Three model-free methods for calculation of activation energy in TG

Two well-known isoconversion methods, the first one developed by Ozawa-Flynn-Wall and the second one developed by Friedman, are confronted with calculations made using modulated thermogravimetry (MTG). The latter variant is free from a number of assumptions and restrictions made in the isoconversion computations. In particular, it allows the use of a single decomposition curve and it remains in force even in the case of multistage decomposition with conjugated processes.To obtain the model-fitting methods from the model-free methods one should replace some functions averaged over isoconversion levels by the functions calculated on the basis of kinetic models. In the Ozawa-Flynn-Wall method it is the averaged reduced time (integral of Arrhenius exponential over time). In the method of Friedman it is the averaged differential conversion function.In MTG, the perturbations caused by the sinusoidal temperature modulation are connected with derivatives of mass loss by simple scaling, where activation energy plays a role of a scaling parameter. The ratio of the experimentally measured perturbations to the experimental derivative is used for the model-free computation of activation energy. If a theoretical derivative replaces the experimental one, this procedure leads to the model-fitting method. Even a rough approximation of the experimental derivative should not lead to an excessive error in activation energy. If in a vicinity of peaks maxima in derivatives of mass loss the decomposition is controlled by single rate-limiting processes, modulated thermogravimetry should give realistic activation energies for these processes. Inasmuch as the results of MTG are weakly sensitive to selection of kinetic models, this method should have a high predictive force.     

A study of the tautomerism of 5-as-triazinones by mass spectrometry

The tautomeric equilibria of variously substituted 5-triazinones have been studied by comparing their mass spectra with those of their methylated derivatives. The results for 6-methyl-5-triazinone have been confirmed by comparison with the mass analysed ion kinetic energy spectra of ions generated from N-ethyl derivatives. The equilibria are dependent upon the nature of the substituents in the 3- and 6-positions.     

Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules

A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each 4.2 to 18.2%. This fourfold increase in the second derivative error dramatically demonstrates the importance of bond anharmonicity in the ab initio potential energy surface. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/ torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. © 1994 by John Wiley & Sons, Inc.     

Force field calculations (MM3) on glyoxal,quinones, and related compounds

A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.     

Quantum-chemical Treatment of Cyclization and Recyclization Reactions: XXVI. Effects of Substituents in the Thermal Rearrangement of Methylenecyclopropane

Basing on the coupled perturbation Hartree-Fock theory an effect of substituents on the thermal rearrangement of methylenecyclopropane derivatives was considered. The effect is described in the second order of the theory. The activation energy depends both on the first and second power of the parameter characterizing the substituent, and introduction of several groups as a rule cannot be described in the framework of an additive scheme and requires accounting for the interactions between the substituents. The results of computation are in good agreement with the results of kinetic measurements.     

Adaptive biasing force method for scalar and vector free energy calculations

In free energy calculations based on thermodynamic integration, it is necessary to compute the derivatives of the free energy as a function of one (scalar case) or several (vector case) order parameters. We derive in a compact way a general formulation for evaluating these derivatives as the average of a mean force acting on the order parameters, which involves first derivatives with respect to both Cartesian coordinates and time. This is in contrast with the previously derived formulas, which require first and second derivatives of the order parameter with respect to Cartesian coordinates. As illustrated in a concrete example, the main advantage of this new formulation is the simplicity of its use, especially for complicated order parameters. It is also straightforward to implement in a molecular dynamics code, as can be seen from the pseudocode given at the end. We further discuss how the approach based on time derivatives can be combined with the adaptive biasing force method, an enhanced sampling technique that rapidly yields uniform sampling of the order parameters, and by doing so greatly improves the efficiency of free energy calculations. Using the backbone dihedral angles Phi and Psi in N-acetylalanyl-N'-methylamide as a numerical example, we present a technique to reconstruct the free energy from its derivatives, a calculation that presents some difficulties in the vector case because of the statistical errors affecting the derivatives.     

An all-atom force field for metallocenes

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations.     

Ionic dehydration reactions: The effect of location of the activated complex on kinetic energy release

A broad range of kinetic energy release has been found for the 1,4 elimination of water in a series of ortho substituted benzyl alcohols and benzoic acids. It is suggested that the trend reflects, in part, the position of the activated complex on the reaction coordinate. More specifically, reactions which proceed via an ‘early’ transition state release only small quantities of energy, whereas those processes occurring ‘later’ release a larger fraction of the available energy. Consequently, the o- methyl derivatives give large kinetic energy release compared to o- amino or hydroxy substituted compounds. Father verification is obtained from the small kinetic energy release observed for the 1,4 ionic dehydration in simple,acyclic alcohols.     

