Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory

A new method for the characterization of molecules based on the model approach of molecular surfaces is presented. We use the topographical properties of the surface as well as the electrostatic potential, the local lipophilicity/hydrophilicity, and the hydrogen bond density on the surface for characterization. The definition and the calculation method for these properties are reviewed shortly. The surface is segmented into overlapping patches with similar molecular properties. These patches can be used to represent the characteristic local features of the molecule in a way that is beyond the atomistic resolution but can nevertheless be applied for the analysis of partial similarities of different molecules as well as for the identification of molecular complementarity in a very general sense. The patch representation can be used for different applications, which will be demonstrated in subsequent articles.     

Hybrid molecular orbitals for interacting systems. reactive region and reaction sites

It is shown how the reactive region is determined in a molecule and how the reaction sites are specified in the reactive region by the use of hybrid molecular orbitals.     

Model for the fast estimation of basis set superposition error in biomolecular systems

Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds.     

Pyrimidine dimer splitting in covalently linked dimer-arylamine systems.

Cyclobutadipyrimidines (pyrimidine dimers) undergo photosplitting which is sensitized by electron donors. We prepared a series of compounds in which a dimer is directly linked to an arylamine, which acts as sensitizer for dimer splitting. Two diastereomers of the dimer-arylamine exhibited very different splitting efficiencies. Also studied were N-methyl, ring methoxy, as well as deuterated derivatives of the sensitizer. These dimer-arylamines had an absorption band with lambda max approximately 300 nm. In each case intramolecular photosensitization of dimer splitting was highly dependent on the solvent, ranging in one instance from phi spl = 0.02 in water to a high value of 0.31 in the least polar solvent mixture examined (1,4-dioxane: isopentane, 1:99). A mechanism is proposed which involves photoinduced electron transfer from arylamine to dimer and splitting of the dimer radical anion. The dependence of splitting on the solvent was rationalized on the basis of retardation of back electron transfer due to Marcus inverted behavior of the charge-separated species. Photolyases might achieve their high efficiency of dimer splitting in part by employing a hydrophobic active site to slow back electron transfer in a similar manner.     

Parameter estimation in modulated, unbranched reaction chains within biochemical systems

Modern biology is increasingly developing techniques for measuring time series of global gene expression and of many simultaneous proteins or metabolites. These data contain valuable information on the dynamics of cells, which has to be extracted with computational means. Given a suitable mathematical model, this extraction is in principle a straightforward regression task, but the complexity and nonlinearity of the differential equations that describe biological systems cause severe difficulties when the systems are of realistic size. We propose a method of stepwise regression that can be applied effectively to linear portions of pathways. The method may be combined with other estimation methods and either directly yields reasonable parameter estimates or at least provides appropriate start values for subsequent nonlinear search algorithms. We illustrate the method with the analysis of in vivo NMR data describing the dynamics of glycolytic metabolites in Lactococcus lactis.     

A general set of order parameters for molecular crystals

Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.     

A critical study of basis set effects and the use of approximate natural orbitals in SCF-CI calculations of molecular geometries and heats of reaction

SCF-CI calculations have been performed on a number of chemical reactions between closed shell molecules in order to determine the heats of reaction. Contracted Gaussian type atomic basis sets of three different qualities were used and the CI calculations were performed in a truncated approximate natural orbital space. The conclusions to be drawn from these calculations are rather pessimistic. For heats of reaction, errors up to 6 kcal/mole are obtained on the SCF-level with a double zeta plus polarization atomic basis. A further improvement is only possible if extended basis sets are used. Correlation effects on heats of reaction are of the same size and CI calculations are therefore only meaningful with large atomic basis sets.For the CI calculations a one-electron space of approximate natural orbitals, obtained from second order RS perturbation theory, was used. Different truncations, using the occupation number as criterion, were tested. The general conclusion is that errors in energy differences obtained with a truncated basis set are of the same magnitude as the error in the total correlation energy. In practice this means that not more than 20–30% of the approximate natural orbitals can be deleted if the error is to be kept less than a few kcal/mole.Finally the truncation error in calculations of bond distances was tested for a few cases. Errors of around 10% of the total change due to correlation were found when 30% of the lowest occupied natural orbitals were deleted.     

A set of molecular models for alkali and halide ions in aqueous solution

This work presents new molecular models for alkali and halide ions in aqueous solution. The force fields were parameterized with respect to the reduced liquid solution density at 293.15 K and 1 bar, considering all possible ion combinations simultaneously. The experimental target data are reproduced with a high accuracy over a wide range of salinity. The ion models predict structural properties of electrolyte solutions well, such as pair correlation functions and hydration numbers. The force fields provide good predictions of the properties studied here in combination with different models for water.     

Vibronic and spin-orbit splitting in spectra of systems exhibiting Jahn-Teller-Effect

Simple two- and three-dimensional models have been used to investigate the vibronic states of molecules exhibiting Jahn-Teller-Effect. According to the topology of the adiabatic potential surface, two cases have to be distinguished, which may (A) or may not (B) be treated in the Born-Oppenheimer approximation. In the latter case B strong Jahn-Teller coupling leads to a splitting of an A E absorption line into three peaks instead of the usual two ones. This additional splitting originates from transitions into the first and second metastable level of the upper potential well. However, the vibronic splitting will often be smeared out by coupling of the Jahn-Teller effect to a distortion of a Jahn-Teller inactive vibration. The effective spin-orbit splitting of an absorption band with unresolved vibrational structure is larger than in the case of vanishing Jahn-Teller coupling, contrary to the spin-orbit splitting of single vibronic levels. An experimental example of this effect is discussed. In Jahn-Teller case B it may be interpreted as a superposition of the vibronic and the spin-orbit splitting effects.

