ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces

The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy‐to‐use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Design of RLS Wiener fixed-lag smoother using covariance information in linear discrete stochastic systems

In this paper, we propose a new design for the recursive least-squares (RLS) Wiener fixed-lag smoother and filter in linear discrete-time wide-sense stationary stochastic systems. It is assumed that the signal is observed with additive white observation noise. The signal is uncorrelated with the observation noise. The estimators require knowledge of the system matrix, the observation matrix and the variance of the state vector. These quantities can be obtained from the auto-covariance function of the signal. In the estimation algorithms, moreover, the variance of the observation noise is assumed to be known, as a priori information.     

Synthesis of aromatic tetracyclic tin compounds by template and transmetallation reactions: Alkyl vs aryl migration from tin to nitrogen

The syntheses of [bis(3,5-di-tert-butyl-2-hydroxy-2-phenyl)amine]diphenyltin (1) and [bis(3,5-di-tert-butyl-2-hydroxy-2-phenyl)amine]dichloro-phenyl-stannate (2) by template reactions using 3,5-di-tert-butylcatechol, aqueous ammonia and SnPh₂Cl₂ are reported. We also report the syntheses of compounds 2, [bis(3,5-di-tert-butyl-2-hydroxy-2-phenyl)amine]trichloro-stannate (4), [bis(3,5-di-tert-butyl-2-hydroxy-2-phenyl)methylamine]chloro-methyltin (5), and [bis(3,5-di-tert-butyl-2-hydroxy-2-phenyl)-n-butylamine]n-butyl-chlorotin (6) and [bis(3,5-di-tert-butyl-2-hydroxy-2-phenyl)amine]n-butyl-dichloro-stannate (7), performed by transmetallation reactions of the octahedral zinc coordination compound Zn[3,5-di-tert-butyl-1,2-quinone-(3,5-di-tert-butyl-2-hydroxy-1-phenyl)imine]₂ (3) with SnPhCl₃ or SnPh₂Cl₂, SnCl₄, SnMe₂Cl₂, Sn(nBu)₂Cl₂ and Sn(nBu)Cl₃, respectively. The X-ray diffraction structures of compounds 1, 2, 4 and 6 are reported. The transmetallation reactions with Sn(alkyl)₂Cl₂ afforded pentacoordinated tin compounds, where an alkyl group migrated from tin to nitrogen, while similar reactions with Sn-Ph compounds did not present any phenyl group migration.     

Synthesis and characterization of PMMA/silylated MMTs

Commercially available Sodium clay (Dellite HPS) and organo-clay (Dellite 72T) are modified via a silylation reaction. These silylated clays are characterized by IR, XRD, thermogravimetric analyses, and their equilibrium contact angles are measured. They are used to prepare nanocomposites at different loading percentage (1, 3, 5% wt) by in situ intercalative polymerization of Methyl methacrylate and morphology and thermal properties of nanocomposites are examined. SEM images of nanocomposites fractured surface show the absence of clays aggregates, confirming a good dispersion and distribution of montmorillonites in the polymer matrix. The effects of modified clays on the thermal properties of nanocomposites are analyzed by differential scanning calorimetry and thermogravimetric analyses showing an increase of glass and decomposition temperatures of all nanocomposites respect to homopolymer ones. The best results are obtained in the presence of silylated montmorillonites, clearly the organosilane improves the compatibility between polymer matrix and clay and as effect the properties of nanocomposites.     

The Synthesis of Some Fused Pyrazolo‐1,4‐Naphthoquinones

New fused pyrazolo‐1,4‐naphthoquinones were prepared from the reaction of hydrazines with 6‐(4‐methyl‐3‐pentenyl)‐1,4‐naphthoquinone. The reaction was extended to hydroxylamine to afford the corresponding isoxazolo‐1,4‐napthoquinone compound.     