Effect of milled fluidised bed cracking catalyst waste on hydration of calcium aluminate cement and formation of binder structure

The effect of Bi addition on precipitation and dissolution, in Cu–9at% In and Cu–5at% Sb supersaturated solid solutions, has been studied by several complementary techniques. Differential Dilatometry and Differential Scanning Calorimetry permit only the analysis of the δ phase dissolution kinetic in sufficiently aged samples. Delayed spheroidization due to Bi segregation around the precipitated lamellae, observed by Transmission Electron Microscopies in the first alloy, gives a residual interfacial energy leading to accelerated δ phase dissolution with decreased activation energy. Kinetics parameters evolution indicates a progressive δ phase continuous dissolution which makes available a small chemical driving force at high temperatures and leads to an increasing activation energy during dissolution. However, Bi dispersed particles in the second alloy haven’t effect on the dissolution but they cause a contraction above 833 K. Kinetics parameters evolution indicates rapid δ phase dissolution that shifted to high temperatures where an important chemical driving force for solution treatment is available. It leads to almost constant activation energy.

     

Stability and aromaticity of tautomers and kinetics of proton transfer in 6-methylpentafulvene and its exo-substituted derivatives: a computational study

Thermodynamic and kinetic aspects of the tautomeric equilibrium of 6-methylpentafulvene and its exo-substituted derivatives were investigated at the B3LYP/6-311 ++G(d,p) level of theory for 17 substituents. It was found that in the case of CF₃ and COCN derivatives, the most stable form is the tautomer in which the proton migrated from the exo-methyl group to a ring carbon atom. The activation energy for such proton transfer is in the range of 53–61 kcal/mol depending on the substituent, NH₂ derivative being an exception with a very high value of 114 kcal/mol. Proton transfers between consecutive ring carbon atoms are associated with much lower activation energies, in general below 30 kcal/mol. The aromaticity of tautomers and transition states of substituted 6-methylpentafulvene was analyzed by employing geometric (HOMA) and electronic (pEDA) indices. It was found that the aromaticity of the nominal form of the molecule is the main driving force behind the stability order of the tautomers. In the case of most substituents, the aromatization of transition states is substantial comparing to the nominal form and is an important factor lowering the activation energy. Solvent effects were modeled by means of PCM and SMD methods.     

Energy transfer from adenosine triphosphate

We suggest a direct molecular mechanism of energy transfer from adenosine triphosphate (ATP) in hydrolysis and phosphorylation reactions, from chemical energy into mechanical energy. Upon hydrolysis of ATP, say bound to a protein, the electrostatic energy of Coulombic repulsion of the ions adenosine diphosphate and phosphate is available to assert a force on a neighboring molecular group in the protein and can do work on that group, or as the ions recede from each without asserting such a force, they gain relative kinetic energy, which, in the absence of dissipative collisions that turn this kinetic energy into heat, can be converted into any other form of energy and work by an impulse, a collision with a neighboring group, without restrictions. Either possibility can be used as a source of activation energy for reactions, as a source of energy to surmount energy barriers in conformational changes, and as a source of work to be done, as in muscle. In some systems where the Gibbs free energy change is fully utilized, all of this energy is turned into mechanical energy, and we suggest a similar mechanism. From the literature we cite some experimental evidence and several quotations indicative of the possibility of our suggestion.     

Atom-atom partitioning of total (super)molecular energy: the hidden terms of classical force fields

Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom-atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange).     

两种组氨酸酰胺衍生物的合成及其与人血清白蛋白的结合

L-组氨酸对生物有机体有着良好的亲和能力,通过修饰其化学结构以期寻找药理活性和生物利用度高的衍生物。本文将L-组氨酸分别与反式肉桂酸和对甲氧基肉桂酸反应,合成了两种组氨酸酰胺类衍生物,利用傅里叶变换红外光谱、质谱、氢谱/碳谱核磁共振谱进行了结构表征。采用分子操作环境(MOE)软件分子对接技术、荧光光谱法、同步荧光光谱法(SFS)、紫外-可见光谱法(UV-Vis),共同研究了两种衍生物分别和人血清白蛋白(HSA)相结合的机理。MOE对接结果显示,这两种衍生物与HSA的模拟结合能分别为-13.82和-16.25 kcal/mol,主要是通过范德华力和疏水作用结合在HSA亚结构域ⅡA(即siteⅠ)的疏水腔内。荧光猝灭数据表明,衍生物与HSA相互作用并形成了新的基态配合物,荧光猝灭过程为静态猝灭;不同温度(300、305和310 K)下衍生物与HSA相互作用的结合常数分别为1.773×104、6.354×10~3、1.260×10~3和5.314×10~4、4.614×10~3、1.420×10~3;由热力学参数得到衍生物与HSA的结合过程是由范德华力驱动;SFS表明,衍生物使得HSA的二级结构发生了变化。结合UV-Vis的结果可以确定,在体外生理条件下,组氨酸酰胺类衍生物均可以通过范德华力与HSA结合,并对HSA内源荧光产生静态猝灭及构象影响,这与分子对接结果一致,从而为组氨酸酰胺类衍生物药物的进一步开发提供了参考。     

