Direct measurement of dipole-dipole/CSA cross-correlated relaxation by a constant-time experiment

Relaxation rates in NMR are usually measured by intensity modulation as a function of a relaxation delay during which the relaxation mechanism of interest is effective. Other mechanisms are often suppressed during the relaxation delay by pulse sequences which eliminate their effects, or cancel their effects when two data sets with appropriate combinations of relaxation rate effects are added. Cross-correlated relaxation (CCR) involving dipole-dipole and CSA interactions differ from auto-correlated relaxation (ACR) in that the signs of contributions can be changed by inverting the state of one spin involved in the dipole-dipole interaction. This property has been exploited previously using CPMG sequences to refocus CCR while ACR evolves. Here we report a new pulse scheme that instead eliminates intensity modulation by ACR and thus allows direct measurement of CCR. The sequence uses a constant time relaxation period for which the contribution of ACR does not change. An inversion pulse is applied at various points in the sequence to effect a decay that depends on CCR only. A 2-D experiment is also described in which chemical shift evolution in the indirect dimension can share the same constant period. This improves sensitivity by avoiding the addition of a separate indirect dimension acquisition time. We illustrate the measurement of residue specific CCR rates on the non-myristoylated yeast ARF1 protein and compare the results to those obtained following the conventional method of measuring the decay rates of the slow and fast-relaxing (15)N doublets. The performances of the two methods are also quantitatively evaluated by simulation. The analysis shows that the shared constant-time CCR (SCT-CCR) method significantly improves sensitivity.     

Separating Structure and Dynamics in CSA/DD Cross-Correlated Relaxation: A Case Study on Trehalose and Ubiquitin

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of ¹³C CSA and ¹³C–¹H dipolar coupling in a disaccharide, α,α- -trehalose, at natural abundance of ¹³C as well as interference of amide ¹⁵N CSA and ¹⁵N–¹H dipolar coupling in uniformly ¹⁵N-labeled ubiquitin. We demonstrate that the standard heteronuclear T₁, T₂, and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.     

熔融Cu57团簇在急冷过程中弛豫和局域结构转变的分子动力学研究

采用基于嵌入原子方法的正则系综分子动力学研究熔融Cu₅₇团簇在急冷过程中的弛豫及其局域结构变化.通过对弛豫过程中均方位移、非相干中间散射函数和非Gauss参数三种函数和原子键对随急冷温度不同所发生变化的分析表明,在经过短时间的原子剧烈运动后,急冷温度极大地影响着团簇内原子结构弛豫过程.急冷温度较高时,原子在经历短时间剧烈运动的β弛豫后,进入α弛豫区后以扩散运动为主,随后原子运动表现为非扩散性的原子局域结构重排,团簇内没有出现明显的成核结构.随着温度的降低,原子局域结构的变化在经过短时间原子剧烈运动的β弛豫后,在α弛豫区原子运动表现为扩散性运动,并出现一定数量的不稳定二十面体结构.当急冷温度很低时,在进入α弛豫区后,团簇结构变化逐渐表现为非扩散性原子局域结构重排,形成相当数量的稳定成核二十面体结构.     

The role of (15)N CSA and CSA/dipole cross-correlation in (15)N relaxation in solid proteins

The influence of the (15)N CSA on (15)N longitudinal relaxation is investigated for an amide group in solid proteins in powder form under MAS. This contribution is determined to be typically 20-33% of the overall longitudinal relaxation rate, at 11.74 and 16.45 T, respectively. The improved treatment is used to analyze the internal dynamics in the protein Crh, in the frame of a motional model of diffusion in a cone, using the explicit average sum approach. Significant variations with respect to the determined dynamics parameters are observed when properly accounting for the contribution of (15)N CSA fluctuations. In general, the fit of experimental data including CSA led to the determination of diffusion times (tau(w)) which are longer than when considering only an (15)N-(1)H dipolar relaxation mechanism. CSA-Dipole cross-correlation is shown to play little or no role in protonated solids, in direct contrast to the liquid state case.     

