Theoretical studies of 31P NMR spectral properties of phosphanes and related compounds in solution

Selected theoretical methods, basis sets and solvation models have been tested in their ability to predict 31P NMR chemical shifts of large phosphorous-containing molecular systems in solution. The most efficient strategy was found to involve NMR shift calculations at the GIAO-MPW1K/6-311++G(2d,2p)//MPW1K/6-31G(d) level in combination with a dual solvation model including the explicit consideration of single solvent molecules and a continuum (PCM) solvation model. For larger systems it has also been established that reliable 31P shift predictions require Boltzmann averaging over all accessible conformations in solution

The Chronus Quantum (ChronusQ) Software Package

The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge-including atomic orbitals (GIAO). ChronusQ is a parallel electronic structure code written in modern C++ which utilizes both message passing (MPI) and shared memory (OpenMP) parallelism. In addition to the examination of the current state of code base itself, a discussion regarding ongoing developments and developer contributions will also be provided.Comment: 43 pages, 2 figure

High sensitivity of 17O NMR to p-d hybridization in transition metal perovskites: first principles calculations of large anisotropic chemical shielding

A first principles embedded cluster approach is used to calculate O chemical shielding tensors, sigma, in prototypical transition metal oxide ABO_3 perovskite crystals. Our principal findings are 1) a large anisotropy of sigma between deshielded sigma_x ~ sigma_y and shielded sigma_z components (z along the Ti-O bond); 2) a nearly linear variation, across all the systems studied, of the isotropic sigma_iso and uniaxial sigma_ax components, as a function of the B-O-B bond asymmetry. We show that the anisotropy and linear variation arise from large paramagnetic contributions to sigma_x and sigma_y due to virtual transitions between O(2p) and unoccupied B(nd) states. The calculated isotropic delta_iso and uniaxial delta_ax chemical shifts are in good agreement with recent BaTiO_3 and SrTiO_3 single crystal 17O NMR measurements. In PbTiO_3 and PbZrO_3, calculated delta_iso are also in good agreement with NMR powder spectrum measurements. In PbZrO_3, delta_iso calculations of the five chemically distinct sites indicate a correction of the experimental assignments. The strong dependence of sigma on covalent O(2p)-B(nd) interactions seen in our calculations indicates that 17O NMR spectroscopy, coupled with first principles calculations, can be an especially useful tool to study the local structure in complex perovskite alloys.Comment: 12 pages, 3 figures, and 3 Table

GIAO-PCM Calculations on Alanine Diamide Models Aimed at Predicting Protein Secondary Structures

In this paper we extend our theoretical studies dealing with the dependence of relative proton and carbon chemical shifts (CSs) of protein backbone atoms on their conformational position. In an earlier paper (A. Czajlik, I. Hudáky, A. Perczel, J Comp Chem 2011, 32, 3362) we reported on a fair agreement between calculated and observed backbone CSs as a function of backbone conformation. Applying the polarizable continuum model (PCM) in this work, we compare relative CSs of fully optimized alanine diamide conformers with gas phase calculations and experimental results. Along a path on the Ramachandran surface, we collated calculated relative CSs obtained with and without explicit water molecules, as well as with and without considering the PCM reaction field. Furthermore, we traced the energetically relevant reaction paths along the torsional angle ψ connecting the lowest energy minima (helical, extended, polyproline II and inverse γ-turn) on the Ramachandran plot, with the prospect to facilitate identifying them by their relative CSs. We found that consideration of the solvent effect of the environment around a diamide model improves the agreement with experimental findings on abundant conformers. This agreement is of the level achieved previously by a thorough gas phase investigation on considerably larger oligoalanine models. By relating DeltaδCα, DeltaδHα and DeltaδCβ values of polyproline II and inverse γ-turn to the experimentally well characterized helical and extended data, our calculations contribute to protein secondary structure prediction based on nuclear magnetic CS

