分子动力学模拟研究方解石表面润湿性反转机理

利用分子动力学模拟技术从分子尺度探究方解石表面润湿性反转机理.首先,研究方解石表面润湿性反转过程;而后,从原油分子-方解石表面与原油分子-原油分子/水分子相互作用两个方面系统揭示方解石表面润湿性反转机理.结果:(1)水分子能够驱离方解石表面弱吸附的非极性分子造成润湿性的改变,但不能驱离强吸附的极性分子使润湿性反转难以实现;(2)原油分子极性越强与方解石表面相互作用越强,极性分子与方解石表面之间主要为静电力,非极性分子与方解石表面之间主要为范德华力;(3)原油分子极性越相近分子之间的相互作用越强,分子极性相差越大分子之间的相互作用越弱.非极性分子之间主要是范德华力,极性分子之间主要是静电力;(4)原油分子在方解石表面和水分子的共同作用下形成乙酸-吡啶-水-甲苯-己烷的稳定吸附序列.本研究为靶向提高采收率技术的设计与应用提供理论基础.     

Alignment of RNA molecules: Binding energy and statistical properties of random sequences

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energy between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.     

Probing complex RNA structures by mechanical force

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpreted by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia colis 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called kinetic traps, thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Received: 15 September 2003, Published online: 5 February 2004PACS: 87.15.-v Biomolecules: structure and physical properties - 82.37.Rs Single molecule manipulation of proteins and other biological molecules - 87.15.Aa Theory and modeling; computer simulation     

光谱法研究3H-吲哚探针分子与Triton X-100胶束间的相互作用

用光谱法研究了荧光分子2－（对－己基胺基）苯基－3,3－二甲基－5－乙酯基－3H吲哚基－甲基二辛基磺化铵（A）与Triton X-100胶束间的相互作用,测定了A在不同浓度的Trtiton X-100溶液中的吸收光谱,荧光光谱和荧光寿命,实验得到了A与胶束的结合常数Ks,A在胶束中所处环境的极性及其在胶束中发生的pH效应,结果表明,A与胶束间存在较强的相互作用,A在胶束中所处环境的极性及其在胶束中发生的pH效应,结果表明：A与胶束间存在较强的相互作用;A在胶束中所处环境的极性接近于甲醇的极性,并推测出了A的不同基团在胶束中所处的不同位置,同时发现：在Triton X-100胶束中A可探测到两个位置,但当Triton X-100的浓度过大时,A只能探测到一个位置。     

The adsorption of iron phthalocyanine on graphite: A scanning tunnelling microscopy study

Different adsorption phases of iron phthalocyanine (FePc) on highly oriented pyrolitic graphite (HOPG) have been characterized by scanning tunnelling microscopy (STM). Evaporation of FePc onto the graphite (0 0 0 1) surface, kept at room temperature, results in the formation of three-dimensional molecular islands.After annealing to 400 °C different two-dimensional features are identified, depending on the initial coverage. At low doses, domains with well defined boundaries have been observed, within which molecules tend to organise in chains. At higher coverage, islands exhibiting well-ordered densely-packed square or hexagonal molecular arrangement have been resolved. For the adsorption structures corresponding to one monolayer islands our results show that the molecules adsorb with the molecular plane parallel to the surface. The high resolution STM images allow us to resolve the orientation of single molecules and subsequently we suggest that the molecular monolayer is stabilized by van der Waals interactions. The characterization of the observed Moiré contrast and a comparison with other similar systems underlines the importance of the central metal in the molecule-molecule and molecule-substrate interactions, which govern the molecular adsorption geometry.     

Tuning the photophysics of a bio-active molecular probe ‘3-pyrazolyl-2-pyrazoline’ derivative in different solvents: Dual effect of polarity and hydrogen bonding

The solvatochromic behavior of 3-pyrazolyl 2-pyrazoline derivative (PYZ), a newly synthesized molecular probe having pharmaceutical importance, has been studied in various solvents of different polarity. The Kamlet and Taft solvatochromic comparison method was utilized to rationalize the solute-solvent interactions from absorption and emission measurements. Spectroscopic studies reveal that the solvatochromic behavior of the dye depends not only on the polarity of the medium but also on the hydrogen-bonding properties of the solvents. The non-radiative relaxation process is facilitated by an increase in the polarity of the media. The photophysical response of PYZ in different solvents has been explained considering solute-solvent interactions.     

