The problems of reaction kinetics calculations based on thermoanalytical curves

The work, results and estimations are summarized which are related to reaction kinetic calculations using thermoanalytical curves. Mathematical operations applied to the calculations are studied. Calculation methods are evaluated on the basis of our test results. The effect of test conditions on reaction kinetic parameters is analysed. Calculation of half-period is also investigated in the study.     

Quantum nonadiabatic dynamics of hydrogen exchange reactions

In continuation of our earlier effort to understand the nonadiabatic coupling effects in the prototypical H + H₂ exchange reaction [Jayachander Rao et al. Chem. Phys. 333 (2007) 135], we present here further quantum dynamical investigations on its isotopic variants. The present work also corrects a technical scaling error occurred in our previous studies on the H + HD reaction. Initial state-selected total reaction cross sections and Boltzmann averaged thermal rate constants are calculated with the aid of a time-dependent wave packet approach employing the double many body expansion potential energy surfaces of the system. The theoretical results are compared with the experimental and other theoretical data whenever available. The results re-establish our earlier conclusion, on a more general perspective, that the electronic nonadiabatic effects are negligible on the important quantum dynamical observables of these reactive systems reported here.     

Monte carlo simulation of polymers in steady potential flows

This work presents a study of the configurational properties of bead-spring chains in steady-state potential flows. These properties are obtained from off-lattice Monte Carlo simulations. The results of our simulations compare favourably with theoretical results for phantom chains. We investigate the effects of excluded volume and hydrodynamic interaction on the configurations of the chains, and compare our results to the predictions of scaling arguments. The scaling law observed here for the latter case deviates from theoretical predictions but is in agreement with findings reported from molecular dynamics simulations.     

Grand canonical Monte Carlo simulation study of capillary condensation between nanoparticles

Capillary condensation at the nanoscale differs from condensation in the bulk phase, because it is a strong function of surface geometry and gas-surface interactions. Here, the effects of geometry on the thermodynamics of capillary condensation at the neck region between nanoparticles are investigated via a grand canonical Monte Carlo simulation using a two-dimensional lattice gas model. The microscopic details of the meniscus formation on various surface geometries are examined and compared with results of classical macromolecular theory, the Kelvin equation. We assume that the system is composed of a lattice gas and the surfaces of two particles are approximated by various shapes. The system is modeled on the basis of the molecular properties of the particle surface and lattice gas in our system corresponding to titania nanoparticles and tetraethoxy orthosilicate molecules, respectively. This system was chosen in order to reasonably emulate our previous experimental results for capillary condensation on nanoparticle surfaces. Qualitatively, our simulation results show that the specific geometry in the capillary zone, the surface-surface distance, and the saturation ratio are important for determining the onset and broadening of the liquid meniscus. The meniscus height increases continuously as the saturation ratio increases and the meniscus broadens faster above the saturation ratio of 0.90. The change of the radius of curvature of the particle surface affects the dimensions of the capillary zone, which drives more condensation in narrow zones and less condensation in wide zones. The increase of surface-surface distance results in the decrease of the meniscus height or even the disappearance of the meniscus entirely at lower saturation ratios. These effects are significant at the nanoscale and must be carefully considered in order to develop predictive relationships for meniscus height as a function of saturation conditions.     

Competitive reactions model for the pyrolysis of lignocellulose: A critical study

The “two competitive reactions” model for the pyrolysis of lignocellulosic materials finds support in the dependence of charcoal yield on thermal conditions, particularly the reaction temperature. This paper reports a critical study of the model on the basis of our experimental data on the pyrolysis of cellulose and wood. The theoretical bases of the model are briefly reviewed. Experimental results and model predictions — using kinetic parameters calculated from our own data — are compared over a wide range of thermal conditions. The implications for reactor design purposes are briefly discussed.     

Influence of the displacement out of the center of mass and nonaxiality of the dipole on the thermodynamics of liquids composed of linear dipole molecules

We present results for organic liquids modeled as linear rods with an embedded point dipole shifted from the geometrical center. Previously, we have obtained results for the vapor-liquid equilibrium (VLE) of similar systems with centered point dipoles. Our results included both models and applications to real systems. Results presented here are based on a previous work ( Phys. Rev. E 2003, 68, 021201) on the structural properties of these systems where relevant results about the appearance of dimers were found. Now, we have also performed systematic simulations on these systems to calculate the VLE of models with different aspect ratios, dipole shifts, and dipole strengths using the Gibbs ensemble Monte Carlo (GEMC) to calculate equilibrium densities and vapor pressure at each temperature. The applications considered here include some important substances such as 1-amines, acetonitrile, and 1-alcohols whose intermolecular parameters were fitted from our model simulations. Furthermore, we have used quantum chemistry calculations to obtain a reliable charge distribution, and we have applied our model to predict the vapor pressure of alpha,omega-diols where experimental results are rather scarce. Our results show a general improvement of the agreement between experiment and models compared to centered dipole models previously used. Results for amines are particularly remarkable.     

