Distance measurements in the borderline region of applicability of CW EPR and DEER: a model study on a homologous series of spin-labelled peptides

Inter-spin distances between 1 nm and 4.5 nm are measured by continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) methods for a series of nitroxide-spin-labelled peptides. The upper distance limit for measuring dipolar coupling by the broadening of the CW spectrum and the lower distance limit for the present optimally-adjusted double electron electron resonance (DEER) set-up are determined and found to be both around 1.6-1.9 nm. The methods for determining distances and corresponding distributions from CW spectral line broadening are reviewed and further developed. Also, the work shows that a correction factor is required for the analysis of inter-spin distances below approximately 2 nm for DEER measurements and this is calculated using the density matrix formalism.     

A steered molecular dynamics study on the elastic behaviour of knotted polymer chains

In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-end distance, R, results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the ＇entrance＇ to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally, the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected, for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.     

Effect of spin–orbit coupling on spin transport at graphene/transition metal interface

In spite of large spin coherence length in graphene due to small spin–orbit coupling, the created potential barrier and antiferromagnetic coupling at graphene/transition metal (TM) contacts strongly reduce the spin transport behavior in graphene. Keeping these critical issues in mind in the present work, ferromagnetic (Co, Ni) nanosheets are grown on graphene surface to elucidate the nature of interaction at the graphene/ferromagnetic interface to improve the spin transistor characteristics. Temperature dependent magnetoconductance shows unusual behavior exhibiting giant enhancement in magnetoconductance with increasing temperature. A model based on spin–orbit coupling operated at the graphene/TM interface is proposed to explain this anomalous result. We believe that the device performance can be improved remarkably tuning the spin–orbit coupling at the interface of graphene based spin transistor. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Static and dynamic properties of grafted ring polymer: Molecular dynamics simulation

The static and dynamic properties of a system of end-grafted flexible ring polymer chains grafted to a flat substrate and exposed to a good solvent are studied by using a molecular dynamics method. The monomers are described by a coarse-grained bead-spring model. Varying the grafting density ρ and the degree of polymerization or chain length N, we obtain the density profiles of monomers, study the structural properties of the chain (radius of gyration, bond orientational parameters, etc.), and also present the dynamic characteristics such as chain energy and bond force. Compared with a linear polymer brush, the ring polymer brush exhibits different static and dynamic properties for moderate or short chain length, while it behaves like linear polymer brush in the regime of long chain length.     

SiC/C界面辐照性能的分子动力学研究

本文通过分子动力学模拟的方法,研究了5种含不同空间结构的SiC/C界面的材料受辐照后的缺陷分布随时间以及PKA位置的变化关系,并与单质SiC中缺陷分布情况进行对比.利用径向分布函数分析了辐照对界面原子排列情况的影响.研究结果表明,SiC/C界面的抗辐照能力明显低于SiC内部,不同的空间结构对界面缺陷数量存在一定影响.由径向分布函数推得界面区域石墨原子密度高则界面原子排列情况受辐照影响越大.     

氧化硅团簇切削单晶硅粗糙峰的分子动力学模拟研究

应用分子动力学模拟方法研究了氧化硅团簇在不同的切削 深度下切削单晶硅粗糙峰的过程, 考察了切削过程中粗糙峰和氧化硅团簇形态变化、团簇的受力状况、粗糙峰原子配位数和温度分布等. 模拟结果表明: 切削深度小于0.5 nm时, 被去除的材料以原子或者原子簇形式存在, 并黏附在颗粒表面被带走; 当切削深度增大至1 nm时, 材料的去除率增大, 并形成大的切屑. 在切削过程中, 由于压力和温度的升高, 粗糙峰切削区域的单晶硅转变为类似Si-Ⅱ相和Bct5-Si相的过渡结构, 在切削过程后的卸载阶段, 过渡结构由于压力和温度的下降转变为非晶态结构.     

Structure and dynamics of water at liquid–vapour interfaces covered by surfactant monolayers of neutral stearic acid and charged stearate ions

The behaviour of water molecules at liquid–vapour interfaces with a surfactant monolayer of either stearic acid molecules or anionic stearate ions is investigated by means of molecular dynamics simulations. The density and dipolar orientational profiles and also the dynamics of translational and rotational motion of interfacial water molecules are calculated in the present work and the results are compared with the bulk liquid water and also of liquid–vapour interface of surfactant-free water. The present simulation results are also compared with available experimental results of similar interfacial systems with a monolayer of either neutral or ionic surfactants.     