The molecular structure and intermolecular interactions of 1,3:2,4-dibenzylidene-D-sorbitol

The 1,3(R):2,4(S)-dibenzylidene-D-sorbitol (DBS) molecule is a low molar mass organic gelator (LMOG) that is capable of hydrogen-bonding with itself. As a consequence, DBS molecules self-organize into nanofibrillar networks at relatively low concentrations in a wide variety of organic solvents and polymers. In this work, molecular mechanics and molecular dynamics simulations were conducted to elucidate the equilibrium structure of DBS and the molecular interactions that govern DBS self-assembly. Molecular mechanics calculations performed on single DBS molecules with Cerius² and InsightII software reveal that the pheny^l rings tend to adopt an equatorial position and that the pendant hydroxyl group prefers to form an intramolecular hydrogen bond with an acetal oxygen, in contrast to the terminal hydroxyl group. Molecular mechanics and molecular dynamics on DBS dimers reveal that they are capable of forming hydrogen bonds and participating in π interactions, suggesting that the mechanism of nanofibrillar network formation may be complex, involving more than one type of physical interaction.     

Metal-ion binding via a cyclic network of intramolecular halogen-bonded interactions: a theoretical study

A cyclic network of four intramolecular C–I…N interactions is shown to bind Na⁺ and Ca²⁺ with corresponding binding energies of 57 and 175 kcal/mol, respectively. The halogen-bonded network is built by connecting four molecules of 2-iodoimidazole with acetylene and ethylene as convenient linkers. 2-iodoimidazole provides both the halogen bond donor and the halogen bond acceptor moieties. Each of the four iodine atoms participates in the binding of the metal ion as indicated by the presence of bond paths connecting the metal ion with each one of the halogen atoms in the host, and orthogonal to the C–I…N interactions. A similar intermolecular network of C–I…N interactions is also found to form by the interactions of four 2-iodoimidazole molecules. In contrast to its intramolecular counterpart, the intermolecular C–I…N network is at least partly destroyed upon metal-ion binding as the metal ion competes somewhat successfully for the lone pair of the acceptor nitrogen atoms.     

Molecular adsorption and growth of n-butane adlayers on Pt(1 1 1)

The molecular adsorption of n-butane and the growth of n-butane adlayers on Pt(1 1 1) was investigated using molecular beam techniques, temperature-programmed desorption (TPD) and low-energy electron diffraction (LEED). It is found that as the surface coverage of n-butane increases, structural changes occur in the adlayer at surface temperatures near 98 K that are accompanied by changes in the binding energy and mobility of the adsorbed species. The film growth process can be divided into four distinct coverage regimes. At low coverages (θ<0.14 ML, where 1 ML is defined as one butane molecule per Pt atom) a disordered monolayer forms in which the butane molecules prefer to lie parallel to the surface in order to minimize their binding energy. At coverages from 0.14 to 0.20 ML, ordered regions develop within the monolayer in which the butane molecules also lie parallel to the surface. The binding energy in the ordered phase is lower than that in the disordered phase due to repulsive intermolecular interactions. A more densely-packed ordered phase begins to form at 98 K after the low-coverage ordered phase saturates at 0.20 ML. The experimental results suggest that the n-butane molecules tilt away from the surface in the high-coverage ordered phase. Finally, a disordered second layer phase forms after the high coverage ordered phase saturates at 0.35 ML. The molecules in the second layer are very mobile at 98 K and rapidly diffuse to the edges of the beam spot. Interchange of molecules between the second layer and ordered monolayer is found to govern the net rate of second layer diffusion at surface temperatures less than 133 K. The adsorption probability of n-butane on Pt(1 1 1) continuously increases with increasing coverage, with no significant dependencies on the structure of the n-butane adlayer. This finding indicates that the long-range arrangements and molecular orientations of a mobile alkane adlayer have a negligible influence on the intrinsic adsorption dynamics, suggesting that the energy transfer processes that facilitate adsorption are highly localized.     