Solution dynamics of the natural bioactive molecule capsaicin: a relaxation study

Nuclear magnetic resonance spectroscopy is a straightforward technique for studying molecular dynamics that range in timescale from picosecond (motions faster than molecular reorientation) to those that occur in real-time. This approach is important to highlight the behavior of bioactive molecules in solution, and to acquire information about action mechanisms and potential pharmacological effects. Proton and carbon-13 spin–lattice relaxation experiments were performed to calculate the reorientational correlation time for protonated carbons. Capsaicin showed complex dynamical properties and the results revealed two regions with different dynamical properties: the aliphatic region with fast reorientation motions and the aromatic region with slow motions.     

熔融Cu57团簇在急冷过程中弛豫和局域结构转变的分子动力学研究

采用基于嵌入原子方法的正则系综分子动力学研究熔融Cu₅₇团簇在急冷过程中的弛豫及其局域结构变化.通过对弛豫过程中均方位移、非相干中间散射函数和非Gauss参数三种函数和原子键对随急冷温度不同所发生变化的分析表明,在经过短时间的原子剧烈运动后,急冷温度极大地影响着团簇内原子结构弛豫过程.急冷温度较高时,原子在经历短时间剧烈运动的β弛豫后,进入α弛豫区后以扩散运动为主,随后原子运动表现为非扩散性的原子局域结构重排,团簇内没有出现明显的成核结构.随着温度的降低,原子局域结构的变化在经过短时间原子剧烈运动的β弛豫后,在α弛豫区原子运动表现为扩散性运动,并出现一定数量的不稳定二十面体结构.当急冷温度很低时,在进入α弛豫区后,团簇结构变化逐渐表现为非扩散性原子局域结构重排,形成相当数量的稳定成核二十面体结构. 关键词： 团簇 分子动力学 计算机模拟 表面     

Chain dynamics in a chiral C phase by deuteron spin relaxation study

Molecular reorientations and internal conformational transitions of an aligned chiral liquid crystal (LC) 10B1M7 are studied by means of deuterium spin-lattice relaxation in its smectic A (SmA) and smectic C* (SmC*) phase. The motional model which is applicable to uniaxial phases of many LCs is found to be adequate even when the phase is a tilted SmC* phase. The deuterium NMR spectrum in this phase cannot discern rotations of the molecular director about the pitch axis. The basic assumption is that the phase biaxiality is practically unobservable. However, the relaxation rates can be accounted for by the tilt angle between the molecular director and the layer normal in the SmC* phase. The tumbling motion appears to show a higher activation energy upon entering from the uniaxial SmA into the SmC* phase.     

Measurement of transverse relaxation in coupled spin systems by semi-selective refocusing: Evidence for interference of CSA and dipolar relaxation

A novel spin-echo experiment is proposed that uses semiselective Gaussian pulse cascades for refocusing in systems with homonuclear couplings. The experiment allows one to obtain evidence of differential T₂ effects due to cross-correlation of proton chemical shift anisotropy and proton-proton dipolar interactions in a small aromatic compound at 9.4 T. The spin-echo experiment is also applied to measure transverse relaxation rates for selected multiplets of the cyclic undecapeptide cyclosporin. Possible extensions to multiple-quantum spin echo-spectroscopy are indicated.     

共轭高分子中激子演化过程的非绝热动力学研究

有机共轭高分子受光激发或被电荷掺杂后可能会产生各种激发状态的激子,激子的演化过程对有机发光光谱有着至关重要的影响.通过非绝热动力学演化的方法模拟了受光激发后有机高分子中激子驰豫的动力学过程,结果表明高激发态激子不稳定,由于电声耦合作用,高激发态激子会持续向低激发态激子演化,同时,低激发态激子的复合发光会发生红移.稳定的激子复合发光光谱中,基态激子发光强度最大,可高达70-80%;第一激发态激子及其它激发态激子发光强度的总和不超过20%.     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.     

