Dynamical structure of peptide molecules: Fourier transform microwave spectroscopy and ab initio calculations of N-methylformamide

Rotational spectra of both trans and cis forms of the N-methylformamide normal as well as deuterated (HCONDCH₃, referred to as N-D) species were observed by Fourier transform microwave spectroscopy in the frequency region from 5 to 118 GHz. Samples were prepared in the form of a beam by a pulsed jet valve maintained at 50 °C and were introduced in a high-vacuum cavity cell, with either Ne or Ar as a carrier gas at a backing pressure of 100 kPa. The observed spectra were analyzed to yield molecular parameters including rotational constants and barrier, V₃, to CH₃ internal-rotation: 53.9 (6) and 301 (4) cm⁻¹ for the trans and cis forms of the normal species, respectively, and 41.9 (6) and 309 (4) cm⁻¹ for the trans and cis forms of the N-D species, respectively. Spectra of four trans isotopologues with ¹³C, ¹⁵N, or ¹⁸O singly-substituted in the internal-rotation A state were observed and analyzed to derive the r_s structure of the trans form. For comparison with the experimental data, ab initio calculations were carried out at MP2/6-31G∗∗ level to derive molecular structure, potential barrier to CH₃ internal rotation, and the energy difference between the cis and trans forms. An extensive coupling was found between the CH₃ internal rotation and N-H out-of-plane bending, suggesting that the potential function for the CH₃ internal-rotation deviates considerably from a simple cos(3α) form. The effects of the V₆ term is briefly discussed.     

Comparative kinetic stability of classical and non-classical fullerenes C46

Molecular dynamics is used to study the kinetic stability of a classical fullerene C₄₆ and its non-classical analog with a square. The lifetimes of both clusters till the moments of their isomerization are directly calculated as functions of temperature. The activation energies _Ea$E_a$ of isomerization processes are determined from the fits of the results obtained to the Arrhenius law. For the non-classical fullerene, the value of _Ea=3.1±0.2 eV$E_a=3.1\pm 0.2\text{eV}$ is found to be considerably below that for the classical one, _Ea=4.5±0.3 eV$E_a=4.5\pm 0.3\text{eV}$. In view of rather low kinetic stability of non-classical C₄₆, its experimental registration in a gas phase seems to be problematic.     

Accurate and analytical strain mapping at the surface of Ge/Si(0 0 1) islands by an improved flat-island approximation

We propose an extension of the well-known flat-island approximation in (1 + 1) dimensions which, while keeping simple analytical relations, allows one to better describe the strain field on the facets of steeper islands, and on the wetting layer between them. The results of atomistic molecular dynamics simulations using the Tersoff potential are used as a benchmark. The simple continuum approach is also shown to predict the correct trend of the strain gradients characterizing closely-spaced interacting islands, which has been recently observed to produce lateral motion of large Ge dots on Si(0 0 1).     

Ab initio study of S dynamics on iron surfaces

Density functional theory was employed to examine the interactions of atomic sulfur with the Fe(1 0 0) and Fe(1 1 0) surfaces. Vibrational frequency calculations were performed to determine the nature of stationary points at the high symmetry atop, bridge and hollow adsorption sites and to indicate the direction the adsorbate would move across the surface. The values were also used in the determination of the rate constant for hopping of S from one energy minimum site to another. Ab initio molecular dynamics (MD) simulations were then performed to monitor the mobility of the S atom on the (1 0 0) surface at different temperatures up to the melting point of Fe (1808 K) and were compared to our previously obtained ab initio MD results for S/Fe(1 1 0) [N. Todorova, M.J.S. Spencer, I. Yarovsky, Australian Institute of Physics 16th Biennial Congress, 2005, Canberra, Australia, ISBN 0-9598064-8-2].     

