Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Switchable vortex beam polarization state terahertz multi-layer metasurface

We propose a switchable vortex beam polarization state terahertz multi-layer metasurface, which consists of three-layer elliptical metal crosses, four-layer dielectrics, and two-layer hollow metal circles, which are alternately superimposed. Under the normal incidence of left-handed circularly polarized (LCP) wave and the right-handed circularly polarized (RCP) waves, the proposed structure realizes three independent control functions, i.e., focused and vortex beam, vortex beam with different topological charges, and polarization states switching, and azimuth switching of two vortex beams with different polarization states. The results show that the proposed metasurface provides a new idea for investigating the multifunctional terahertz wave modulation devices.     

纤锌矿InGaN staggered量子阱中的激子态和光学性质

本文将基于有效质量近似下的变分法,理论研究了纤锌矿InGaN/GaN staggered 量子阱中的激子态和光学性质。数值结果显示了InGaN量子阱中的量子尺寸和staggered受限垒对束缚于量子阱中的激子态和光学性质有着明显地影响。当阱宽增加时,量子受限效应减弱,激子结合能降低, 带间发光波长增加。另一方面,当量子阱中staggered受限势增加时,量子受限效应增强,激子结合能升高,带间发光波长降低。本文的理论结果证明了可以通过调节staggered垒高和量子尺寸来调控纤锌矿InGaN staggered 量子阱中的激子态和光学性质。     

电化学合成聚苯胺涂层防护性能的研究

采用循环伏安法在Q235钢表面电化学合成了聚苯胺涂层,通过极化曲线评价了扫描方式、电位区间、扫描速率、循环次数等电聚合参数对聚苯胺涂层在Q235钢耐腐蚀性能方面的影响,结果表明:合成条件对聚苯胺涂层的防护性能影响显著.在0.1 mol/L苯胺+0.3 mol/L草酸溶液中,循环电位区间–0.5~1.6 V,扫速10 m V/s,连续扫描5个循环,可获得最佳防护性能.该涂层在3.5%Na Cl溶液中对Q235钢具有较好的保护作用.扫描电镜观察表明:聚苯胺膜具有颗粒状纤维状结构.     

透过式光纤陀螺偏振特性的分析

偏振波动是谐振式光纤陀螺(R-FOG)的主要噪声之一,它对信号检测精度具有重要影响。通过矩阵法得到了透过式R-FOG中由偏振波动引起的系统零漂与偏振噪声相关参数、环形谐振腔结构参数间的关系表达式。在一定的透过式R-FOG系统结构参数下,对上述解析表达式进行了数值拟合,通过估算可满足高精度透过式R-FOG系统对偏振相关参数的要求,为偏振波动噪声的理论分析和R-FOG系统的实际搭建提供了理论基础。     

固体核磁共振Multiple-CP定量技术的参数优化与应用研究

固体核磁共振Multiple-CP定量技术可实现对不同体系、 不同定量信息的检测. 然而, Multiple-CP对样品属性的宽容度较低, 其中有关样品属性的核磁共振参数包括氢的自旋晶格弛豫时间(T_1,H)、 交叉弛豫时 间(T_CH)和自旋锁定场下氢的自旋晶格弛豫时间(T_{\mathrm{1}\rho }^{\text{?}\mathrm{H}})等. 因而需要系统地掌握Multiple-CP各种实验参数与样品上述特性参数之间的关系, 从而确定Multiple-CP技术可适用的体系范围以及最优的实验参数范围. 基于此, 首先以L-丙氨酸为模型样品, 探讨在Multiple-CP实验中弛豫恢复时间(t_d)、 交叉极化接触时间(t_p)和交叉极化次数(n) 3种实验参数对分子中基团比例测量结果的影响规律. 并以L-缬氨酸、 L-丙氨酸/L-缬氨酸的混合物为模型样品, 探讨样品特性参数的差异性对Multiple-CP实验参数范围的影响. 实验结果表明, t_p受T_CH和\text{?}{T}_{\mathrm{1}\rho }^{\text{?}\mathrm{H}}的影响较大. 对于纯净物或均相体系, T_CH是影响t_p参数设置的关键. 依据实验数据发现, 当样品中各基团T_CH差异度小于8%时, 实验对t_p的宽容度较高; 对于混合物体系, 需同时考虑混合物中组分\text{?}{T}_{\mathrm{1}\rho }^{\text{?}\mathrm{H}\text{?}}差异度的影响. 当组分\text{?}{T}_{\mathrm{1}\rho }^{\text{?}\mathrm{H}\text{?}}差异度为32%、 各基团T_CH差异度为21%时, Multiple-CP对t_p的宽容度高, 可在较宽的参数范围内实现定量检测. 而当T_CH差异度较大时, 获取定量结果时t_p的参数范围较小, 实验条件较苛刻. Multiple-CP定量方法更适用于T_CH和\text{?}{T}_{\mathrm{1}\rho }^{\text{?}\mathrm{H}\text{?}}差异度较小的样品体系的定量研究. 通过研究样品T_CH和\text{?}{T}_{\mathrm{1}\rho }^{\text{?}\mathrm{H}\text{?}}对实验参数的影响, 总结了Multiple-CP方法所适用的样品体系特征, 为使用Multiple-CP进行定量检测提供可参考的参数设置方案.     

