Molecular dynamics and spatial distribution of TOAC spin-labelled peptaibols studied in glassy liquid by echo-detected EPR spectroscopy

2,2,6,6-tetramethylpiperidine-l-oxyl-4-carboxylic acid (TOAC) spin-labelled analogues of the Aib-rich peptide (peptaibol) Trichogin GA IV are investigated in a glassy methanol/glycerol (70/30 v/v%) system, using conventional CW EPR and electron spin echo spectroscopy. Echo-detected (ED) EPR spectra indicate that the labels undergo restricted orientational motion (libration). Comparison with the small molecular spin probe Tempone shows that the dynamics of peptide molecules is determined by their structure and not by the surrounding medium. At the terminal positions (position 1 and 8) TOAC residues were found to be more flexible than at the central 4th position. Instantaneous diffusion mechanism in electron spin echo, which also contributes to the ED EPR spectra, was employed for deriving the local concentration of peptaibols. This approach may serve as a tool for investigation of peptide aggregation. In the studied model glassy solution the peptaibols were found to be randomly distributed.     

CW EPR, echo-detected EPR, and field-step ELDOR study of molecular motions of nitroxides ino-terphenyl glass: Dynamical transition, dynamical heterogeneity and β-relaxation

Continuous-wave electron paramagnetic resonance (CW EPR), echo-detected (ED) EPR, and field-step electron-electron double resonance (FS ELDOR) were simultaneously applied to study molecular motions of nitroxide spin probes of two different types in glassyo-terphenyl. A strong linear temperature dependence of the overall splitting of the CW EPR lineshape was found for nitroxide Tempone and only a weak one for a phenyl-ring-containing imidasoline nitroxide. The linear temperature dependence of the splitting is explained within the model of harmonic librations. The assessed libration frequency for Tempone is of the order of 3·10¹² rad/s. The observed remarkable difference between the two nitroxides is explained by the different strength of interactions between guest and host molecules and by dynamical heterogeneity of the glass. The nonlinear temperature dependence above 250 K is attributed to the onset of anharmonic motion that is postulated in a number of neutron scattering and Mössbauer spectroscopy studies for molecular glasses and proteins (the so-called dynamical transition). Above 245 K also ED EPR spectra change drastically, which may be explained on the same ground. Magnetization transfer was observed in FS ELDOR for nitroxide Tempone, with a time constant around 10^?5 s. It was found to be almost temperature-independent between 160 K and 265 K and was attributed to the Johari-Goldstein β-relaxation process. For the phenyl-ring-containing imidasoline nitroxide this transfer was not observed, which may be explained again by the dynamical heterogeneity of the glass and by small effectivity of the β-relaxation process in this case.     

Conformational dynamics of triradical nitroxides as studied by EPR

The EPR spectra of a flexible nitroxide triradical are recorded in a large temperature range. A detailed analysis of the spectral features is performed and the spectra are compared with computer simulations. An excellent agreement with the experimental spectra is obtained by using a dynamic model based on the conformation interconversion of different molecular structures, characterized by the electron exchange interactions between pairs of free radicals. The energy barrier for the interconversion process and the temperature variation of the constant for the equilibrium among the conformations have been obtained. The results show that EPR spectra of nitroxide triradicals spin labelled polymers could be of valuable use for studying subtle details of molecular dynamics.     

Librational relaxation of molecular impurities in host crystals

A study is made of phonon-assisted transitions between closely spaced librational levels of an impurity molecule in a host crystal. The contributions to librational relaxation of direct, of Orbach-type and of Raman processes are evaluated as a function of temperature. It is found for a model case of NH(³ π) in solid Ar, that below T = 16 K, the direct process dominates, while for T > 20 K relaxation takes place mainly by the Raman mechanisms. The calculation predicts a nanosecond time scale for the relaxation at 4 K, and a picosecond time-scale for the relaxation at T = 24 K.     

纳米铜团簇凝结规律的分子动力学研究

采用分子动力学方法对包含147，309和561个原子数的液态纳米铜团簇凝结过程进行模拟研 究，结果表明降温速率及团簇原子数对凝结得到常温下的固态团簇结构有重要影响：在模拟 时间内，降温速度越慢，团簇原子数越少，凝结得到铜团簇越倾向生成二十面体结构，反之 则倾向生成面心立方结构.同时探讨了该现象的物理机理. 关键词： 铜团簇 凝结 结构 分子动力学     

Low-frequency molecular dynamics studied by spin-lock field cycling imaging

Spin-lock adiabatic field cycling imaging (SLOAFI) relaxometry was shown to be a useful technique for obtaining a fast study of spin-lattice relaxation dispersion in the rotating frame. The aim of the present article is to describe some technical aspects of the experiment in more detail, while showing simple examples that can be compared with laboratory frame relaxation. We also present here a general discussion of the equations for an off-resonance experiment used to analyze low-frequency molecular dynamics.     

