Chemical shift driven geometry optimization

A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out.     

Matrix isolation infrared and ab initio study of the hydrogen bonding between formic acid and water

The infrared spectra of the formic acid-water complexes isolated in argon matrices are reported. Both supersonic jet expansion and a conventional effusive source followed by trapping in solid argon at 10K are used to obtain the matrices. The experimental IR spectra are compared to the data obtained from high level ab initio (MP2) and DFT (B3LYP) calculations with 6-311++G(d,p) and aug-cc-pVTZ basis sets. The complex formation results in red shifts in the C=O and O-H stretching vibrations and a blue shift in the C-O stretching vibration of formic acid. The O-H stretching modes of water also exhibit pronounced red shifts. Both the MP2 and B3LYP calculations located three minima corresponding to cyclic HCOOH...H2O complexes with two hydrogen bond interactions. The binding energies are -10.3, -5.1, and -3.5 kcal mol(-1), respectively, for the three complexes at the MP2/ aug-cc-pVTZ level, corrected for the basis set superposition error (BSSE) using the Boys-Bernardi counterpoise scheme. Comparison of the calculated frequencies of the three complexes with the matrix IR spectrum reveals that the lowest energy complex is formed. In addition, a complex of formic acid with two water molecules is observed.     

Influence of precursor solvent extraction on stable isotope signatures of methylamphetamine prepared from over-the-counter medicines using the Moscow and Hypophosphorous routes

A number of methods of clandestine manufacture of methylamphetamine involve the extraction and subsequent reaction of pseudoephedrine hydrochloride with other essential chemicals. The precursor can be easily extracted from over-the-counter medication widely available in the UK and elsewhere. Essential chemicals such as iodine and red phosphorous are also readily available and can be extracted from iodine tinctures and matchboxes, respectively. This work reports the repetitive preparation of methylamphetamine using two popular routes (the Moscow and Hypophosphorous synthesis). The focus was on the extraction solvent used for isolation of the precursor chemical and any consequential isotopic variation which may arise in the final product. Six batches of methylamphetamine were prepared under precisely controlled conditions for each synthetic route and for each of three different precursor extraction solvents. Synthesis of the final product from laboratory grade precursor using the synthetic methods described was used as a template for comparison. The resultant IRMS data from all 48 prepared samples suggests some underlying trends in the identification of the synthetic route which may aid in the interpretation of IRMS data derived from clandestine samples.     

Heavy-Atom Tunneling in Semibullvalenes: How Driving Force,Substituents, and Environment Influence the Tunneling Rates

The Cope rearrangement of selectively deuterated isotopomers of 1,5-dimethylsemibullvalene 2 a and 3,7-dicyano-1,5-dimethylsemibullvalene 2 b were studied in cryogenic matrices. In both semibullvalenes the Cope rearrangement is governed by heavy-atom tunneling. The driving force for the rearrangements is the small difference in the zero-point vibrational energies of the isotopomers. To evaluate the effect of the driving force on the tunneling probability in 2 a and 2 b , two different pairs of isotopomers were studied for each of the semibullvalenes. The reaction rates for the rearrangement of 2 b in cryogenic matrices were found to be smaller than the ones of 2 a under similar conditions, whereas differences in the driving force do not influence the rates. Small curvature tunneling (SCT) calculations suggest that the reduced tunneling rate of 2 b compared to that of 2 a results from a change in the shape of the potential energy barrier. The tunneling probability of the semibullvalenes strongly depends on the matrix environment; however, for 2 a in a qualitatively different way than for 2 b .     

The powder X-band electron paramagnetic resonance spectroscopy of septet pyridyl-2,4,6-trinitrene

The first X-band EPR spectrum containing only non-overlapping signals of septet pyridyl-2,4,6-trinitrene and triplet pyridylnitrenes is reported. This spectrum was recorded after photolysis of 2,4,6-triazidopyridine in solid argon at 5 K. The zero-field splitting (ZFS) parameters of this trinitrene as well as of intermediate triplet mononitrenes and quintet dinitrenes formed at early stages of the photolysis were determined using the combination of modern computer line-shape spectral simulations and density functional theory (DFT) calculations. It was found that septet pyridyl-2,4,6-trinitrene has the record negative parameter D_S = −0.1031 cm⁻¹ among all known to date septet pyridyl-2,4,6-trinitrenes and may be of interest as a model multi-qubit spin system for investigations of quantum computation processing.     

Towards a black‐box for biological EXAFS data analysis. II. Automatic BioXAS Refinement and Analysis (ABRA)

In biological systems, X‐ray absorption spectroscopy (XAS) can determine structural details of metal binding sites with high resolution. Here a method enabling an automated analysis of the corresponding EXAFS data is presented, utilizing in addition to least‐squares refinement the prior knowledge about structural details and important fit parameters. A metal binding motif is characterized by the type of donor atoms and their bond lengths. These fit results are compared by bond valance sum analysis and target distances with established structures of metal binding sites. Other parameters such as the Debye–Waller factor and shift of the Fermi energy provide further insights into the quality of a fit. The introduction of mathematical criteria, their combination and calibration allows an automated analysis of XAS data as demonstrated for a number of examples. This presents a starting point for future applications to all kinds of systems studied by XAS and allows the algorithm to be transferred to data analysis in other fields.     

Improved growth of solution‐deposited thin films on polycrystalline Cu(In,Ga)Se2

CdS and Zn(O,S) grown by chemical bath deposition (CBD) are well established buffer materials for Cu(In,Ga)Se₂ (CIGS) solar cells. As recently reported, a non‐contiguous coverage of CBD buffers on CIGS grains with {112} surfaces can be detected, which was explained in terms of low surface energies of the {112} facets, leading to deteriorated wetting of the chemical solution on the CIGS surface. In the present contribution, we report on the effect of air annealing of CIGS thin films prior to the CBD of CdS and Zn(O,S) layers. In contrast to the growth on the as‐grown CIGS layers, these buffer lay‐ ers grow densely on the annealed CIGS layer, even on grains with {112} surfaces. We explain the different growth behavior by increased surface energies of CIGS grains due to the annealing step, i.e., due to oxidation of the CIGS surface. Reference solar cells were processed and completed by i‐ZnO/ZnO:Al layers for CdS and by (Zn,Mg)O/ZnO:Al for Zn(O,S) buffers. For solar cells with both, CdS and Zn(O,S) buffers, air‐annealed CIGS films with improved buffer coverage resulted in higher power‐conversion efficiencies, as compared with the devices containing as‐grown CIGS layers. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)