Experimental design for soil gas radon monitoring

An effort to define and characterize the environmental effects that control the release and mobility of radon in the environment is presented. The results of our preliminary field experiments on the long-term study of our radon activity measurements are reported.     

Structural Characterization of Venom Toxins by Physical Methods and the Perspectives on Structure-Function Correlation of Proteins

This account describes work in our laboratories on the application of physical methods to the structural studies of various toxins during the past few years. A general review of background and the meaningful results obtained from these approaches are described. The results are compared with updated information on related subjects carried out at other laboratories. Examples of structural studies on some small toxins present abundantly in Formosan cobra (Naja naja atra), one of the indigenous toxic snakes in Taiwan, are given with the emphasis on the identification and characterization of complex toxic protein components based on near-infrared Fourier transform Raman Spectroscopy. We will also describe our initial efforts in solving the solution structures of several small proteins and peptides by means of two-dimensional nuclear magnetic resonance (2D-NMR) and computer-simulated modeling. The structural information obtained by these modem physical techniques provides the framework for unraveling the complex structure-activity relationships engendered by these biomolecules.     

Phase transitions of methane using molecular dynamics simulations

Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.     

Vibrational molecular quantum computing: basis set independence and theoretical realization of the Deutsch-Jozsa algorithm

The phase of quantum gates is one key issue for the implementation of quantum algorithms. In this paper we first investigate the phase evolution of global molecular quantum gates, which are realized by optimally shaped femtosecond laser pulses. The specific laser fields are calculated using the multitarget optimal control algorithm, our modification of the optimal control theory relevant for application in quantum computing. As qubit system we use vibrational modes of polyatomic molecules, here the two IR-active modes of acetylene. Exemplarily, we present our results for a Pi gate, which shows a strong dependence on the phase, leading to a significant decrease in quantum yield. To correct for this unwanted behavior we include pressure on the quantum phase in our multitarget approach. In addition the accuracy of these phase corrected global quantum gates is enhanced. Furthermore we could show that in our molecular approach phase corrected quantum gates and basis set independence are directly linked. Basis set independence is also another property highly required for the performance of quantum algorithms. By realizing the Deutsch-Jozsa algorithm in our two qubit molecular model system, we demonstrate the good performance of our phase corrected and basis set independent quantum gates.     

Density-functional-based molecular-dynamics simulations of molten salts

The physicochemical properties of two molten salts, namely, KCl and NaCl, have been studied with a molecular-dynamics approach using a density-functional-based tight-binding (DFTB) model. The obtained results have been compared with a number of previously reported simulations, carried out on smaller systems and using classical force-field techniques. A good agreement has been found for both structural parameters and macroscopic properties, such as self-diffusion coefficients. Furthermore, our DFTB results are very close to the available experimental data. From a more general point of view, our results demonstrate the applicability of DFTB as an efficient tool in the modeling of melts. At the same time, the quality of the obtained results supports the use of this as a reliable alternative to the more expensive ab initio dynamics approaches, if accurate parameters are provided.     

Comment on “kinetic models for the CH4(ν3) deactivation in CH4CH4 collisions. Interpretation of experimental results” by J. Laterrasse and M. Huetz-Aubert

The paper by Laterrasse and Huetz-Aubert under comment here indicates models for optoacoustic analysis following ν₃ excitation in methane. It uses published results from my group. They purport to show (i) that our models and analysis were wrong, and (ii) that their analysis does not fit our results and therefore our results are wrong. The comments below respond to these claims.     

Transport Coefficients of Two-temperature Lithium Plasma for Space Propulsion Applications

Lithium has been proposed as an attractive metal propellant for advanced electric propulsion. In our current work, transport coefficients including the viscosity, thermal conductivity, and electrical conductivity of lithium plasma under both the equilibrium and non-equilibrium conditions are calculated based on a two-temperature model. The collision integrals used in calculating the transport coefficients are significantly more accurate than values used in previous theoretical studies, resulting in more reliable values of the transport coefficients. Results are computed for different degrees of thermal non-equilibrium, i.e. the ratio of electron to heavy particle temperatures, from 1 to 15, with the electron temperature ranging from 300 to 60,000 K in a wide pressure range from 0.0001 to 100 atm. We compare our calculated results with existing published results and discrepancies are found and explained.     

The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years

The future of the advancement as well as the reputation of computer-aided drug design will be guided by a more thorough understanding of the domain of applicability of our methods and the errors and confidence intervals of their results. The implications of error in current force fields applied to drug design are given are given as an example. Even as our science advances and our hardware become increasingly more capable, our software will be perhaps the most important aspect in this realization. Some recommendations for the future are provided. Education of users is essential for proper use and interpretation of computational results in the future.     