Molecular simulation of sodium butyl benzene sulfonate at air–water interface and in aqueous solution

Molecular mechanics(MM) calculations for interfacial behaviour of sodium n-butyl benzene sulfonate (NaNBBS), sodium iso-butyl benzene sulfonate (NaIBBS) and sodium tert-butyl benzene sulfonate (NaTBBS) show a significant effect of the butyl group geometry on the surface area occupied by these molecules at the air–water interface. NaNBBS, in comparison with NaIBBS and NaTBBS, shows a closer molecular packing at the interface. The simulation predicts minimum hydrotrope concentration of each hydrotrope to reach surface saturation and molecular surface area at the interface match with good accuracy. The shape, size and charge of the hydrotrope aggregates obtained by molecular dynamics simulation also match well with the results of small angle neutron scattering experiments on the same hydrotrope. The simulation shows non-regular and ellipsoidal hydrotropes aggregates with substantial charge on the surface. The aggregates are also more open structures as compared to surfactant micelles. The water accessible surface area of a NaNBBS aggregate was 25% lower in comparison to that of NaTBBS aggregate, indicating closer packing of NaNBBS molecules. The fractional charge on the NaNBBS aggregate decreases with the increase in the number of NaNBBS molecules in the aggregate indicating more counter-ion association.     

Synthesis of copper monolayer and particles at aqueous–organic interface

Using aqueous–organic interface (water–oleic acid) reduction of Cu²⁺ by ascorbic acid, hydrophobic copper monolayer and copper particles have been prepared and characterized. The resultant monolayer could be transferred from the interface onto solid substrate or be dissolved to yield an organosol and copper nanoparticles.     

Synthesis of high fluorescent silica hybrid materials by immobilization of orange peel extract in silica‐silsesquioxane matrix

Sol–gel chemistry can be easily modified to the changing needs of society to produce fine‐tuned sol–gel nanostructured materials for relevant applications. In this context, there is an increasing need for natural and versatile raw materials as well as biocompatible compounds that could be extensively used as biomarkers for bioimaging in diagnosis or therapy. Silica‐based materials are widely used in the field of biomedicine due to their chemical inertness and biocompatibility. In the present paper, orange peel extract was immobilized inside inorganic silica and hybrid silica‐silsesquioxane polymeric networks. Silica and organo‐modified silica matrices were synthesized through a templated sol–gel route of TEOS and an organosilsesquioxane (octaisobutyltetracyclo[7.3.3.1^5,11] octasiloxane‐endo‐3,7‐diol), with D ‐glucose as template, and for comparison a non‐ionic surfactant (tetraethylene glycol mono‐hexadecyl ether) was also used. The bioactive properties of the molecules from orange peel extract were preserved after immobilization in both silica and silica‐silsesquioxane networks. Moreover, the fluorescence properties were amplified by 10–20 times more than the native orange peel extract. The structural properties of the final materials have been studied by FT‐IR, UV–Vis‐NIR, and fluorescence spectroscopy. Dynamic light scattering measurements and transmission electron microscopy were used to estimate the size and morphology of the hybrid materials with orange peel extract immobilized in silica networks. Copyright © 2009 John Wiley & Sons, Ltd.     

EPR and NMR study of molecular components mobility and organization in goat milk under ultrasound treatment

The effect of ultrasound treatment on molecular mobility and organization of the main components in raw goat milk was studied by EPR and NMR spectroscopies. NMR relaxation studies showed an increase in the spin–lattice T₁ and spin–spin T₂ relaxation times in goat milk products (cream, anhydrous fat) and change in the diffusion of proton-containing molecules during ultrasound treatment. The diffusion became more uniform and could be rather accurately approximated by one effective diffusion coefficient D_eff, which indicates homogenization of goat milk components, dispersion of globular and supermicellar formations under sonication. EPR studies have shown that molecular mobility and organization of hydrophobic regions in goat milk are similar to those observed in micellar formations of surfactants with a hydrocarbon chain length C12–C16. Ultrasound treatment did not affect submicellar and protein globule organization. Free radicals arising under ultrasound impact of milk reacted quickly with components of goat milk (triglycerides, proteins, fatty acids) and were not observed by spin trapping method.     

