A simple model of hydrogen bonding with particular application to trends in hydrogen‐bonded dimers

A simple model has been proposed to explain trends in the computed interaction energy, bond length changes, frequency shifts and infrared intensities for the chlorofluoromethanes CF_nCl_mH, FH and FArH on complexation with the isoelectronic diatomics BF, CO, N₂ and the rare gas atoms Kr, Ar, Ne to form a series of linear or nearly linear hydrogen‐bonded complexes. The dipole moment derivative of the proton donor (with respect to the stretching coordinate) and the chemical hardness of the hydrogen‐bonded atom of the proton acceptor are identified as two useful parameters for rationalizing the changes in some of the molecular properties of the proton donor when the hydrogen bond is formed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A comparative computational study of hydrogen and lithium-bonded complexes

A computational study of hydrogen-bonded complexes of F(3)CH and C1H and of lithium-bonded complexes of F(3)CLi and CILi, with small molecules such as N(2) and H(2)O was undertaken at the MP2/6-311++G(d,p) level of theory. Bond extensions and redshifts were obtained for the Cl[Single Bond]H bond in the ClH complexes, while bond contractions and blueshifts were obtained for the C[Single Bond]H bond in the F(3)CH complexes. By contrast, bond extensions and blueshifts were obtained for all of the lithium-bonded species. These results were rationalized using a model derived from perturbation theory.     

Detection of genetic modification in cured tobacco leaf: proficiency testing using polymerase chain reaction-based methods

The Cooperation Centre for Scientific Research Relative to Tobacco (CORESTA; Paris, France) "Task Force Genetically Modified Tobacco-Detection Methods" investigated the performance of qualitative and quantitative methods based on the polymerase chain reaction (PCR) for the detection and quantitation of genetically modified (GM) tobacco. In the 4 successful rounds of proficiency testing, the cauliflower mosaic virus 35S RNA promoter (CaMV 35S) and the Agrobacterium tumefaciens nopaline synthase terminator (NOS) were selected as target sequences. Blind-coded reference materials containing from 0.1 to 5.0% and from 0.15 to 4% GM tobacco were used in 2 rounds of qualitative and quantitative PCR, respectively. Eighteen laboratories from 10 countries participated in this study. Considering all methods and 2 rounds, the different laboratories were able to detect GM tobacco at the 0.1% level in 46 out of 58 tests in qualitative assays. The results of the proficiency test indicate that both end point screening and real-time quantitative methods are suitable for the detection of genetically modified organisms in tobacco leaf samples having a GM content of 0.1% or higher. The CORESTA proficiency study represents a first step towards the interlaboratory evaluation of accuracy and precision of PCR-based GM tobacco detection, which may lead to the harmonization of analytical procedures and to the enhancement of comparability of testing results produced by different laboratories.     

Bayesian analysis and inference from QSAR predictive model results

QSAR models have been under development for decades but acceptance and utilization of model results have been slow, in part, because there is no widely accepted metric for assessing their reliability. We reapply a method commonly used in quantitative epidemiology and medical decision-making for evaluating the results of screening tests to assess reliability of a QSAR model. It quantifies the accuracy (expressed as sensitivity and specificity) of QSAR models as conditional probabilities of correct and incorrect classification of chemical characteristic, given a true characteristic. Using Bayes formula, these conditional probabilities are combined with prior information to generate a posterior distribution to determine the probability a specific chemical has a particular characteristic, given a model prediction. As an example, we apply this approach to evaluate the predictive reliability of a CATABOL model and base on it a "ready" and "not ready" biodegradability classification. Finally, we show how predictive capability of the model can be improved by sequential use of two models, the first one with high sensitivity and the second with high specificity.     