Photoinduced electron transfer and spin dynamics in mixed porphyrin-quinone solutions studied by time-resolved EPR

From time-resolved direct detection cw EPR with pulsed laser excitation, the photoinduced electron transfer and spin dynamics (CIDEP) in mixed zinc-tetraphenylporphyrin (ZnTPP)/benzo-1,4-quinone (BQ) ethanol solutions were determined as functions of temperature and BQ concentration. At lower temperatures the EPR spectra reveal that mixing of the S and T_?1 states in the charge separated radical pair gains in importance relative to the ST₀ mixing. Furthermore, at lower temperatures, the EPR spectra of the spin-correlated radical pairs of ZnTPP⁺ and BQ⁷ could also be observed. From the temperature/viscosity dependence of the electron transfer rates and of the polarization contributions from the triplet and radical pair mechanisms, deviations from a macroscopic diffusion behaviour are inferred at lower temperatures.     

The dynamical transition in proteins of bacterial photosynthetic reaction centers observed by echo-detected EPR of specific spin labels

An echo-detected electron paramagnetic resonance (ED EPR) approach was used to study molecular dynamics in photosynthetic reaction centers (RCs) fromRhodobacter sphaeroides R26, employing the specific spin label methanethiosulfonate and 3-maliemido proxyl. ED EPR has recently been shown to be sensitive to so-called dynamical transition in disordered media, which is characterized by the transition from a harmonic-like librational motion of a molecule to an anharmonic one or to a stochastic wobbling motion. ED EPR line shapes studied over a wide temperature range reveal a sharp transition occurring above 180 K. The possible relation of the found transition to the temperature dependence of electron transfer reactions in RC is discussed.     

Energy transfer under impact load studied by molecular dynamics simulation

The process of amorphous silica clusters impact on a crystal silicon substrate is studied by molecular dynamics simulation, focusing on the energy transfer between clusters and the substrate under different impact conditions such as cluster size, impact velocity, and incidence angle. The impact process is divided into cluster deformation stage, cluster resilience stage, and cluster rebound stage according to the courses of energy change during the impact process. The simulation elucidates that the time of impact process of every cluster is only related to cluster size and is independent of impact velocity and incidence angle. The translational energy loss of the cluster and the potential energy increment of the substrate during cluster deformation stage, and the dissipation energy of system are independent of cluster size under the same impact energy and incidence angle. And the translational energy loss of the cluster during cluster rebound stage changes from energy absorption to energy release after the incidence angle becomes more than 60°. The rotational energy of the cluster may be omitted when the incidence angle is less than 15°. The ratios of the rotational energy increment of the cluster, the kinetic energy increment, and the potential energy increment of the substrate to the translational energy loss of the cluster are obviously influenced by impact conditions. And the ratios of the increment of the other categories of energy to the translational energy loss of the cluster are not sensitive to impact conditions.     

Determination of absolute concentration of nitroxide radical by radio-frequency EPR imaging

The absolute concentrations of a nitroxide radical in samples in a loop-gap resonator (LGR) were determined by using a radio-frequency (about 720 MHz) electron paramagnetic resonance (EPR) imaging system. EPR imaging of phantoms containing a nitroxide radical, 3-carbamoyl-2,2,5,5-tetramethylpyrrolidin-1-yloxy (carbamoyl-PROXYL), dissolved in various concentrations of an aqueous sodium chloride solution was made to investigate the influence of dielectric losses and sample position within the LGR. As it was found that these influences on the signal intensity were sufficiently small (less than 6%), it is possible to use identical radical solutions in which the radical is dissolved in a known concentration as an internal marker. Two phantoms containing aqueous solutions of 3 mM (as a marker) and 1, 2, 3, 4, or 5 mM (as a sample) carbamoyl-PROXYL were placed together in the LGR. From EPR images of these phantoms, the absolute concentration of the sample could be calculated by using the gray-scale value (i.e., the signal intensity) of the marker and sample within a small margin of error (about 4%).     

Transport properties of cholesteric liquid crystals studied by molecular dynamics simulation

We have studied the transport properties of a cholesteric liquid crystal by molecular dynamics simulation. The molecules consist of six soft ellipsoids of revolution, the axes of which are perpendicular to the line connecting their centres of symmetry. The angle between the symmetry axes of two adjacent ellipsoids is 7.5°, so the molecules are twisted. At high densities they form a cholesteric phase where their twist axes are oriented around the cholesteric axis and the symmetry axes of the ellipsoids are approximately parallel to the local director. We have been particularly interested in thermomechanical coupling or the Lehmann effect, which arises when a temperature gradient parallel to the cholesteric axis induces a torque that rotates the director. The converse is also possible: rotation of the director can drive a heat current. The thermal conductivity, the twist viscosity, the cross-coupling coefficient between the temperature gradient and the torque, and the cross-coupling coefficient between the director angular velocity and the heat current have been calculated by non-equilibrium molecular dynamics simulation methods (NEMD) and by evaluation of the Green-Kubo relations from equilibrium simulations. Two ensembles have been utilized: the ordinary canonical ensemble and another ensemble where the director angular velocity is constrained to be a constant of motion. All the methods give consistent results for the twist viscosity and the thermal conductivity. The NEMD estimates of the cross-coupling coefficients agree within a relative error of 20%. This is consistent with the Onsager reciprocity relations that state that the two cross-coupling coefficients should be equal. The relative error of the Green-Kubo estimates is about 100% even though the order of magnitude is the same as that of the NEMD estimates.     