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Zusammenfassung Mittels einfacher zwei- und dreidimensionaler Modelle wurden die vibronischen Zustände von Molekülen untersucht, die einen Jahn-Teller-Effekt zeigen. Entsprechend der Topologie der adiabatischen Potentialfläche sind zwei Fälle A und B zu unterscheiden, die im Rahmen der Born-Oppenheimer-Näherung behandelt werden können bzw. wo dies nicht möglich ist. Im letzteren Falle B führt eine sehr starke Jahn-Teller-Kopplung zur Aufspaltung einer AE Absorptionslinie in drei statt wie üblich in zwei Peaks. Diese zusätzliche Aufspaltung rührt her von Übergängen in die ersten beiden metastabilen Resonanzzustände der oberen Potentialmulde. In vielen Fällen wird mit einer Jahn-Teller-Kopplung der asymmetrischen Schwingung eine Verschiebung der Gleichgewichtslage einer Jahn-Teller inaktiven Schwingung einherlaufen: Die vibronischen Aufspaltungen sollten daher durch Schwingungsverbreiterung teilweise verschmiert sein. Während die Spin-Bahn-Aufspaltung einzelner vibronischer Niveaus durch Jahn-Teller-Kopplung verringert wird, wird die effektive Spin-Bahn-Aufspaltung einer Absorptionslinie mit nichtaufgelöster Schwingungsstruktur vergrößert. Ein experimentelles Beispiel für diesen Effekt wird diskutiert. Im Jahn-Teller-Fall B kann er als Überlagerung der vibronischen und der Spin-Bahn-Aufspaltung interpretiert werden.

     

A mini review of the crossed molecular beam apparatus in molecular reaction dynamics

This review has introduced some experimental techniques of crossed molecular beam apparatus in chemical reaction dynamics. First of all, the history of crossed molecular beam equipment is retrospected in this paper. The detectors of both the universal crossed molecular beam machine and Hydrogen-atom Rydberg-tagging apparatus have been discussed. Other types of crossed molecular beam instruments have also been reviewed. Each experimental apparatus makes a compromise among the resolution, sensibility and universality. As a matter of fact, it is these equipments that make many breakthroughs happen in chemical reaction dynamics. This review aims to provide the readers and researchers with some information about the experiments in molecular reaction dynamics. We believe that new types of experimental techniques can emerge and contribute to the development of molecular reaction dynamics and relevant research fields.     

A contracted bromine basis set for use in calculation of molecular energies

A contracted [9s6p2d] basis set derived from Dunning's (14s11p5d) primitive Gaussian set for bromine has been used in ab initio molecular orbital calculations of the dissociation energies of HBr, CH₃Br, and Br₂, the ionization potentials of Br and HBr, and the electron affinity of Br. The calculated energies are within 0.1 eV of the experimental values. This is similar to the accuracy obtained in a previous study, also using a contracted [9s6p2d] basis set, of the dissociation and ionization energies of the GeH_n, AsH_n, and SeH_n hydrides.     

A mixed basis set of slater and gaussian functions for molecular calculations

A procedure for using simultaneously Slater and Gaussian basis functions in molecular calculations is presented here. The analytic expressions of the integral prototypes involving both Slater and Gaussian functions are explicitly derived.     

Transition-element hexafluoride systems in ionic lattices. A Suhf molecular orbital study

An unrestricted Hartree-Fock SCFMO method, based on the MCZDO method of Brown and Roby, suitable for computing spin densities in transition-element compounds, is described. The method is used to study spin densities on fluorine in Cs₂MnF₆, K₂NaCrF₆, K₂MnF₆, K₂NaFeF₆, KMnF₃, RbMnF₃ and KNiF₃ using a “cluster” approximation in which a MF ₆ ^n? unit is explicitly considered. Excellent agreement is obtained between calculated and experimental spin parameters. The effect of the lattice is incorporated by using the electrostatic approximation of Brown, O'Dwyer and Roby. The lattice potential for these highly symmetric systems is found to have little effect on spin densities and charge distributions, but it effects substantial stabilization of the anion molecular orbitals. A general feature of the results is that central-atom 4p orbitals are scarcely involved in bonding, this being confined to the 3d and to some extent the 4s orbitals. Comments are offered on the lack of spin symmetry in the unrestricted Hartree-Fock wavefunctions of these systems, and the need to evaluate the core hamiltonian as accurately as possible.     

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right phi angle) in the Y position.     

Thermal risk assessment and rankings for reaction hazards in process safety

Thermal degradation of copolymers, prepared from glycidyl methacrylate and acrylonitrile in varying molar ratios using 2,2′-azobisisobutyronitrile as an initiator, was studied by thermogravimetry, derivative thermogravimetry, differential thermal analysis and mass spectrometry. The fragmentation patterns in the mass-spectra were interpretable by comparison with the known degradation patterns of the related materials. Thermal kinetic parameters, including activation energies and order of reaction of the degradation of the prepared copolymers, were calculated from their thermoanalytical data. These parameters suggest an overall increase in thermal stability with increasing content of acrylonitrile in the copolymers.     

A molecular geometry invariant property of energy level set boundaries in z space

Boundaries of electronic energy level sets in the nuclear charge space ^wZ can be parametrized as single valued functionals for any nuclear geometry of molecules, which property, combined with the general convexity of such level sets, leads to various electronic energy inequalities.