In silico prediction of drug solubility. 3. Free energy of solvation in pure amorphous matter

The solubility of drugs in water is investigated in a series of papers. In this work, we address the process of bringing a drug molecule from the vapor into a pure drug amorphous phase. This step enables us to actually calculate the solubility of amorphous drugs in water. In our general approach, we, on one hand, perform rigorous free energy simulations using a combination of the free energy perturbation and thermodynamic integration methods. On the other hand, we develop an approximate theory containing parameters that are easily accessible from conventional Monte Carlo simulations, thereby reducing the computation time significantly. In the theory for solvation, we assume that DeltaG* = DeltaGcav + ELJ + EC/2, where the free energy of cavity formation, DeltaGcav, in pure drug systems is obtained using a theory for hard-oblate spheroids, and ELJ and EC are the Lennard-Jones and Coulomb interaction energies between the chosen molecule and the others in the fluid. The theoretical predictions for the free energy of solvation in pure amorphous matter are in good agreement with free energy simulation data for 46 different drug molecules. These results together with our previous studies support our theoretical approach. By using our previous data for the free energy of hydration, we compute the total free energy change of bringing a molecule from the amorphous phase into water. We obtain good agreement between the theory and simulations. It should be noted that to obtain accurate results for the total process, high precision data are needed for the individual subprocesses. Finally, for eight different substances, we compare the experimental amorphous and crystalline solubility in water with the results obtained by the proposed theory with reasonable success.     

On the mode-coupling theory of vibrational line broadening in near-critical fluids

Molecular-dynamics simulations of a neat atomic fluid, coupled with a simple model for vibrational frequency perturbations, are used to investigate vibrational line broadening near the liquid-gas critical point. All features of our simulations are in qualitative agreement with recent Raman experiments on nitrogen. We also use our simulation results to assess the validity of the mode-coupling theories that have been used to analyze experiment. We find that the theoretical results are not in good agreement with simulation, both for the temperature dependence of the linewidth, and for the frequency time-correlation functions. However, the mode-coupling prediction that critical line broadening is due to the diverging correlation time of the frequency fluctuations is shown to be correct.     

Computer simulation of adsorption kinetics of surfactants on solid surfaces

Adsorption kinetics of surfactants on solid surfaces has been studied by using computer simulation. Both bulk surfactant concentration and diffusion region are explicitly integrated in our model. Depending on the head-surface interaction, our simulation results indicate that there exist two different kinetic modes in adsorption process of surfactants on solid surfaces. One is the four-regime mode and the other is step-wise mode. For the strongly attractive head-surface interaction, four distinct regimes of surfactant adsorption are found: a diffusion-controlled regime, a self-assembly controlled regime, an intermediate coverage regime and a saturated regime. In particular, the adsorption in second regime displays a power-law time dependence with an exponent unrelated to bulk concentrations and diffusion coefficients. While for the weaker adsorption surfaces, the step-wise mode is found. The mode includes a low-coverage nucleation regime and the saturated regime after a sudden aggregation of surfactants on the substrates which occurs stochastically. Besides the head-surface interaction, in this work, the effects of surfactant diffusivity, bulk concentration, the length of diffusion zone and surfactant architecture on the adsorption kinetics are also considered. The simulated adsorption kinetics is compared qualitatively with experimental results.     

Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes

Detection and quantitative characterization of the internal cavities in proteins remain an important topic in studying protein structure and function. Here we propose a new analytical method for detecting the existence of cavities in proteins. The method is based on constructing the special enveloping triangulation enclosing the cavities. Based on this method, we develop an algorithm and a fortran package, CAVE, for computing volumes and surface areas of cavities in proteins. We first test our method and algorithm in some artificial systems of spheres and find that the calculated results are consistent with exact results. Then we apply the package to compute volumes and surface areas of cavities for some protein structures in the Protein Data Bank. We compare our calculated results with those obtained by some other methods and find that our approach is reliable.     

Application of fluorescence polarization to enzyme assays and single nucleotide polymorphism genotyping: some recent developments

This article describes some recent developments in the field of fluorescence polarization (FP) as applied to enzyme assays and single nucleotide polymorphism (SNP) genotyping. First, we present our recent progress on the application of fluorescence polarization to high throughput screening (HTS). We show how the use of a 2-thiopyridinone-based, mixed disulfide biotinylation reagent can shorten the assay time of our recently reported kinase assay method based on thiophosphorylation and biotinylation from several hours to a few minutes. We also summarize our recent findings on a new approach for HTS of kinases, proteases and phosphatases based on the use of a cationic poly-amino acid such as polyarginine. We show how the careful selection of the polyarginine concentration and the ionic strength of the solution during the FP measurement allow one to expand the range of substrates that can be assayed. Both of these methods are valuable additions to the existing techniques for HTS. Most importantly, both of these methods can be applied to the assay of kinases without the need for any antibodies. In the area of genomics, we present some results from our studies on a new single nucleotide polymorphism typing approach based on the polymerase catalyzed extension of 3' fluorescein labeled primers. Contrary to our initial expectations, we observed that the enzymatic extension of these primers results in a significant decrease of the fluorescence polarization value. Possible explanations of this phenomenon are discussed.     

Reductive cleavages of homochiral acetals: inversion of the stereoselectivity

Reductive cleavages of homochiral acetals using Lewis acid-hydride systems and of alkynyl acetals using organoaluminum reagents are described. Stereochemical outcomes are found to be the opposite compared with our previous results on the aluminum hydride reduction of the acetal.