直角坐标系中的分子和分子晶体振动光谱分析

本文介绍在直角坐标系中用简单的弹性力常数模型分析振动光谱的方法,这种方法在处理孤立分子时与传统的 GF 矩阵法等效,而对于分子晶体振动的动力学计算具有一定的优越性。它利用统一的数学公式来描述晶体中分子内外的相互作用从而同时获得分子外部振动频率和内部模式在晶体场中分裂的信息。     

Librational and relaxational motion of molecular impurities in crystals

The dynamics of a single impurity with rotational degrees of freedom in the static crystal field of the host lattice is revisited. We use numerical simulation techniques to calculate the time-dependent correlation functions accurately up to very long times. Then we carry out a spectral analysis of these results, thus obtaining good estimates for the contribution of different representations to the incoherent scattering cross-sections. For some representations we find non-ergodic behaviour, giving rise to delta-function contributions at zero frequency. In the real crystal these contributions will be broadened because the rotator is coupled dynamically to the phonons of the host crystal, which is not taken into account in our simple model.     

分子动力学模拟钠硼硅酸盐玻璃电子辐照诱导的结构演化效应

钠硼硅酸盐玻璃作为高放射废物玻璃固化体的候选材料之一,已有大量实验对该类玻璃开展了电子或重离子的辐照效应研究.然而,在理论计算与模拟方面的工作却很少,目前主要集中于重离子的辐照效应,对电子的辐照效应的模拟尚未见报道.本文利用分子动力学工具提出一种新的方法,以实现对电子辐照诱导的玻璃结构演化进行模拟.该方法基于实验中玻璃的结构变化特点,即实验中的拉曼结果已经证实:在大剂量的电子辐照后的玻璃中存在分子氧的事实,由于这些分子氧不会与其他粒子发生相互作用,因而可以通过从体系中逐步地移除一定数量氧原子的方式,以达到模拟大剂量电子辐照的情形,进而得到电子辐照后的玻璃的结构信息.模拟结果显示:随着移除氧原子的数量增加,玻璃中的Si—O—Si平均键角逐渐减小;而且玻璃中的小环数量会因氧的逐渐减少而逐渐增加;玻璃中部分[BO4]结构会转变为[BO3]结构,最终这种转变会达到饱和;大量移除氧之后,玻璃中的钠元素也出现明显的相分离.这些模拟辐照的玻璃结构特性能较好地与实验中的硼硅酸盐玻璃电子辐照诱导的结构变化符合.因此,本文提出的方法有望为通过分子动力学模拟硼硅酸盐玻璃的电子辐照效应提供新思路.     

The effect of donor self-association on EPR studies of transient complex formation between nitroxide radicals and solvent molecules

Nitroxide radical-hydrogen donor systems in which the donor can self-associate are examined by EPR techniques. Data for CH₃OH and CH₃COOH and the nitroxide radical TMPO are first fitted by using methods developed for transient complex formation between hydrogen donors and nitroxides. TheK _assoc and hyperfine coupling constants obtained are inconsistent with previous correlations with thepK _a of the hydrogen donor. An alternative method of analysis that incorporates donor self-association is developed and applied to the systems studied.     

超纳米金刚石薄膜结构相变的第一原理分子动力学研究

纳米金刚石薄膜的结构相变非常复杂,对稳定性和物理性质又尤为重要。本文用第一性原理分子动力学模拟研究了超纳米金刚石薄膜的结构相变和表面重构。研究发现,纳米金刚石的表面碳团簇通过断开（111）面的σ键,形成具有碳六元环结构的石墨碎片;内部原子sp3杂化向sp2杂化转化的发生是从（111）面上成对C原子向石墨相转化时形成π键的过程中获得了能量,驱动石墨的转变由表层向心部逐渐进行。转变过程中存在一种洋葱状富勒烯和金刚石结构共存的过渡相——Bucky-diamond,表面悬空键的消除和表层的富勒烯外壳最大限度地降低了表面能和系统总能量,Bucky-Diamond结构稳定存在。     

Light neutron-rich nuclei studied with antisymmetrized molecular dynamics

Structure study of neutron-rich isotopes of Li, Be, B, and C with the antisymmetrized molecular dynamics (AMD) is reported. Good reproduction of various observed data by AMD is demonstrated. AMD wave functions which reproduce data well show large change of structure when neutron number increases. Clustering structure is predicted around neutron driplines of Be and B, while large oblate deformation with neutron skin is predicted around neutron dripline of C.     

Flux trapping in granular superconductors studied by EPR technique

The sensitive and contactless method of microwave absorption has been applied in investigation of the magnetic properties of high-temperature superconductor (HTS). The method allowed the analysis of flux trapping in low magnetic field as a function of texture of the samples.