纳米尺度下Si/Ge界面应力释放机制的分子动力学研究

采用分子动力学方法研究了纳米尺度下硅(Si)基锗(Ge)结构的Si/Ge界面应力分布特征,以及点缺陷层在应力释放过程中的作用机制.结果表明:在纳米尺度下, Si/Ge界面应力分布曲线与Ge尺寸密切相关,界面应力下降速度与Ge尺寸存在近似的线性递减关系;同时,在Si/Ge界面处增加一个富含空位缺陷的缓冲层,可显著改变Si/Ge界面应力分布,在此基础上对比分析了点缺陷在纯Ge结构内部引起应力变化与缺陷密度的关系,缺陷层的引入和缺陷密度的增加可加速界面应力的释放.参考对Si/Ge界面结构的研究结果,可在Si基纯Ge薄膜生长过程中引入缺陷层,并对其结构进行设计,降低界面应力水平,进而降低界面处产生位错缺陷的概率,提高Si基Ge薄膜质量,这一思想在研究报道的Si基Ge膜低温缓冲层生长方法中初步得到了证实.     

Adsorption and spreading of polymers at plane interfaces; theory and molecular dynamics simulations

Nonequilibrium processes play a key role in the adsorption kinetics of macromolecules. It is expected that the competition between transport of polymer towards an interface and its subsequent spreading has a significant influence on the adsorbed amount. An increase of the transport rate can lead to an increase of the adsorbed amount, especially when the polymer has too little time to spread at the interface. In this study we present both molecular dynamics simulations and analytical calculations to describe some aspects of the adsorption kinetics. From MD simulations on a poly(ethylene oxide) chain in vacuum near a graphite surface, we conclude that the spreading process can, in first approximation, be described by either a simple exponential function or by first-order reaction kinetics. Combining these spreading models with the transport equations for two different geometries (stagnation-point flow and overflowing cylinder) we are able to derive analytical equations for the adsorption kinetics of polymers at solid-liquid and at liquid-fluid interfaces. Received: 18 July 1997 / Received in final form: 27 October 1997 / Accepted: 6 November 1997     

Mechanical and tribological properties of Ni/Al multilayers—A molecular dynamics study

Mechanical and tribological properties of multilayers with nanometer thickness are strongly affected by interfaces formed due to mismatch of lattice parameters. In this study, molecular dynamics (MD) simulations of nanoindentation and following nanoscratching processes are performed to investigate the mechanical and tribological properties of Ni/Al multilayers with semi-coherent interface. The results show that the indentation hardness of Ni/Al multilayers is larger than pure Ni thin film, and the significant strength of Ni/Al multilayers is caused by the semi-coherent interface which acts as a barrier to glide of dislocations during nanoindentation process. The confinement of plastic deformation by the interface during nanoscratching on Ni/Al multilayers leads to smaller friction coefficient than pure Ni thin film. Dislocation evolution, interaction between gliding dislocations and interface, variations of indentation hardness and friction coefficient are studied.     

Correlation of size and oxygen bonding at the interface of Si nanocrystal in Si–SiO2 nanocomposite: A Raman mapping study

Raman spectroscopy/mapping is used to investigate the variation of Si phonon wavenumbers, i.e., lower wavenumber (LW ~ 495–510 cm⁻¹) and higher wavenumber (HW ~ 515–519 cm⁻¹) phonons, observed in Si–SiO₂ multilayer nanocomposite (NCp) grown using pulsed laser deposition. Sensitivity of Raman spectroscopy as a local probe to surface/interface is effectively used to show that LW and HW phonons originate at surface (Si–SiO₂ interface) and core of Si nanocrystals, respectively. The consistent picture of this understanding is developed using Raman spectroscopy monitored laser heating/annealing and cooling experiment at the site of the desired wavenumber, chosen with the help of Raman mapping. Raman spectra calculations for Si₄₁ cluster with oxygen and hydrogen termination show strong mode at 512 cm⁻¹ for oxygen terminated cluster corresponding to the vibration of surface Si atoms. This supports our attribution of LW phonons to be originating at the Si–SiO₂ surface/interface. These results along with XPS show that nature of interface (oxygen bonding) in turn depends on the size of nanocrystals and LW phonons originate at the surface of smaller Si nanocrystals. The understanding developed can conclude the ongoing debate on large variation in Si phonon wavenumbers of Si–SiO₂ NCps in the literature. Copyright © 2015 John Wiley & Sons, Ltd.     