光谱法结合分子动力学模拟研究臭氧对肌红蛋白结构的作用机制

臭氧(O₃)是一种具有强氧化性作用的杀菌消毒剂,因其安全无害等特点已被广泛用于肉制品生产加工的减菌处理,但O₃减菌处理对红肉色泽具有较强的负面作用,且其作用机制尚缺乏研究。针对肌红蛋白（Mb）存在状态是决定红色肉色泽关键因素的基础,通过紫外-可见吸收光谱法、荧光光谱法和圆二色光谱法（CD）研究O₃作用下Mb的光谱特性变化,结合蛋白质氧化特征指标分析和分子动力学模拟技术探究O₃对Mb分子的作用效果与机制。光谱研究结果表明,O₃处理可使Mb的紫外-可见光谱图在412 nm左右处的铁卟啉环特征峰及540和580 nm附近的氧合肌红蛋白（OMb）特征峰的强度减弱,其中铁卟啉环特征峰发生蓝移;利用固定激发波长280 nm下测定Mb内源性荧光和同步荧光光谱表明O₃会降低Mb的荧光强度,增大铁卟啉基团贡献的荧光峰强度和造成酪氨酸残基荧光光谱特征峰的蓝移;O₃作用使Mb三维荧光光谱特征峰强度的下降及光散射强度的增加。以上变化推断出O₃会促进Mb的氧化,造成其氨基酸残基疏水基团裸露,使Mb所处微环境及其蛋白构象改变;CD分析表明O₃与肌红蛋白接触时间越久,蛋白质二级结构变化越明显,造成α-螺旋的含量下降,无规则卷曲增加。辅以检测不同强度O₃处理Mb的含量及性质的变化,可知O₃处理使OMb含量下降,高铁肌红蛋白（MMb）含量增加,同时O₃处理Mb的羰基含量增加和巯基含量下降,这也进一步证实O₃作用促进了Mb的氧化,此外,O₃处理Mb表面疏水性的增强,说明O₃造成Mb体系微环境的极性变化。分子动力学模拟结果显示O₃会提高Mb肽链的RMSD值,影响Mb肽链的稳定性,减弱铁卟啉环与Mb肽链的相互作用;RMSF结果表明Mb活性口袋附近氨基酸残基的变化较大;蛋白质二级结构分析与光谱学试验研究结果一致,Mb的α-螺旋的含量下降,无规则卷曲增加。总而言之,O₃可作用于Mb的氨基酸残基,导致蛋白质二级结构和疏水性改变,并发生蛋白氧化及铁卟啉环暴露,进而引起红色肉色泽发生改变。该研究可为生鲜红肉护色技术制定等提供一定理论依据。     

三种蛋白和黄酮结合物中氢键与黄酮稳定性相关性分析研究

运用三维荧光光谱、紫外可见分光光谱以及傅里叶红外光谱等手段研究了蛋白与黄酮分子的相互作用,并结合相关性分析的统计学手段分析了蛋白与黄酮分子相互作用方式对黄酮稳定性的影响。实验结果表明,疏水相互作用是三种蛋白与黄酮分子之间主要的作用力,在牛血清白蛋白与黄酮的结合中有氢键的参与,同时发现在牛血清白蛋白体系中黄酮的稳定性明显增强。通过相关性分析证明蛋白对黄酮稳定性的提高与两者之间的分子间氢键有关,氢键结合作用越强蛋白对黄酮保护越明显。     

Impact of interface relaxation on the nanoscale corrugation in Pb/Si(1 1 1) islands

The nanoscale hexagonal pattern observed in scanning tunneling microscopy (STM) for 3-layer and 4-layer Pb islands on Si(1 1 1) is studied theoretically. We found that besides thickness the atomic rearrangement at the Pb/Si interface plays an important role in determining the STM patterns. Electronic structures of the Pb film on Si(1 1 1) obtained from fully relaxed and unrelaxed Pb films are qualitatively different. Simulated STM images for Pb films with different stacking also show that the corrugation patterns are sensitive to the buried Pb-Si interfacial structure.     

Rotational analysis of weak (4, 6) hot band in the comet-tail (AΠi-XΣ) system of the CO

The ro-vibrational spectrum of the weak (4, 6) hot band in the comet-tail (A²Π_i-X²Σ⁺) system of CO⁺ is observed by employing optical heterodyne and magnetic rotation enhanced velocity modulation spectroscopy. One hundred and twenty-four spectral lines are assigned to this band; thus, precise molecular constants of the levels involved are obtained from a weighted nonlinear least-squares fitting procedure combining with our previous spectrum of the (3, 6) band.     

Study of (1, 4) band in the comet-tail (AΠi-XΣ) system of CO

Ro-vibrational spectrum of the (1, 4) band in the comet-tail system of CO⁺ cation is observed employing the optical heterodyne and magnetic rotation enhanced velocity modulation spectroscopy in the range of 13 189-13 472 cm⁻¹. Two hundred and eighteen spectral lines are assigned to 12 branches of this band for the first time, thus, precise molecular constants of the levels involved are obtained by nonlinear least-squares fitting procedure combining with our previous spectrum of the (1, 2) band.     