Force reversed method for locating transition states

To identify the transition state accurately and efficiently on a high-dimensional potential energy surface is one of the most important topics in kinetic studies on chemical reactions. We present here an algorithm to search the transition state by so-called force reversed method, which only requires a rough reaction direction instead of knowing the initial state and final state. Compared to the nudged elastic band method and the dimer method that require multiple images, the present algorithm with only single image required saves significantly the computational cost. The algorithm was implemented in the first-principle periodic total energy calculation package and applied successfully to several prototype surface processes such as the adsorbate diffusion and dissociation on metal surfaces. The results indicate that the force reversed method is efficient, robust to identify the transition state of various surface processes.     

Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.     

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001     

Absolute partial cross sections and kinetic energy analysis for the electron impact ionization of ethylene

We present absolute partial electron impact ionization cross sections for ethylene in the electron energy range between threshold and 1000 eV measured with a two sector field double focusing mass spectrometer. Ion kinetic energy distribution functions have been measured at all electron energies by applying a deflection field method. Multiplication of the measured relative cross sections by the appropriately determined discrimination factors lead to accurate relative partial cross sections. Normalization of the sum of the relative partial cross sections to an absolute total cross section gives absolute partial cross section values. The initial kinetic energy distributions of several fragment ions show the presence of two or more contributions that exhibit different electron energy dependencies. Differential cross sections with respect to the initial kinetic energy of the ions are provided and are related to specific ion production channels. The electron threshold energies for the direct and numerous other dissociative ionization channels are determined by quantum chemical calculation and these allow the determination of the total kinetic energy release and the electron energy loss for the most prominent dissociative ionization channels.     

Hierarchical expansion of the kinetic energy operator in curvilinear coordinates for the vibrational self-consistent field method

A new hierarchical expansion of the kinetic energy operator in curvilinear coordinates is presented and modified vibrational self-consistent field (VSCF) equations are derived including all kinematic effects within the mean field approximation. The new concept for the kinetic energy operator is based on many-body expansions for all G matrix elements and its determinant. As a test application VSCF computations were performed on the H(2)O(2) molecule using an analytic potential (PCPSDE) and different hierarchical approximations for the kinetic energy operator. The results indicate that coordinate-dependent reduced masses account for the largest part of the kinetic energy. Neither kinematic couplings nor derivatives of the G matrix nor its determinant had significant effects on the VSCF energies. Only the zero-point value of the pseudopotential yields an offset to absolute energies which, however, is irrelevant for spectroscopic problems.     

Mechanisms of formation of [M?HCO]+ and [M?C6H5CO]+ ions from isomers of 1,4-benzodioxin derivatives

It is demonstrated that phenyl and benzocyclobutenyl derivatives of 1,4-benzodioxin interconvert before fragmentation at low internal energy. The mechanisms of the two major fragmentations (HCO and C₆H₅CO losses) are investigated by means of kinetic energy release determination and appearance energy measurements. From these experiments it is concluded that the fragment ions possess a dibenzopyran structure.     

The influence of water on the friction forces of fibers in aramid fabrics

Fabrics based on high-impact organic fibers have an excellent potential to dissipate the energy of a ballistic impact. That is why they are used in protective helmets and flexible armor vests. The work of friction is the main mechanism of energy absorption in fabrics during a transverse impact. The friction forces of fibers were studied via the pullout of several neighboring fibers and via the transverse hardness indentation. The influence of water on indentation forces and pullout forces of Armos and Rusar fibers during their pullout from fabrics is studied. Water enhances friction force several-fold during the pullout of fibers. Consequently, the potential to dissipate the energy of an impact changes during a transverse action. The influence of moisture is irreversible in the Armos fabrics without a water-repellent coating, and drying does not lead to complete recovery of the friction forces of fibers. In the case of Rusar 56319 fabrics with a water-repellent coating, large drops of water roll off the fabric and only small drops influence the friction forces. A substantial variation in the indentation force is detected, thereby apparently providing evidence of the instability of the density of the fabric. An analysis of the mechanisms of energy dissipation is performed. The energy of the elastic deformation in an individual fiber is three times smaller than the kinetic energy of the fiber. Friction work can exceed the sum of kinetic energy and strain energy by an order of magnitude. The estimation of the value of the increase in the temperature of a fiber during an impact is performed. Heat is not emitted during an impact on an individual fiber in the case of the formation of a transverse wave during an inelastic impact. In the process of transmission of transverse and dilatational waves, the energy dissipation is proportionate to the impact velocity raised to the power of 8/3.