First-principles calculations of the structural, electronic, vibrational and magnetic properties of C_{60} and C_{48}N_{12}: a comparative study

In this work, we perform first-principles calculations of the structural, electronic, vibrational and magnetic properties of a novel ${\rm C}_{48}{\rm N}_{12}$ azafullerene. Full geometrical optimization shows that ${\rm C}_{48}{\rm N}_{12}$ is characterized by several distinguishing features: only one nitrogen atom per pentagon, two nitrogen atoms preferentially sitting in one hexagon, ${\rm S}_{6}$ symmetry, 6 unique nitrogen-carbon and 9 unique carbon-carbon bond lengths. The highest occupied molecular orbital of ${\rm C}_{48}{\rm N}_{12}$ is a doubly degenerate level of $a_{g}$ symmetry and its lowest unoccupied molecular orbital is a nondegenerate level of $a_{u}$ symmetry. Vibrational frequency analysis predicts that ${\rm C}_{48}{\rm N}_{12}$ has in total 116 vibrational modes: 58 infrared-active and 58 Raman-active modes. ${\rm C}_{48}{\rm N}_{12}$ is also characterized by 8 $^{13}{\rm C}$ and 2 $^{15}{\rm N}$ NMR spectral signals. Compared to ${\rm C}_{60}$, ${\rm C}_{48}{\rm N}_{12}$ shows an enhanced third-order optical nonlinearities which implies potential applications in optical limiting and photonics.Comment: a long version of our manuscript submitted to J.Chem.Phy

Ab initio calculations of Co shielding in model complexes

Recent ab initio calculations of cobalt NMR shielding show that DFT-GIAO calculations using hybrid functionals are found to reproduce experimental values well. This method is used top calculate the vatriation of the cobalt NMR shielding tensor of square pyramidal nitrosyl complexres with respect to the CoNO geometry and to differing basal ligands. The isotropic shielding is shown to have a large negative derivative with respect to CoX distance where X is a ligating atom; the derivative with respect to NO distance is smaller but still significant. The zz component where z is along the CoN(NO) bond is more sensitive to the basal ligands but the other two principal components are sensitive to the CoNO geometry

Application of Computational Chemical Shift Prediction Techniques to the Cereoanhydride Structure Problem-Carboxylate Complications.

Despite the vast array of techniques available to modern-day chemists, structural misassignments still occur. These misassignments are often only realized upon attempted synthesis, when the spectra of synthesized products do not match previously reported spectra. This was the case with marine natural product cereoanhydride. The originally proposed 7-membered ring anhydride (1) was shown to be incorrect, although a likely precursor to the correct structure (2) in both its laboratory synthesis and biosynthesis. Herein, in addition to showing how NMR computations could have been used to arrive at the correct structure, we show that the conversion of 1 to 2 is indeed energetically viable, and we highlight complications in predicting NMR chemical shifts for molecules with acidic protons

Trichinellosis in Vietnam

Trichinellosis is a zoonotic parasitic disease with a worldwide distribution. The aim of this work was to describe the epidemiological and clinical data of five outbreaks of trichinellosis, which affected ethnic minorities living in remote mountainous areas of northwestern Vietnam from 1970 to 2012. Trichinellosis was diagnosed in 126 patients, of which 11 (8.7%) were hospitalized and 8 (6.3%) died. All infected people had consumed raw pork from backyard and roaming pigs or wild boar at wedding, funeral, or New Year parties. The short incubation period (average of 9.5 days), the severity of the symptoms, which were characterized by diarrhea, abdominal pain, fever, myalgia, edema, weight loss, itch, and lisping, and the high mortality, suggest that patients had ingested a high number of larvae. The larval burden in pigs examined in one of the outbreaks ranged from 70 to 879 larvae/g. These larvae and those collected from a muscle biopsy taken from a patient from the 2012 outbreak were identified as Trichinella spiralis. Data presented in this work show that the northern regions of Vietnam are endemic areas for Trichinella infections in domestic pigs and humans