An N.M.R. study of molecular motion in solid trimethylaminegallane

Continuous wave and pulsed ¹H N.M.R. data have been obtained for solid H₃GaN(CH₃)₃ over the temperature range 63–300 K. A theoretical expression for the relaxation behaviour of a methyl group in a trimethylamine moeity undergoing various motions has been obtained to aid analysis of the data. We find the activation energy to rotation of the -GaH₃ group to be 3·6 ± 0·3 kJ/mole (0·86 ± 0·07 kcal/mole), and to a different motion in the molecule to be 21 ± 2 kJ/mole (5·0 ± 0·5 kcal/mole). In the continuous wave spectra effects due to motion of the -CH₃ groups and the whole -NMe₃ moeity may be distinguished.     

Hydrogen-bonded ferroelectrics: Evidence for Slater configurations from E.P.R. studies of X-irradiated KH2AsO4 and NH4H2AsO4

The temperature dependence of the powder E.P.R. spectrum of the AsO₄ ^4- centre in x-irradiated samples of KH₂AsO₄ and NH₄H₂AsO₄ yields results which can be understood as arising from exchange processes taking place between the six configurations in the Slater model for this type of hydrogen-bonded ferroelectric and antiferroelectric. Knowing that the ⁷⁵As hyperfine parameters have rhombic symmetry in the compounds studied, it is possible to interpret certain specific features in the spectra as being associated with the Slater configurations of higher energy.     

Blue and red shifts in Rg···HCN and Rg···HNC complexes (Rg=He,Ne, Ar,Kr)

The shift in the harmonic vibrational frequency of the H–C stretch of HCN on formation of the linear Rg···HCN complexes, and of the H–N stretch of HNC on the formation of Rg···HNC complexes (Rg?=?He, Ne, Ar, Kr), has been determined by ab initio computations. These shifts are in agreement with predictions from a model based on perturbation theory and involving the first and second derivatives of the interaction energy with respect to displacement of the H–C (H–N) bond length from its equilibrium value in the monomer. Small blue shifts were obtained for He···HCN, Ne···HCN and He···HNC, while red shifts were obtained for the other weakly bound complexes. These vibrational characteristics are rationalized by considering the balance between the interaction energy derivatives obtained from the perturbative model. For all complexes, the IR intensity of the H–C or H–N stretch was increased from the isolated monomer values on complexation.     

Christopher Longuet-Higgins, 1923 to 2004

The structure, harmonic vibrational frequencies, dissociation energies with respect to possible fragmentation pathways, dipole moment, natural bond orbital (NBO) partial atomic charges and time-dependent density functional theory (TD-DFT) excitation energies for the novel molecule periodane, FBeCNLiOB, and three structural analogues were computed using density functional theory (DFT). Two isoelectronic analogues (FBeCNLiNC and FBeBOLiOB) result from the replacement in periodane of the BO fragment with the CN fragment and vice versa, while the third, called hydroperiodane, is formed by replacing the F atom of periodane with a H atom. These three species are predicted to have a stable structural motif based on that of the theoretically predicted planar global minimum of the periodane molecule.     

Prediction of phonon properties of 1D polyatomic systems using concurrent atomistic–continuum simulation

In this work, we present the simulation results of phonon properties, including phonon dispersion relations, group velocities, phonon relaxation time and mode-specific thermal conductivity, of low-dimensional crystals using the newly developed concurrent atomistic–continuum (CAC) method. With significantly less number of degrees of freedoms than all-atom molecular dynamics, the CAC method predicts the phonon properties of one-dimensional (1D) polyatomic crystals at finite temperatures with the full anharmonicity of the atomic interactions being incorporated. Complete phonon branches of polyatomic crystals are obtained by CAC through the phonon spectral energy density analysis. It is shown that CAC allows medium to long-wavelength phonon transport from atomic to coarsely meshed finite element region without the need of special numerical treatment. The frequency-dependent phonon group velocities are explicitly measured in the simulation. Sub-THz phonon lifetimes in 100 -mm-long polyatomic chains containing 400 million of atoms are predicted. Analysis of the phonon mode-specific thermal conductivity shows that the medium to long-wavelength acoustic phonons are contributing to the majority of the heat transport in 1D crystal, suggesting that the long-wavelength phonons effectively act as thermal carriers in 1D system. This work provides a possible explanation for the anomalous heat transport observed in low-dimensional materials.