PDB ligand conformational energies calculated quantum-mechanically

We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 ?. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient (RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy.     

Quantitative analysis of perfumes in talcum powder by using headspace sorptive extraction

Quantitative analysis of perfume dosage in talcum powder has been a challenge due to interference of the matrix and has so far not been widely reported. In this study, headspace sorptive extraction (HSSE) was validated as a solventless sample preparation method for the extraction and enrichment of perfume raw materials from talcum powder. Sample enrichment is performed on a thick film of poly(dimethylsiloxane) (PDMS) coated onto a magnetic stir bar incorporated in a glass jacket. Sampling is done by placing the PDMS stir bar in the headspace vial by using a holder. The stir bar is then thermally desorbed online with capillary gas chromatography-mass spectrometry. The HSSE method is based on the same principles as headspace solid-phase microextraction (HS-SPME). Nevertheless, a relatively larger amount of extracting phase is coated on the stir bar as compared to SPME. Sample amount and extraction time were optimized in this study. The method has shown good repeatability (with relative standard deviation no higher than 12.5%) and excellent linearity with correlation coefficients above 0.99 for all analytes. The method was also successfully applied in the quantitative analysis of talcum powder spiked with perfume at different dosages.     

Oligomer Formation Pathways in Secondary Organic Aerosol from MS and MS/MS Measurements with High Mass Accuracy and Resolving Power

Secondary organic aerosol (SOA) is formed when organic molecules react with oxidants in the gas phase to form particulate matter. Recent measurements have shown that more than half of the mass of laboratory-generated SOA consists of high molecular weight oligomeric compounds. In this work, the formation mechanisms of oligomers produced in the laboratory by ozonolysis of α-pinene, an important SOA precursor in ambient air, are studied by MS and MS/MS measurements with high accuracy and resolving power to characterize monomer building blocks and the reactions that couple them together. The distribution of oligomers in an SOA sample is complex, typically yielding over 1000 elemental formulas that can be assigned from an electrospray ionization mass spectrum. Despite this complexity, MS/MS spectra can be found that give strong evidence for specific oligomer formation pathways that have been postulated but not confirmed. These include aldol and gem-diol reactions of carbonyls as well as peroxyhemiacetal formation from hydroperoxides. The strongest evidence for carbonyl reactions is in the formation of hydrated products. Less compelling evidence is found for dehydrated products and secondary ozonide formation. The number of times that a monomer building block is observed as a fragmentation product in the MS/MS spectra is shown to be independent of the monomer vapor pressure, suggesting that oligomer formation is not driven by equilibrium partitioning of a monomer between the gas and particle phases, but rather by reactive uptake where a monomer collides with the particle surface and rapidly forms an oligomer.     

Structure-based tuning of T(m) in lipid-like ionic liquids. Insights from Tf2N- salts of gene transfection agents

Ionic liquids of cations bearing two lipid-like aliphatic tails are shown to have values of T(m) that can be very low, and that can be tuned up or down by the addition, deletion, or combination of dipolar modules and side-chain double bonds.     

Identifying well-bleached quartz using the different bleaching rates of quartz and feldspar luminescence signals

When dating older sedimentary deposits using quartz, there are no unambiguous methods for identifying the presence of incomplete bleaching. Current statistical analysis of dose distributions depends entirely on the assumption that incomplete bleaching and mixing are the main causes of any excess dispersion in the distribution; the only existing way to test this assumption is using independent age control. Here we suggest a new approach to this question, based on the differential bleaching rates of quartz and feldspar luminescence signals. We first present data that confirm the differences in relative bleaching rates of quartz optically stimulated luminescence (OSL) and feldspar luminescence stimulated at 50 °C by infrared light (IR₅₀) and feldspar luminescence stimulated at 290 °C by infrared light after a stimulation at 50 °C (pIRIR₂₉₀), and use recently deposited samples to determine the likely significance of the difficult-to-bleach residual feldspar signals in non-aeolian samples. For a set of mainly Late Pleistocene non-aeolian sediments, large aliquot quartz doses are then used to predict feldspar doses (based on a knowledge of the sample dose rates). The differences between observed and predicted feldspar doses as a function of the quartz dose, combined with a conservative assumption concerning the relative feldspar and quartz residual signals after natural bleaching prior to deposition, are used to identify those samples for which the quartz is very likely to be well bleached (20 out of 24). Two of these apparently well-bleached samples are then examined using single-grain quartz dose distributions; one of these is consistent with the well-bleached hypothesis, and one indicates poor bleaching or a multi-component mixture. However, independent age control makes it clear that the large aliquot data are more likely to be correct. We conclude that a comparison of quartz and feldspar doses provides a useful independent method for identifying well-bleached quartz samples, and that it is unwise to apply statistical models to dose distributions without clear evidence for the physical origins of the distributions.     

Polynomial identities for the ternary cyclic sum

We simplify the results of Bremner and Hentzel [J. Algebra 231 (2000) 387–405] on polynomial identities of degree 9 in two variables satisfied by the ternary cyclic sum [a, b, c] = abc + bca + cab in every totally associative ternary algebra. We also obtain new identities of degree 9 in three variables which do not follow from the identities in two variables. Our results depend on (i) the LLL algorithm for lattice basis reduction, and (ii) linearization operators in the group algebra of the symmetric group which permit efficient computation of the representation matrices for a non-linear identity. Our computational methods can be applied to polynomial identities for other algebraic structures.     

A polynomial identity for the bilinear operation in Lie–Yamaguti algebras

We use computer algebra to demonstrate the existence of a multilinear polynomial identity of degree 8 satisfied by the bilinear operation in every Lie–Yamaguti algebra. This identity is a consequence of the defining identities for Lie–Yamaguti algebras, but is not a consequence of anticommutativity. We give an explicit form of this identity as an alternating sum over all permutations of the variables in a nonassociative polynomial with 8 terms. Our computations show that no such identities exist in degrees less than 8.     

The reaction force constant: an indicator of the synchronicity in double proton transfer reactions

Earlier work, both experimental and computational, has drawn attention to the transition region in a chemical reaction, which includes the traditional transition state but extends along the intrinsic reaction coordinate ξ from perturbed forms of the reactants to perturbed forms of the products. The boundaries of this region are defined by the reaction force F(ξ), which is the negative gradient of the potential energy V(ξ) of the system along ξ. The reaction force constant κ(ξ), the second derivative of V(ξ), is negative throughout the transition region. We have now demonstrated, for a series of twelve double proton transfer processes, that the profile of κ(ξ) in the transition region is an indicator of the synchronicity of the two proton migrations in each case. When they are fully or nearly fully synchronous, κ(ξ) has a single minimum in the transition region. When the migrations are considerably nonsynchronous, κ(ξ) has two minima separated by a local maximum. Such an assessment of the degree of synchronicity cannot readily be made from an examination of the transition state alone, nor it is easily detected in the profiles of V(ξ) and F(ξ).     

Autostereogram resonators

Autostereograms, or “Magic Eye” pictures, are repeating patterns designed to give the illusion of depth. Here we discuss optical resonators that create light patterns which, when viewed from a suitable position by a monocular observer, are autostereograms of the three-dimensional shape of one of the mirror surfaces.