数据进行解析和描述, 从重叠严重的光谱数据中同时得到作用体系的定量和定性信息。从解析得到的浓度趋势图中, 说明体系在LMG∶BSA=2∶1时达到动态平衡, 并可确认复合物LMG₂-BSA的生成; 解析得到的与所测量的BSA荧光和CD图符合, 印证由MCR-ALS获得的浓度趋势图的可靠性和正确性; 通常由重叠光谱中无法辨别的LMG₂-BSA复合物荧光光谱和CD谱图也可由数学解析获得, 进一步印证了复合物的存在。原子力显微镜(AFM)测量结果表明BSA与LMG结合后, BSA的形貌发生改变, 表面粗糙度(RMS)由(1.24±0.28) nm增至(13.47±0.53) nm; 同时由CD实验结果可知LMG与BSA作用达到平衡时, α-螺旋结构的含量从46.5%降低到42.3%, 推测是BSA所处微环境和构象发生变化所致。荧光探针实验发现经典site Ⅰ标记物华法林加入后, LMG-BSA的猝灭常数由2.65×106 L·mol-1降低为1.88×106 L·mol-1, 但加入site Ⅱ标记物布洛芬后, LMG-BSA的猝灭常数变化不明显, 由此推断LMG可能结合在蛋白质的亚域ⅡA, 即site Ⅰ位。分子对接证实BSA的Ⅰ位有足够的空间容纳LMG, 且LMG与BSA之间的主要作用是疏水作用力。该研究从分子水平了解LMG与生物大分子的作用机制, 并为LMG的毒副作用研究提供重要的信息。     

Molecular orbital calculations of the dissociative adsorption of a hydrogen molecule on a 14 atom nickel cluster

MINDO/SR molecular orbital calculations have been performed for the Ni₁₄H₂ system in order to study the various steps of the dissociative chemisorption process of H₂ over nickel. Particular attention was placed in the determination of physisorbed “precursor” states. It was found that such states may occur at border sites of our model cluster and that dissociative chemisorption may take place preferentially over a two-fold nickel site. The present results indicate that starting from this site, dissociation occurs following an essentially barrierless path. Changes in both electronic and binding properties along the path were studied in order to determine the relative importance of the several factors affecting chemisorption. In this respect, the role of d orbitals has been carefully analyzed with reference to the changes in density of states. The present results also indicate that after dissociation, the hydrogen atoms may easily move away from the border, into the surface, through low-barrier potential energy channels.     

Molecular potential energy surface constructed from ab initio interpolation for HCN− + H reaction and deuterated analogues

A classical study for constructing potential energy surface from ab initio electronic energy of molecular fragments was presented for HCN^? + H reaction and deuterated analogues. The classical trajectory was studied on this surface to determine the reaction probability. Reaction probability was used to calculate others observable properties like rate constant and cross section. Rate constants expressions were reported for all reactions. Influence of translation energy of fragments on the reaction probability and reaction cross section was also studied. Nonlinear least-squares fitting was also used to calculate the rate constants expressions. Deuterium was used instead of hydrogen atom to observe the effect of mass of attacking atoms and target molecule on the reaction probability and reaction rate.     

The stability of gadolinium-based contrast agents in human serum: A reanalysis of literature data and association with clinical outcomes

PurposeTo reanalyze literature data of gadolinium (Gd)-based contrast agents (GBCAs) in plasma with a kinetic model of dissociation to provide a comprehensive assessment of equilibrium conditions for linear GBCAs.MethodsData for the release of Gd from GBCAs in human serum was extracted from a previous report in the literature and fit to a kinetic dissociation/association model. The conditional stabilities (logK_cond) and percent intact over time were calculated using the model rate constants. The correlations between clinical outcomes and logK_cond or other stability indices were determined.ResultsThe release curves for Omniscan®, gadodiamide, OptiMARK®, gadoversetamide Magnevist® and Multihance® were extracted and all fit well to the kinetic model. The logK_conds calculated from the rate constants were on the order of ~ 4–6, and were not significantly altered by excess ligand or phosphate. The stability constant based on the amount intact by the initial elimination half-life of GBCAs in plasma provided good correlation with outcomes observed in patients.ConclusionsEstimation of the kinetic constants for GBCA dissociation/association revealed that their stability in physiological fluid is much lower than previous approaches would suggest, which correlates well with deposition and pharmacokinetic observations of GBCAs in human patients.     

Estimation of the Electron–Phonon Coupling Constants for Graphene and Metallic and Nonmetallic Substrates

Two modes of graphene–substrate interaction have been considered: a weak van der Waals bond and a strong covalent bond. The Lennard–Jones potential and Harrison bond-orbital method are used in the former and latter cases, respectively. Analytical expressions for the electron–phonon interaction constants, which contain only two parameters (binding energy E _B for graphene and a substrate and distance d between them) have been obtained. The constants have been calculated for metallic, semiconductor, and dielectric substrates.

     

Coriolis Coupling in a Very Nearly Symmetric-Top Molecule

Abstract

Methyl arsine is very nearly a prolate symmetric-top molecule. Although its exact structure is not known, the moments of inertia can be calculated from a reasonable (assumed) structure (see Fig. 1). The rotational constants (A″ = 2.160 cm^?1, B″ = 0.2951 cm^?1, C″ ?0.2940 cm^?1) obtained from this structure are not greatly different from those of another study (1) and reflect the near symmetric-top character of the molecule. Indeed, most of the perpendicular bands show very small splitting of the two components (A′ and A″ for C_s point group to which methyl arsine belongs) which would be exactly degenerate in the symmetric-top molecule, in which two of the three rotational constants are identical.     