Indirect carbon–carbon spin–spin couplings across one,two and three bonds in pyridine and diazine systems: experiment and theory

An excellent linear correlation is found between a large body of experimental spin–spin carbon–carbon couplings, J(CC), across one, two and three bonds in pyridine and diazine ring systems and the corresponding B3PW91/6‐311++G(d,p)//B3PW91/6‐311++G(d,p) computations. The correlation does not differ significantly from the simplest relationship possible, J(CC)_exp. = J(CC)_calcd., within a small and random spread of about 1 Hz. There are 276 experimental values considered, and 124 out of these are new and come from the present work. The aromatic carbon–carbon couplings vary from ?7.6 through +78.5 Hz. It is shown that the correlation provides a reliable tool for predictions of the signs of aromatic J(CC)'s even if the magnitudes of the latter are of the order of 1 Hz. It is demonstrated, for the first time, that the relatively weak ² J(CC) couplings, in the heteroaromatic systems studied, can bear either sign and span a considerable range of about 11 Hz. The character of the correlation indicates that rovibronic effects on aromatic J(CC)'s and those of nuclear motions on aromatic J(CC)'s are practically negligible. All of this is in a perfect agreement with our recent extensive studies on aromatic J(CC)'s in analogous benzene ring system. Substituent effects on the aromatic J(CC)'s turn out to be significant not only for ¹J(CC)'s but also for most of ³J(CC)'s and ² J(CC)'s, and the computation neatly reciprocates these trends. Copyright © 2008 John Wiley & Sons, Ltd.     

Intricate packing in the hydrophobic core of barstar through a CH–π interaction

Identification of specific packing interactions within in the hydrophobic core of proteins is important for understanding the integrity of protein structure. Finding such interactions is challenging because few tools allow monitoring of a specific interaction in the presence of several non‐specific forces that hold proteins together. It is important to understand how and when such interactions develop during protein folding. In this study, we have used the intrinsic tryptophan residue, Trp53, as an ultraviolet resonance Raman probe to elucidate the packing interactions in the hydrophobic core of the protein barstar. Barstar is extensively studied for its folding, unfolding and aggregation properties. The Trp53 residue is known to be completely buried in the hydrophobic core of the protein and is used extensively as an intrinsic probe to monitor the folding and unfolding reactions of barstar. A comparison of the resonance Raman cross sections of some bands of Trp53 with those observed for N‐acetyl‐tryptophanoamide in water suggests that Trp53 in barstar is indeed isolated from water. Intensity ratio of the Fermi doublet suggests that Trp53 is surrounded by several aliphatic amino acid residues in corroboration with the crystal structure of barstar. Importantly, we show that the side chain of Trp53 is involved in a unique CH–π interaction with CH groups of Phe56 as well as a steric interaction with the methyl group of Ile5. Copyright © 2014 John Wiley & Sons, Ltd.     

Origin of significant solvent effects on 1J(CC) spin–spin coupling in some acetylenes: hydrogen bonding and solvent polarity

It is demonstrated that some acetylenes, those of the R? C?CH structure, display anomalously high sensitivity to solvent effects of their ¹J(C?C) coupling while R? C?CR acetylenes fail to show that. The solvent‐induced variation in the latter coupling does not exceed 3 Hz; this seems to be the upper limit of variation of any J(CC) and J(CH) coupling in the molecular system studied which included: acetylene (in 13 solvents), phenylacetylene (in 12 solvents), 1‐phenylpropyne, and 2‐hexyne (two solvents each), and the only exceptions are ¹J(C?C) in acetylene, which is shown to vary within about 13 Hz, and that in phenylacetylene where the range amounts to about 8 Hz. These apparent anomalies are explained in the present study in terms of two effects of prime importance, solvent polarity and the solute‐to‐solvent hydrogen bonds where the CH moiety in R? C?CH acetylenes acts as a donor of hydrogen bonds to acceptor sites in the solvent concerned. Copyright © 2009 John Wiley & Sons, Ltd.     

A study of the valence shell photoionisation dynamics of CH3CN and CF3CN

Valence shell angle resolved photoelectron spectra of CH₃CN and CF₃CN have been recorded in the photon energy range 14–120 eV, thereby allowing asymmetry parameters and branching ratios to be derived. The carbon and nitrogen K-shell photoabsorption spectra of these two molecules exhibit features ascribed to shape resonantly enhanced transitions. Energy dependent variations observed in the asymmetry parameters and branching ratios provide evidence of shape resonances influencing the valence shell photoionisation dynamics. In addition to the main lines associated with single-hole states, complex satellite structure appears in the inner valence region of the photoelectron spectrum due to many-electron effects. The experimental spectra have been interpreted using previously reported ionisation energies and spectral intensities obtained from Green's function calculations.