ENDOR and related EMR methods applied to flavoprotein radicals

Flavoproteins are involved in a wide range of biological processes, owing to the versatility of the isoalloxazine moiety of flavin, which can undergo both one- and two-electron reactions with the formation of three oxidation states. Paramagnetic semiquinone radical states are stabilised in some flavoproteins and appear as transient intermediates in the reaction of many others. The apoprotein controls the reactivity of flavin semiquinones, including redox potentials, protonation states and access to substrates. Most flavoproteins are involved in oxidation-reduction processes, but some catalyze different types of reactions involving radical intermediates. Anionic and neutral flavin radicals are found in flavoproteins and are distinguished by their line widths in X-band electron paramagnetic resonance. Electron-nuclear double resonance, electron spin echo envelope modulation and hyperfine sublevel correlation spectroscopy make it possible to observe biological electron transfer and catalysis at the level of the electronic structure of the intermediate states. They provide information about the protein environment of flavin semiquinone radicals and their interactions with nearby nuclear and electron spins. Hyperfine couplings, particularly to the 8-methyl protons on the flavin ring, are a sensitive probe of perturbations of the flavin environment. They demonstrate differences in polarity of the flavin binding site and changes that occur in flavoenzymes during binding of substrates.     

Influence of the polarity of a medium on the photonics of a merocyanine dye with a high quadratic polarizability

The influence of the polarity of a medium on the spectral and luminescent properties of 2-[(2E,4E)-6-(1,3,3-trimethyl-2,3-dihydro-1H-2-indolyliden)-2,4-hexadienyliden]malononitrile (THDM) in solutions and polymer matrices is studied at room temperature under conditions of steady-state and pulsed laser excitation. A large bathochromic shift of the absorption spectra observed upon an increase in the polarity of a solvent is caused by a strong increase in the molecular dipole moment μ due to a transition of molecules from the ground state (μ_g = 7.6 D) to an excited Franck-Condon state (μ^FC = 33.5 D). Based on the solvatochromic data, the quadratic polarizability was calculated to be β = (3.2 ± 0.6) × 10^?28 esu, which is close to the experimentally determined value β_ex = (3.9 ± 0.2) × 10^?28 esu. A strong narrowing of the fluorescence spectra in comparison with the absorption spectra is observed upon an increase in the solvent polarity. This narrowing is explained by a decrease in the bond length alternation parameter and by weakening of vibronic interactions in the singlet excited state. The dynamic solvatofluorochromism of THDM in the picosecond range is caused by reorientations of molecules of the polar environment occurring during a time period consistent with the dielectric relaxation time of these molecules.     

Selection rules for electric multipole transition of diatomic molecule in scattering experiments

The knowledge of the energy level structures of atoms and molecules is mainly obtained by spectroscopic experiments.Both photoabsorption and photoemission spectra are subject to the electric dipole selection rules(also known as optical selection rules). However, the selection rules for atoms and molecules in the scattering experiments are not identical to those in the optical experiments. In this paper, based on the theory of the molecular point group, the selection rules are derived and summarized for the electric monopole, electric dipole, electric quadrupole, and electric octupole transitions of diatomic molecules under the first Born approximation in scattering experiments. Then based on the derived selection rules, the electron scattering spectra and x-ray scattering spectra of H2, N2, and CO at different momentum transfers are explained, and the discrepancies between the previous experimental results measured by different groups are elucidated.     

DFT study of dihydrogen interactions with lithium containing organic complexes C4H4-mLim and C5H5-mLim （m = 1, 2）

The interactions of dihydrogen with lithium containing organic complexes C₄H_4-mLi_m and C₅H_5-mLi_m (m = 1, 2) were studied by means of density functional theory (DFT) calculation. For all the complexes considered, each bonded lithium atom can adsorb up to five H₂ molecules with the mean binding energy of 0.59 eV/H₂ molecule. The interactions can be attributed to the charge transfer from the H₂ bonding orbitals to the Li 2s orbitals. The kinetic stability of these hydrogen-covered organolithium molecules is discussed in terms of the energy gap between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). The results indicate that these organiclithium structures can perhaps be used as building units for potential hydrogen storage materials.     

Molecular Interactions of Flavonoids to Hyaluronidase: Insights from Spectroscopic and Molecular Modeling Studies

In the work described on this paper, the interactions between eight flavonoids and hyaluronidase (HAase), an important enzyme involved in a promoting inflammation pathway, were investigated by spectroscopic and molecular modeling methods. The results revealed that all flavonoids could interact with HAase to form flavonoid-HAase complexes. The binding parameters obtained from the data at different temperatures indicated that flavonoids could spontaneously bind with HAase mainly through electrostatic forces and hydrophobic interactions with one binding site. According to synchronous and three-dimensional fluorescence spectra and the molecular docking results, all flavonoids bound directly into the enzyme cavity site and the binding of flavonoid into the enzyme cavity influenced the microenvironment of the HAase activity site which led to the reduced enzyme activity. The present study provides direct evidence at a molecular level to understand the mechanism of inhibitory effect of flavonoid against HAase and explain the anti-inflammatory mechanism of the Traditional Chinese Medicines as anti-inflammatory drugs.     