Proposal for a laser control of vibrational cooling in Na(2) using resonance coalescence

With a specific choice of laser parameters resulting in a so-called exceptional point (EP) in the wavelength-intensity parameter plane, it is possible to produce the coalescence of two Floquet resonances describing the photodissociation of the Na(2) molecule, which is one of the candidates for the formation of samples of translationally cold molecules. By appropriately tuning laser parameters along a contour encircling the exceptional point, the resonances exchange their quantum nature. Thus a laser-controlled transfer of the probability density from one field-free vibrational level to another is achieved through adiabatic transport involving these resonances. We propose an efficient scenario for vibrational cooling of Na(2) referring to cascade transfers involving multiple EPs and predicted to be robust up to a 78% rate against laser-induced dissociation.     

Calculated sextic centrifugal distortion constants of polyatomic molecules

By a perturbation treatment of the vibration-rotation Hamiltonian, expressions are derived for the sextic centrifugal distortion constants of a polyatomic molecule in terms of the basic molecular parameters. The calculation can be simplified by reordering the terms in the perturbation expansion. The theoretical expressions for the sextic distortion constants contain the cubic anharmonic potential constants, for which they are a possible source of information. The formulas are applied to molecules of various types of symmetry, and numerical results are computed for sulfur dioxide, ammonia and methane from published anharmonic force fields. The agreement with the observed distortion constants is good for SO₂ and reasonable for NH₃, but poor for CH₄. These results probably reflect the present state of knowledge of the cubic potentials of these three molecules.     

Mechanistic Insights into the Inhibition of Endo-β 1,4 Xyloglucan Hydrolase by a Classical Aspartic Protease Inhibitor

This is the first report of inactivation of xyloglucanase from Thermomonospora sp by pepstatin A, a specific inhibitor towards aspartic proteases. The steady state kinetics revealed a reversible, competitive, two-step inhibition mechanism with IC ₅₀ and K _i values of 3.5?±?0.5 μM and 1.25?±?0.5 μM respectively. The rate constants determined for the isomerization of EI to EI^* and the dissociation of EI* were 14.5?±?1.5?×?10^?5?s^?1 and 2.85?±?1.2?×?10^?8?s^?1 respectively, whereas the overall inhibition constant K _i ^* was 27?±?1 nM. The conformational changes induced upon inhibitor binding to xyloglucanase were monitored by fluorescence analysis and the rate constants derived were in agreement with the kinetic data. The abolished isoindole fluorescence of o-phthalaldehyde (OPTA)-labeled xyloglucanase and far UV analysis suggested that pepstatin binds to the active site of the enzyme. Our results revealed that the inactivation of xyloglucanase is due to the interference in the electronic microenvironment and disruption of the hydrogen-bonding network between the essential histidine and other residues involved in catalysis.     

丹参酮ⅡA等中草药有效成分与白蛋白结合反应的光谱研究

在β－环糊精存在的缓冲体系中,利用光谱法研究了丹参酮ⅡA等有效成分与人血清蛋白(HSA)折结合反应。结果表明：丹参酮ⅡA等与HSA结合后,紫外吸收有红移现象,且吸收强度增加;它们对HSA的荧光有较强的猝灭作用。根据Lineweaver-Burk双倒数图,求得了它们与HSA的解离常数,基于Foerster无辐射能量转移机理,确定了它们的第一结合部位与HSA中214位色氨酸残基的距离。     

Ground states of the hydrogen molecule and its molecular ion in the presence of a magnetic field using the variational Monte Carlo method

ABSTRACT

By using the variational Monte Carlo (VMC) method, we calculated the 1sσ_g-state energies, the dissociation energies, and the binding energies of the hydrogen molecule and its molecular ion in the presence of an aligned magnetic field regime between 0 and 10?a.u. The present calculations are based on using two types of compact and accurate trial wave functions, which are put forward for consideration in calculating energies in the absence of a magnetic field. The obtained results are compared with the most recent accurate values. We conclude that the applications of the VMC method can be successfully extended to cover the case of molecules under the effect of a magnetic field.     

Chemical contribution to surface-enhanced Raman scattering

We present a new mechanism for the chemical contribution to surface-enhanced Raman scattering (SERS). The theory considers the modulation of the polarizability of a metal nanocluster or a flat metal surface by the vibrational motion of an adsorbed molecule. The modulated polarization of the substrate coupled with the incident light will contribute to the Raman scattering enhancement. We show that for a metal cluster and for a flat metal surface this new chemical contribution may enhance the Raman scattering intensity by a factor of approximately 102 and approximately 104, respectively. The new SERS process is determined by the electric field parallel to the surface of the metal substrate at the molecular binding site.     

Isomerization and dissociation of small (CH <Emphasis Type="Bold">3</Emphasis>CN) <Emphasis Type="Bold">n</Emphasis> molecular clusters: a computational study

The isomerization and evaporation processes in the neutral homogeneous (CH₃CN)_n molecular clusters (n = 2-7) have been investigated using classical molecular dynamics simulations. The evaporation rate constants and the kinetic energy release in the dissociation have been analysed as a function of the cluster size and as a function of the internal energy in the parent cluster. The competition between monomer and dimer ejections has been also carefully studied. All the dynamical properties in these dissociative processes have been discussed in relation to the static properties of the clusters involved in the dissociation and also in relation to the solid-liquid like transition which appears in these homogeneous molecular clusters. Received 19 November 2002 / Received in final form 5 February 2003 Published online 29 April 2003 RID="a" ID="a"e-mail: pascal.parneix@ppm.u-psud.fr RID="b" ID="b"Laboratoire associé à l'université Paris-Sud.