Simulations of the chain length dependence of the melting mechanism in short-chain n-alkane monolayers on graphite

The melting transition in solid monolayers of a series of short-chained n-alkanes, n-octane (n-C₈H₁₈), n-decane (n-C₁₀H₂₂), and n-dodecane (n-C₁₂H₂₆) physisorbed onto the graphite basal plane are studied through use of molecular dynamics simulations. Utilizing previous experimental observations of the solid phase behavior of these monolayers, this study investigates the temperature dependence of the phases and phase transitions in these three monolayers during the solid-fluid phase transition, and compares the observed melting behavior to previous studies of hexane and butane monolayers. In particular, this study seems to indicate a greater dependence of the melting transition on the formation of gauche defects in the alkyl chains as the chain length is increased. In light of the previously proposed “footprint reduction” mechanism and variations where the formation of gauche defects are energetically negated, simulations seem to suggest that decane and dodecane monolayers are generally equally as dependent upon the formation of gauche defects for the melting transition to take place, whereas octane monolayers seem to have less dependence, but follow a trend that is established in previous studies of melting in butane and hexane monolayers. Also, the phase transition from a solid herringbone phase into an orientationally ordered “intermediate” phase is found to exhibit some differences as compared to a recent study of hexane monolayers, which may be interpreted as originating from the greater influence of gauche defects. Comparison to experimental melting temperatures is provided where possible, and applications involving thin film manipulation and lubrication is discussed.     

Study of the spectrum of (3, 1) band in the dΔ-aΠ system of CO

Six hundred and sixty-one spectral lines of the (3, 1) band in the d³Δ-a³Π system of CO in the range of 13,410-13,920 cm⁻¹ were observed employing optical heterodyne magnetic rotation enhanced concentration modulation spectroscopy. Improved molecular constants of the upper vibrational level involved were obtained by a non-linear least-squares weighted fitting procedure using effective Hamiltonians with those of the lower levels fixed at the values obtained in the sub-millimeter region, and the improvements are around one order of magnitude.     

Surface relaxation and near-surface atomic displacements in the N/Cu(1 0 0) self-ordered system

The atomic displacements of Cu atoms induced by nitrogen adsorption on Cu(1 0 0) have been studied by channelling–blocking of swift ⁴He ions. This study has been performed at two adsorption stages. The first one corresponds to the formation of a dense, two-dimensional, self-ordered array of square-shaped islands covered by nitrogen. The second one corresponds to uniform coverage at saturation. We have determined by nuclear reaction analysis the absolute quantity of nitrogen adsorbed at these two stages. The values obtained, when confronted to previous observations of these stages by low energy electron diffraction and by scanning tunnelling microscopy, demonstrate that nitrogen remains mostly at the sample surface and that the N concentration in bulk Cu could not exceed 1%. However, channelling measurements show that this surface adsorption generates atomic displacements of Cu atoms down to depths of a few ten (1 0 0) interplanar distances. In the mean time, blocking measurements reveal that nitrogen adsorption induces a strong surface expansion: the interplanar distance between the first two (1 0 0) planes increases of about 0.2 Å, in contrast with the weak contraction observed on bare Cu(1 0 0) surfaces. This observation supports the hypothesis that, when nitrogen is adsorbed, the surface is submitted to stress variations, from tensile to compressive stress for, respectively, bare and nitrogen-covered surface regions. The surface forces corresponding to such variations have been introduced in molecular dynamics simulations. For coverage leading to self-ordering, these simulations do indeed predict displacements of subsurface Cu atoms. The adjustment of these displacements to those measured by channelling gives the amplitude of the stress variation.     

A theoretical investigation of the binding of TiCln to MgCl2

The structure of the (0 0 0 1) surface of the -MgCl₂ crystal has been investigated using DFT-GGA periodic calculations. The calculated surface relaxation is in agreement with LEED measurements. Motivated for the use of MgCl₂ as support for the Ziegler–Natta reaction, we have studied the adsorption of the catalyst (titanium chlorides as monomers or dimers) on the (1 0 0) and (1 1 0) MgCl₂ surfaces. The structures of adsorbed species are close to those previously found on cluster models: bridging chlorine atoms connect the Ti to the Mg atoms and the systems remain in high spin states. The (0 0 0 1) surface is the most stable face of the -MgCl₂ crystal; however it is Cl-terminated and henceforth poorly reactive; it had been suggested to deposit metallic Mg in order to improve its reactivity. Our modelling explains the failure of this tentative; the interaction between the deposited metal and the surface is repulsive and uncharged Mg atom does not bind.     

Friction between α-Al2O3(0 0 0 1) surfaces and the effects of surface hydroxylation

Molecular dynamics simulations were performed to study the friction between hydroxylated α-Al₂O₃(0 0 0 1) surfaces at the temperature of 300 K. Effects of the degree of surface hydroxylation and sliding velocity have been discussed. Results indicate that the friction coefficient decreases with increased degrees of hydroxylation. For all degrees of surface hydroxylation, the friction law crosses over from thermal activation to viscous damping at sliding velocity of 80 m/s.     