超精细结构对激光与二能级原子相互作用的影响

应用半经典理论建立了一个简化模型,对157Gd原子在激光作用下17795267cm-1(9D3)←→532977cm-1(9D4)的能级跃迁进行计算并给出了计算结果,提出相应的理论解释,分析了超精细结构对激光与二能级原子相互作用的影响 关键词： 超精细结构 原子蒸气激光同位素分离 二能级原子 钆原子     

Influence of line defects on relaxation properties of graphene: A molecular dynamics study

The relaxation properties of single layer graphene sheets containing line defects were investigated using molecular dynamics simulation with AIROBE bond-order interatomic potential. The dynamic evolution of graphene sheets during relaxation condition was analyzed. The simulation results show that the single layer graphene sheets are not perfectly flat in an ideal state, and the graphene sheet shows a significant corrugations at the verge of sheet. The graphene sheet is bent with the line defects at the end of the sheet, and the extent of this bend also increases with the increase of the defect number. Furthemore, the graphene sheet transforms into a paraboloid with the line defects at the middle of the sheet.     

第一原理研究界面弛豫对InAs/GaSb超晶格界面结构、能带结构和光学性质的影响

通过广义梯度近似的第一原理全电子相对论计算, 研究了不同界面类型InAs/GaSb超晶格的界面结构、电子和光吸收特性. 由于四原子界面的复杂性和低对称性, 通过对InAs/GaSb超晶格进行电子总能量和应力最小化来确定弛豫界面的结构参数. 计算了InSb, GaAs型界面和非特殊界面(二者交替)超晶格的能带结构和光吸收谱, 考察了超晶格界面层原子发生弛豫的影响.为了证实能带结构的计算结果, 用局域密度近似和Hartree-Fock泛函的平面波方法进行了计算. 对不同界面类型InAs/GaSb超晶格的能带结构计算结果进行了比较, 发现界面Sb原子的化学键和离子性对InAs/GaSb超晶格的界面结构、 能带结构和光学特性起着至关重要的作用.     

Determination of the Maier-Saupe strength parameter from dielectric relaxation experiments: a molecular dynamics simulation study

Molecular dynamics simulations have been performed to investigate the rotational motion in the nematic and isotropic phases of a model mesogenic system in which the interactions between the molecules are represented by the Gay-Berne potential. First-rank end-over-end rotational relaxation times, analogous to those measured using dielectric relaxation spectroscopy for real mesogens with a longitudinal electric dipole, have been determined as a function of temperature and density. The relaxation times at temperatures throughout the nematic region are found to be larger than the values extrapolated from the isotropic phase to the same temperature. The simulation results are compared with the extended Debye theory for dielectric relaxation in the nematic phase. This relates the reduction in the relaxation rate to the retardation factor which depends on the Maier-Saupe strength parameter, and in turn is defined uniquely by the second-rank orientational order parameter. The simulations indicate that the retardation factor at constant strength parameter is density dependent, a feature neglected in the relaxation theory. We compare the simulation results where possible with experiment.     

NMR relaxation study of molecular dynamics in columnar and smectic phases of a PAMAM liquid-crystalline co-dendrimer

We present the first results obtained by proton (¹H) nuclear magnetic relaxation studies of molecular dynamics in a supermolecular liquid-crystal dendrimer exhibiting columnar rectangular and smectic-A phases. The ¹H spin-lattice relaxation time (T₁) dispersions are interpreted using two relaxation mechanisms associated with collective motions and local molecular reorientations of the dendritic segments in the low- and high-frequency ranges, respectively. The T₁ values show a drop around 2.3 MHz that is attributed to a contribution coming from cross-relaxation between ¹H and nitrogen nuclear spins. In the high-frequency range the motions appear to be of similar nature in both mesophases and are ascribed to reorientations of dendritic segments (belonging to the core and/or to the mesogenic units) characterized by two correlation times. Notable differences in the dynamics between the columnar and layered phases are observed in the low-frequency range. Depending on the mesophase they are discussed in terms of elastic deformations of the columns and layer undulations. In this study we find that the dendritic core influences the dynamics of the mesogenic units both for local and collective motions. These results can be understood in terms of spatial constraints imposed by the dendritic architecture and by the supermolecular arrangement in the mesophases.     