氢键对2-(N-甲基)氨基-5-硝基吡啶分子非线性光学性质的影响

本文在杂化密度泛函理论水平上研究了溶剂对2-(N-甲基)氨基-5-硝基吡啶分子非线性光学性质的影响.在溶剂中,构造了包括氢键作用的超分子体系,在优化结构的基础上分别研究了由极化连续模型模拟的溶剂与该分子的长程相互作用、溶剂与该分子的氢键相互作用以及溶剂与包括氢键作用的超分子体系整体的相互作用对分子的几何结构、非线性光学性质、紫外吸收光谱和电荷分布等特性的影响.结果表明,溶剂中分子电偶极矩、线性极化率和第一超极化率都增大,而溶剂与溶质分子通过氢键形成的超分子结构与单体有着明显区别.因此,氢键对分子结构和性质的影响较大,从而将明显的影响该类分子的非线性光学性质.     

Effect of reduced cooperativity on growth-induced polarity formation: a comparison between different growth models

We investigate the influence of the growth process on macroscopic polarity formation in molecular crystals consisting of polar molecules with two directional states. Specifically, layer-by-layer growth is compared with growth along surface steps, and growth at kink sites. Idealized models for these growth processes are presented, being characterized by the thermal equilibrium formation of a domain of molecules on the surface, ranging from an entire adlayer to a single molecule only (reduced cooperativity). Longitudinal and lateral Ising-type nearest neighbour interactions are taken into account. Formerly attached and thermalized molecules are kept frozen upon growth and therefore, bulk polarity results. Growth models are studied by means of Monte Carlo simulations. Results show that a reduced cooperativity between neighbouring molecules on the crystal surface increases the probability of orientational disorder. However, in the asymptotic limit of infinite growth and for sufficiently strong longitudinal couplings, phenomenologically, evolution of polarity for step and kink growth remains the same as for layer-by-layer growth, being mainly a thermodynamically driven process. Despite their strong out-of-equilibrium character, step and kink growth processes feature a continuous phase transition as layer-by-layer growth and are reasonably well described by an effective lateral coordination number within a mean field approach.     

Nonintrusive measurement of field-free molecular alignment

A technique was provided to nonintrusively quantify the field-free alignment of molecules by measuring the transient birefringence caused by the aligned molecules. Pure heterodyne alignment signals were obtained from the difference of the signals under an external electric field with opposite polarity and equal magnitude. The results demonstrated that the pure heterodyne alignment signal directly reproduced the revival structure of molecular alignment and its Fourier transform spectroscopy represented the actual populations of the different J states in the rotational wave packet.     

Investigation of Solvent Effects on Photophysical Properties of New Aminophthalimide Derivatives-Based on Methanesulfonate

Novel aminophthalimide derivatives were synthesized starting from (3aR,7aS)-2-(2-hydroxypropyl)-3a,4,7,7a–tetrahydro-1H-isoindole-1,3(2H)-dione (9) , and solvent effects on the photo-physical properties of these newly synthesized aminophthalimide derivatives (compounds 14 and 15) were investigated using UV-Vis absorption spectroscopy, steady-state and time-resolved fluorescence measurements. Both absorption and fluorescence spectra exhibited bathochromic shift with the increased polarity of the solvents for both molecules. Solute-solvent interactions were analyzed using the Lippert-Mataga and Bakhshiev polarity functions, and Kamlet-Taft and Catalan multiple linear regression approaches. The results revealed that these two molecules experienced specific interactions. Furthermore, photo-physical parameters were calculated for both molecules in all of the solvents, such as the fluorescence quantum yield, fluorescence lifetime, radiative (k_r) and non-radiative (k_nr) rate constant values. It was observed that the fluorescence quantum yield values decreased linearly with increasing solvent polarity. This study proved the new dyes including isopropyl methanesulfonate group displayed different behavior from previous studies of aminophthalimide derivatives in water. It was recommended that these new dyes having interesting properties by changing solvent can be used various applications such as environmentally sensitive fluorescent probes, labels in biology, laser industry.