Kr/Xe气体在塑料闪烁体表面的吸附与扩散行为研究

采用基于Compass力场的分子动力学(MD)方法,研究了惰性气体氙(Xe)和氪(Kr)在塑料闪烁体(聚乙烯基对甲苯)的平整和粗糙表面的吸附和扩散行为.由惰性气体吸附曲线的均方根位移(MSD),得到了Xe/Kr气体在聚乙烯基对甲苯表面的扩散系数.研究结果表明,Kr/Xe气体均被稳定地吸附在塑料闪烁体表面,其稳定性随着温度的升高而增加,Xe分子的吸附性强于Kr分子. Kr/Xe气体在聚乙烯基对甲苯表面具有较强的扩散性能,扩散深度随着温度与厚度的增加而增加,最大为22.865?,Kr分子扩散能力强于Xe分子.基底粗糙表面增加了两种惰性气体分子的吸附和扩散.     

Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water

应用分子动力学模拟方法研究了室温条件下四氟硼酸钠(NaBF₄)/水混合体系中水分子的微观结构、IR光谱以及转动动力学. 考察了混合物体系中水分子的摩尔分数浓度分别为6.25%、25.0%、50.0%、75.0%、90.0% 和99.6%时体系的结构和动力学性质. 研究显示在不同水分子含量的混合物中水分子以自由分子存在,随着混合物中水分子摩尔分数的增加,水分子的转动和弯曲振动带红移,而O-H伸缩振动蓝移,混合物中水分子内和分子间的氢键和非谐性相互作用增强,分子平动和转动变得困难和缓慢,研究结果与实验观测一致.     

System size and trajectory length dependence of the static structure factor and the diffusion coefficient as calculated from molecular dynamics simulations: The case of SPC/E water

The effect of the applied trajectory length on the convergence of the self-diffusion coefficient was examined for the SPC/E water model in the NVT ensemble with different system sizes at 293 K. Temperature dependence and isotope effects, via using D₂O instead of H₂O, were also investigated. A simulation for the polarizable SWM4-DP model was also carried out to compare the effect of different potential models. Radial distribution functions and the neutron weighted structure factor were also calculated; they were found to be insensitive to changing the system size in the range of 216 to 16,000 molecules. On the other hand, the diffusion coefficient is rather sensitive to the applied trajectory length, system size and the method of calculation. The diffusion coefficient is therefore not appropriate for assessing, and distinguishing between, potential models of water, whereas the structure factor could serve as a more stable measure.     

Theoretical calculations on the adhesion, stability, electronic structure, and bonding of Fe/WC interface

The adhesion, stability, electronic structure, and bonding of Fe/WC interfaces were studied using first-principles calculations. The preferred stacking sequence is HCP structure that Fe atoms continue the natural stacking sequence of the bulk WC. For two different interfaces with HCP stacking geometry (C-HCP and W-HCP), the work of adhesion of the optimized Fe/WC interfaces are 9.7 J m⁻² for C-HCP and 5.1 J m⁻² for W-HCP, respectively. The effects of the interface on the electronic structures of both the metal Fe and ceramic WC are mainly localized within the first and second layers of the interface. C-HCP interface has strong covalency and W-HCP interface is dominated by metallic bonds. The magnetic moments of Fe atoms at interface are decreased in both interfaces. Calculations of the interfacial energies provide theoretical evidence for the excellent wear behaviors of Fe/WC composites. Besides, the chemical bonding properties for the interfacial atoms are also discussed in this paper based on Milliken population method.     

Effect of ultrasonic power on the stability of low-molecular-weight oyster peptides functional-nutrition W1/O/W2 double emulsion

Ultrasonic-assisted treatment is an eco-friendly and cost-effective emulsification method, and the acoustic cavitation effect produced by ultrasonic equipment is conducive to the formation of stable emulsion. However, its effect on the underlying stability of low-molecular-weight oyster peptides (LOPs) functional-nutrition W₁/O/W₂ double emulsion has not been reported. The effects of different ultrasonic power (50, 75, 100, 125, and 150 W) on the stability of double emulsions and the ability to mask the fishy odor of LOPs were investigated. Low ultrasonic power (50 W and 75 W) treatment failed to form a well-stabilized double emulsion, and excessive ultrasound treatment (150 W) destroyed its structure. At an ultrasonic power of 125 W, smaller particle-sized double emulsion was formed with more uniform distribution, more whiteness, and a lower viscosity coefficient. Meanwhile, the cavitation effect generated by 125 W ultrasonic power improved storage, and oxidative stabilities, emulsifying properties of double emulsion by reducing the droplet size and improved sensorial acceptability by masking the undesirable flavor of LOPs. The structure of the double emulsion was further confirmed by optical microscopy and confocal laser scanning microscopy. The ultrasonic-assisted treatment is of potential value for the industrial application of double emulsion in functional-nutrition foods.