Formation dynamics of bipolaron in a metal/polymer/metal structure

Charge injection process from metal electrode to a nondegenerate polymer in a metal/ polymer/ metal structure has been investigated by using a nonadiabatic dynamic method. We demonstrate that the dynamical formation of a bipolaron sensitively depends on the strength of applied electric field, the work function of metal electrode, and the contact between the polymer and the electrode. For a given bias applied to one of the electrode (V₀) and coupling between the electrode and the polymer (t^′), such as V₀=0.79 eV and t^′=1 eV, the charge injection process depending on the electric field can be divided into the following three cases: (1) in the absence of the electric field, only one electron tunnels into the polymer to form a polaron near the middle of the polymer chain; (2) at low electric fields, two electrons transfer into the polymer chain to form a bipolaron; (3) at higher electric fields, bipolaron can not be formed in the polymer chain, electrons are transferred from the left electrode to right electrode through the polymer one by one accompanying with small irregular lattice deformations.     

Thermal structure and relaxation rates of the perturbed atmosphere: a study with a photochemial radiative convective model

Summary We have developed a radiative-photochemical model to evaluate the temperature distribution in the Earth's atmosphere between the ground and 70 km. The model takes into account the interaction between photochemistry and temperature. We report results of a number of experiments performed with this model to assess the climatic effects of varying the ozone distribution and the ozone overburden. An evaluation of the relaxation rates of both ozone and temperature is also reported. In particular, the importance of the ozone distribution with respect to the ?greenhouse effect? is further investigated.

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Riassunto è stato sviluppato un modello fotochimico-radiativo-convettivo dell'atmosfera terrestre per calcolare la distribuzione di temperatura fra la superficie e 70 km. Il modello tiene conto dell'interazione fra fotochimica e temperature. Si riportano i risultati di alcuni esperimenti effettuati con il modello atti a studiare gli effetti climatici dovuti alle variazioni del carico e distribuzione di ozono. Si riporta anche una valutazione dei tempi di rilassamento per l'ozono e la temperatura. Inoltre è ulteriormente studiata l'influenza della distribuzione di ozono sull'effetto serra.

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Резюме Мы развиваем радиационную-фотохимическую модель ддя оценки распределения температур в атмосфере земли от поверхности до 70 км. Модель учитывает взаимодействие между фотохимией и температурой. Мы приводим результаты ряда чэкспериментов, выполненных с помощьу предложенной модели для оценки климатических эффектов изменения распределения озона. Проводится оценка интенсивностей релаксации распределений озона и температуры. В частности, исследуется важность распределения озона.

     

The structure,dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2 (aq) aqueous solutions

Systematic long time (5–20 ns) molecular dynamics (MD) simulations have been carried out to study the structural and dynamical properties of CaCl₂ aqueous solutions over a wide range of concentrations (≤9.26 m) in this study. Our simulations reveal totally different structural characteristics of those yielded from short time (≤1 ns) MD simulations [A.A. Chialvo and J.M. Simonson, J. Chem. Phys. 119, 8052 (2003); T. Megyes, I. Bako, S. Balint, T. Grosz, and T. Radnai, J. Mol. Liq. 129, 63 (2006)]. An apparent discontinuity was found at 4–5 m of CaCl₂ in various properties including ion–water coordination number and self-diffusion coefficient of ions, which were first noticed by Phutela and Pitzer in their thermodynamic modelling [R.C. Phutela and K.S. Pitzer, J. Sol. Chem. 12, 201 (1983)]. In this study, residence time was first taken into consideration in the study of Ca²⁺–Cl^? ion pairing, and it was found that contact ion pair and solvent-sharing ion pair start to form at the CaCl₂(aq) concentrations of about 4.5 and 4 m, respectively, which may be responsible for the apparent discontinuity. In addition, the residence time of water molecules around Ca²⁺ or Cl^? showed that the hydration structures of Ca²⁺ and Cl^? are flexible with short residence time (<1 ns). It needs to be pointed out that it takes much longer simulation time for the CaCl₂–H₂O system to reach equilibrium than what was assumed in previous studies.