Entropy evaluation using the kinetic method: is it feasible?

The kinetic method is one of the most widely used experimental techniques for the measurement of thermochemical parameters by mass spectrometry. Recently it has been realized that it can also be used to determine reaction entropies, but the validity of this approach has not been established. This Perspective evaluates kinetic method plots in cases where there is a significant entropy difference between the competing fragmentation channels (i.e. between sample and reference compounds in the dissociating cluster ion). The concept underlying this study is to calculate mass spectra theoretically, based on known thermochemical parameters and as a function of experimental conditions. This can be done accurately using the RRKM-based MassKinetics software. The resulting mass spectra are then interpreted by the kinetic method, yielding DeltaH and DeltaS values. These values are, in turn, compared with the true values used to generate the calculated mass spectra. The results show that the reaction entropy difference between sample and reference has a very large influence on kinetic method plots. This should always be considered when studying energy-dependent mass spectra (using metastable ions or low- or high-energy collision-induced dissociation (CID)), even if only DeltaH is to be determined. Kinetic method plots are not strictly linear and this becomes a serious issue in the case of small molecules showing a large entropy effect. In such cases, results obtained at a low degree of excitation are more accurate. Energy and entropy effects can be evaluated in a relatively straightforward manner: first, the apparent Gibbs energy (DeltaG(app)) and effective temperature (T(eff)) are determined from kinetic method plots (intercept and slope, respectively), obtained from experiments using various degrees of excitation. Second, the resulting DeltaG(app) is plotted against T(eff), the slope yielding DeltaS while the intercept (extrapolation to zero temperature) yields DeltaH. This data evaluation yields more accurate results than alternative methods used in the literature. The resulting DeltaH values are fairly accurate, with errors, in most cases, <4 kJ mol(-1). On the other hand, DeltaS is systematically underestimated by 20-40%. Empirically scaling DeltaS values determined by the kinetic method by 1.35 results in a DeltaS value within 20% (or 10 J mol(-1) K(-1)) of the theoretical value.     

炼铝用碳阳极中碱金属氧化物作用机理的量子化学研究

本文应用CNDO/2法研究了炼铝用碳阳极中添加碱金属氧化物的吸附行为, 通过优化得到了吸附的最佳模型, 考察了吸附结合能随分子间距的变化, 进而给出了碱金属氧化物在碳阳极中作用的机理。量子化学计算结果表明: 碱金属氧化物添加到炼铝用碳阳极中起传输电子的电桥作用, 是碳阳极在空气中氧化反应以及铝电解时生成氧气的氧化反应的催化剂; 理论计算和实验结果二者吻合较好, 可以用来解释若干实验结果。     

负载型TiO2-聚酰亚胺亲水复合膜的制备与分离性能

采用溶解－流涎法，湿相转换法和干湿相转换法制轩了负载型ＴｉＯ２－聚酰亚胺亲水复合膜，采用扫描电镜，红外光谱，压汞和透气性实验等手段对该膜的孔径分布，表面结构及扩散性能进行了表征，并讨论了制备亲水对膜孔结构的影响，实验结果表明，三种膜均具有很好的亲水性能，而干湿相转换膜具有良好的孔径分布和分离性能。     

DSC study on the effect of isocyanates and catalysts on the HTPB cure reaction

The urethane forming cure reactions of hydroxyl terminated polybutadiene (HTPB) binder with three different isocyanate curatives, viz., toluene diisocyanate (TDI), isophorone diisocyanate (IPDI) and 4,4-methylene bis(cyclohexyl isocyanate) (MCHI), were investigated by differential scanning calorimetry (DSC). The effect of two cure catalysts, viz., dibutyl tin dilaurate (DBTDL) and ferrric tris-acetylacetonate (FeAA) on the cure reactions was also studied. Cure kinetics was evaluated using the multiple heating rate Ozawa method. The reactivities of the three isocyanates and catalytic efficiencies were compared based on the DSC reaction temperatures, activation energies and rate constants. Viscosity build-up in these systems at isothermal temperature was also studied and compared with the results from DSC.     

A hybrid approach combining energy density analysis with the interaction energy decomposition method

We propose a new analysis technique for characterizing molecular interactions that combines an energy decomposition scheme, such as the Kitaura-Morokuma decomposition method, with energy density analysis, which partitions the total energy of the system into atomic contributions. The combined scheme, termed Interaction-EDA, enables us to estimate the local contribution of interaction energy components, such as electrostatic, exchange, polarization, and charge transfer. The evaluation of the local interaction energy is rather important in large systems. For a numerical assessment, the Interaction-EDA method is applied to the process of CO adsorption on Si(100) - (2 x 1) surface.     

Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.     

Comments on the primary and scatter dose-spread kernels used for convolution methods

The basic primary and scatter dose-spread kernels used for convolution methods are usually produced by Monte Carlo simulations with the interaction point forced to the center of a large water phantom. However, it is still not clear whether such Monte Carlo based kernels allow accurate dose calculations with a wide range of field sizes and depths, especially in thorax phantoms. Using the differential primary and scatter concept, this paper proposes another type of basic kernel, with which perfectly accurate primary and scatter absorbed dose calculations can be performed under conditions that the beam is parallel, the incident beam intensity is uniform within and zero outside the field, and the primary beam attenuation coefficient along raylines is not a function of depth and off-axis distance.     

Adaptive approach for nonlinear sensitivity analysis of reaction kinetics

We present a unified approach for linear and nonlinear sensitivity analysis for models of reaction kinetics that are stated in terms of systems of ordinary differential equations (ODEs). The approach is based on the reformulation of the ODE problem as a density transport problem described by a Fokker-Planck equation. The resulting multidimensional partial differential equation is herein solved by extending the TRAIL algorithm originally introduced by Horenko and Weiser in the context of molecular dynamics (J. Comp. Chem. 2003, 24, 1921) and discussed it in comparison with Monte Carlo techniques. The extended TRAIL approach is fully adaptive and easily allows to study the influence of nonlinear dynamical effects. We illustrate the scheme in application to an enzyme-substrate model problem for sensitivity analysis w.r.t. to initial concentrations and parameter values.     

Competitive adsorption and desorption of a bi-solute mixture: effect of activated carbon type

This study aims to clarify the effects of carbon activation type and physical form on the extent of adsorption capacity and desorption capacity of a bi-solute mixture of phenol and 2-chlorophenol (2-CP). For this purpose, two different PACs; thermally activated Norit SA4 and chemically activated Norit CA1, and their granular countertypes with similar physical characteristics, thermally activated Norit PKDA and chemically activated Norit CAgran, were used. The thermally activated carbons were better adsorbers for phenol and 2-CP compared with chemically activated carbons, but adsorption was more reversible in the latter case. 2-CP was adsorbed preferentially by each type of activated carbon, but adsorption of phenol was strongly suppressed in the presence of 2-CP. The simplified ideal adsorbed solution (SIAS) model underestimated the 2-CP loadings and overestimated the phenol loadings. However, the improved and modified forms of the SIAS model could better predict the competitive adsorption. The type of carbon activation was decisive in the application of these models. For each activated carbon type, phenol was desorbed more readily in the bi-solute case, but desorption of 2-CP was less compared with single-solute. This was attributed to higher energies of 2-CP adsorption.