UV-vis spectroscopic Investigation on γ-irradiated alkali aluminoborate glasses

This research paper reports about the change in optical spectra of alkali aluminoborate glasses under high dose of gamma irradiation. Effect of irradiation on visible spectra finds remarkable applications in optoelectronic materials.Glasses with a host matrix composed of M₂O (where M=Na, K)_, Al₂O_3, B2O3 were prepared by conventional melt quench technique. Gamma irradiation was performed at a dose-rate of 573 Gy/h to a total dose of 50 kGy. Samples were characterised before and immediately after irradiation by UV-vis transmission spectra in the range of 200-800 nm. The induced absorption coefficient and loss of transmission due to irradiation were attributed to the nature of alkali metals as well as the host matrix.     

Theory of spin polarization in mesoscopic spin–orbit coupling systems

We establish a general formalism of the bulk spin polarization (BSP) and the current-based spin polarization (CSP) for mesoscopic ferromagnetic and spin–orbit interaction (SOI) semiconducting systems. Based on this formalism, we reveal the basic properties of BSP and CSP and their relationships. The BSP describes the intrinsic spin polarized properties of devices. The CSP depends on both intrinsic parameters of device and the incident current. For the non-spin-polarized incident current with the in-phase spin-phase coherence, CSP equals to BSP. We give analytically the BSP and CSP of several typical nanodevice models, ferromagnetic nanowire, Rashba nanowire and rings. These results provide basic physical behaviors of BSP and CSP and their relationships.     

Field-induced phase transitions in chiral smectic liquid crystals studied by the constant current method

In ferroelectric liquid crystals, phase transitions can be induced by an electric field. The current constant method allows these transition to be quickly localized and thus the(E, T) phase diagram of the studied product can be obtained.In this work, we make a slight modification to the measurement principles based on this method. This modification allows the characteristic parameters of ferroelectric liquid crystal to be quantitatively measured. The use of a current square signal highlights a phenomenon of ferroelectric hysteresis with remnant polarization at null field, which points out an effect of memory in this compound.     

On the frequency of oscillations in the pair plasma generated by a strong electric field

We study the frequency of the plasma oscillations of electron–positron pairs created by the vacuum polarization in a uniform electric field with strength E   in the range 0.2Ec<E<10Ec$0.2E_c<E<10E_c$. Following the approach adopted in Ruffini, et al. (2007) [1] we work out one second order ordinary differential equation for a variable related to the velocity from which we can recover the classical plasma oscillation equation when E→0$E\to 0$. Thereby, we focus our attention on its evolution in time studying how this oscillation frequency approaches the plasma frequency. The time-scale needed to approach to the plasma frequency and the power spectrum of these oscillations are computed. The characteristic frequency of the power spectrum is determined uniquely from the initial value of the electric field strength. The effects of plasma degeneracy and pair annihilation are discussed.