Using molecular dynamics and quantum mechanics calculations to model fluorescence observables

We provide a critical examination of two different methods for generating a donor-acceptor electronic coupling trajectory from a molecular dynamics (MD) trajectory and three methods for sampling that coupling trajectory, allowing the modeling of experimental observables directly from the MD simulation. In the first coupling method we perform a single quantum-mechanical (QM) calculation to characterize the excited state behavior, specifically the transition dipole moment, of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on each snapshot and use the complete transition densities to calculate the electronic coupling without need for the IDA. The resulting coupling trajectories are then sampled using three methods ranging from an independent sampling of each trajectory point (the independent snapshot method) to a Markov chain treatment that accounts for the dynamics of the coupling in determining effective rates. The results show that the IDA significantly overestimates the energy transfer rate (by a factor of 2.6) during the portions of the trajectory in which the probes are close to each other. Comparison of the sampling methods shows that the Markov chain approach yields more realistic observables at both high and low FRET efficiencies. Differences between the three sampling methods are discussed in terms of the different mechanisms for averaging over structural dynamics in the system. Convergence of the Markov chain method is carefully examined. Together, the methods for estimating coupling and for sampling the coupling provide a mechanism for directly connecting the structural dynamics modeled by MD with fluorescence observables determined through FRET experiments.     

Time resolved spectroscopy of 2-(dimethylamine)fluorene. Solvent effects and photophysical behavior

The effect of different solvents on the fluorescent properties of 2-(dimethylamine)fluorene (DAF) were studied. In aprotic solvents we detected a strongly emissive intramolecular charge transfer (ICT) state that decayed by intersystem crossing to triplet. In proton-accepting solvents DAF exhibits in the excited state an intramolecular proton transfer. An ionized species is postulated, which simultaneously twists to a rotated conformation in the excited state. Thus, the specific solvent interactions supplement but do not replace the twist mechanism and accompany the charge transfer accepted as the prerequisite for twisted intramolecular charged transfer (TICT) state formation.     

Structure prediction, disorder and dynamics in a DMSO solvate of carbamazepine

We have applied crystal structure prediction methods to understand and predict the formation of a DMSO solvate of the anti-convulsant drug carbamazepine (CBZ), in which the DMSO molecules are disordered. Crystal structure prediction calculations on the 1:1 CBZ:DMSO solvate revealed the generation of two similar low energy structures which differ only in the orientation of the DMSO molecules. Analysis of crystal energy landscapes generated at 0 K suggests the possibility of solvent disorder. A combined computational and experimental study of the changes in the orientation of the DMSO within the crystal structure revealed that the nature of the disorder changes with temperature. At low temperature, the DMSO disorder is static whilst at high temperature the DMSO configurations can interconvert by a 180° rotation of the DMSO molecules within the lattice. This 180° rotation of the DMSO molecules drives a phase change from a high temperature dynamically disordered phase to a low temperature phase with static disorder. Crystallisation of a DMSO solvate of the related molecule epoxycarbamazepine resulted in a different degree of DMSO disorder in the crystal structure, despite the similarity of the carbamazepine and epoxycarbamazepine molecules. We believe consideration of disorder and its contribution to entropy and crystal free energies at temperature other than 0 K is fundamental for the accuracy of future energy rankings in crystal structure prediction calculations of similar solvated structures.     

O-Alkylation of 3-hydroxy-1-phenyl-2-pyrazolin-5-one

3-Hydroxy-1-phenyl-2-pyrazolin-5-one 1 reacts with primary, secondary and allylic alcohols under catalytic acidic conditions and in the presence of 3 Å molecular sieves, to afford 3-alkoxy-1-phenyl-2-pyrazolin-5-ones 3 .     

A Model for Community Nursing in a Rural County

A model for the working day of the community nurse is proposed. This takes into account the attachment of the nurse to the patients registered with assigned general practices and the effect that this will have on her travelling time, visiting time and administrative duties. It also leads to a method of dividing the country into nursing team regions, assessing the level of nursing service thereby provided.