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     

On the cavitation energy of water

Free-energy-perturbation theory from molecular dynamics calculations has been used to obtain the DeltaG of adjoining cavities' formation in water. The DeltaGs for systems with three, five and seven cavities are compared with that of a single cavity of the same volume, and found to be in good agreement. The conditions under which the analytical formulation of the energy of cavity formation proposed by Pierotti holds are discussed. The data for a single cavity have been tabulated and can lend themselves to a simple numerical implementation in standard quantum chemical packages, which can be used when high accuracy for DeltaG(cav) is required.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Chemical mass shifts in resonance ejection experiments in the quadrupole ion trap

Chemical mass shifts were measured in a Paul ion trap operated in the mass-selective instability scan with resonance ejection using a custom-built instrument. These shifts, which can be as much as 2%, decrease with increasing endcap electrode separation owing to changes in the higher order contributions to the electric field. They also decrease with decreasing helium buffer gas pressure. Both of these effects are analogous to those found with boundary ejection. This suggests that the previously proposed chemical mass shift mechanism based on compound-dependent collisional modification of the ejection delay produced by field faults near the endcap electrode apertures holds true also for resonance ejection. The influence of the resonance frequency on chemical mass shifts was also investigated and it is shown that at certain working points (values of the Mathieu parameter q(z) and a(z)) non-linear resonances greatly reduce the ejection delay for all ions, regardless of their chemical structures, and thus reduce the magnitude of the chemical mass shift. Energetic collisions leading to dissociation can take place at an earlier stage during the ejection process in the mass analysis scan when using resonance ejection compared with boundary ejection. This leads to even larger chemical mass shifts of fragile ions in resonance ejection. Increasing the resonance voltage amplitude can enhance this effect. The chemical mass shifts of fragile ions increase with increase in the resonance voltage amplitude, whereas negligible changes occur for structurally stable ions.     

Study on δ‐form complex in syndiotactic polystyrene–organic molecules systems. IV. Formation of complexes with a mixture of solvents and structural changes during the sorption of solvents by syndiotactic polystyrene mesophase membranes

The syndiotactic polystyrene (sPS) δ form was crystallized from mixtures with different compositions of p‐chlorotoluene–chlorobenzene (p‐CT–CB) and p‐chlorotoluene–1,1,2‐trichloroethane (p‐CT–TCE). The presence of the δ form and TTGG helical conformation was confirmed by Fourier transform infrared and wide‐angle X‐ray diffraction (WAXD) analyses. In sPS/p‐CT–CB and sPS/p‐CT–TCE δ‐form membranes, the relative absorbance (RA) of the p‐chlorotoluene (p‐CT) solvent peak was very high even at very low concentrations of p‐CT in comparison with the RA of higher concentrations of chlorobenzene (CB) or 1,1,2‐trichloroethane (TCE) in the mixtures. However, the RAs of both CB and TCE solvent peaks decreased with decreasing concentrations of CB and TCE in the mixtures. A negligible decrease in the RA of the TTGG helical content was observed with a decreasing concentration of CB or TCE. The WAXD results showed that the 2θ peak positions of the [010] and [ 10] planes of the sPS/p‐CT–CB and sPS/p‐CT–TCE δ‐form membranes appeared in the same position and were almost equal to those of the sPS–p‐CT δ‐form membrane. The mesophases of the sPS–p‐CT [p‐CT (A‐M)] and sPS–TCE [TCE (A‐M)] membranes were used for the sorption studies with different concentrations of various solvents. The sorption amount of aromatic solvents by both p‐CT (A‐M) and TCE (A‐M) mesophase membranes was higher than that of aliphatic solvents, regardless of the size, shape, and nature of the molecular cavity. The 2θ peak of the [010] plane of the sPS membranes slowly approached the original δ‐form value when the sPS mesophase membranes were immersed in various solvents of different concentrations for 48 h. The shifting of the 2θ peak of the [010] plane to the original δ form depended on the nature and concentration of the immersion solvents. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2380–2387, 2005     

Orientation of a chiral smectic C elastomer by mechanical fields

It is well known that, with respect to the director, nematic elastomers can be macroscopically aligned by uniaxial mechanical fields. Extending this method to a chiral smectic C elastomer, depending on the experimental set-up either smectic layer orientation or director orientation parallel to the stress axis occurs. In order to align the director and the smectic layers a biaxial mechanical field (e.g. shear field) consistent with the phase symmetry has to be used to achieve a macroscopically uniform orientation of the untwisted smectic C^* structure.     

Influence of the variable wall thickness of the sample tubes and a quartz Dewar on the EPR signal intensity in a single TE102 and double TE104 rectangular cavity

The response of a single TE₁₀₂ and double TE₁₀₄ rectangular cavity to the insertion of samples contained in tubes with variable wall thickness and a quartz Dewar into the cavity has been analyzed. A direct, indirect, and concurrent (positive or negative) “lens effect” inside the double TE₁₀₄ rectangular cavity is discussed. The experimental dependence of the EPR signal intensity on the wall thickness of the sample tube, δ, for the line-like samples with identical length of the sample material column, L=30 mm, recorded in the microwave cavity showed a directly proportional increase of the relative “lens effect” with the increase of the wall thickness of the tube in the interval, δ∈<0.1 mm, >0.5 mm. The insertion of the variable-temperature double-wall quartz Dewar (home-built, resonant frequency shift, ca. −300 MHz) into the single TE₁₀₂ rectangular cavity showed the same relative “lens effect”, with ca. 1.5-time increase of the EPR signal intensity, for a point-like sample and the line-like samples with material columns of diameter of 1 and 1.3 mm, and wall thickness of the sample tubes, δ∈<0.1 mm, >0.5 mm. The increased effect of the Dewar arises because the active volume of the quartz Dewar tube walls is always much more larger than the active volume of the sample tube wall. In the case of the double TE₁₀₄ rectangular cavity, the insertion of the quartz Dewar: (i) into the same cavity, in which the sample is present, caused a direct “lens effect”, with ca. 1.8-fold increase of the EPR signal intensity; however, (ii) into the complementary cavity, in which the sample is absent, caused an indirect “lens effect”, with ca. 0.6-fold decrease of the EPR signal intensity. With the Dewar and sample in one cavity and a large empty sample tube in the complementary cavity, a concurrent (positive or negative) “lens effect” can be observed. Thus, the possible increase/decrease of the EPR signal intensity depends on the volume ratio of the quartz Dewar tube walls and large sample tube wall inserted into the double TE₁₀₄ rectangular cavity. Each of the above phenomena may be a significant source error in quantitative EPR spectrometry unless the samples to be compared in the quantitative EPR analysis are contained in sample tubes having the same wall thickness and each EPR spectra should be recorded inside an identical quartz Dewar.