Mourning the Loss of a Leader

Deuteronomy 3

Jolly Guardsmen : March

https://digitalcommons.library.umaine.edu/mmb-ps/1974/thumbnail.jp

Calculation of Raman optical activity spectra for vibrational analysis

By looking back on the history of Raman Optical Activity (ROA), the present article shows that the success of this analytical technique was for a long time hindered, paradoxically, by the deep level of detail and wealth of structural information it can provide. Basic principles of the underlying theory are discussed, to illustrate the technique's sensitivity due to its physical origins in the delicate response of molecular vibrations to electromagnetic properties. Following a short review of significant advances in the application of ROA by UK researchers, we dedicate two extensive sections to the technical and theoretical difficulties that were overcome to eventually provide predictive power to computational simulations in terms of ROA spectral calculation. In the last sections, we focus on a new modelling strategy that has been successful in coping with the dramatic impact of solvent effects on ROA analyses. This work emphasises the role of complementarity between experiment and theory for analysing the conformations and dynamics of biomolecules, so providing new perspectives for methodological improvements and molecular modelling development. For the latter, an example of a next-generation force-field for more accurate simulations and analysis of molecular behaviour is presented. By improving the accuracy of computational modelling, the analytical capabilities of ROA spectroscopy will be further developed so generating new insights into the complex behaviour of molecules

The Raman optical activity of β-D-xylose: where experiment and theory meet

Besides its applications in bioenergy and biosynthesis, β-D-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure–spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved

Distinguishing epimers through raman optical activity

The Raman optical activity spectra of the epimers β-d-glucose and β-d-galactose, two monosaccharides of biological importance, have been calculated using molecular dynamics combined with a quantum mechanics/molecular mechanics approach. Good agreement between theoretical and experimental spectra is observed for both monosaccharides. Full band assignments have been carried out, which has not previously been possible for carbohydrate epimers. For the regions where the spectral features are opposite in sign, the differences in the vibrational modes have been noted and ascribed to the band sign changes

First-principles analysis of the interplay between electronic structure and volume change in colquiriite compounds during Li intercalation

A main source of capacity fading in lithium-ion batteries is the degradation of the active cathode materials caused by the series of volume changes during charge and discharge cycles. The quaternary colquiriite-type fluorides Li$_x$CaFeF$\mathrm{_6}$ and Li$_x$CaCoF$\mathrm{_6}$ were reported to have negligible volume changes in specific Li concentration ranges, making the underlying colquiriite structure a promising candidate for so-called zero-strain behavior. Using first-principles electronic structure calculations based on density functional theory with a Hubbard-$U$ correlation correction on the transition-metal ions, we systematically investigate the equilibrium volumes of the colquiriite-type fluorides Li$_x$CaMF$\mathrm{_6}$ with M =Ti, V, Cr, Mn, Fe, Co, and Ni at the Li concentrations $x$=0, 1, and 2. We elucidate the connection between the total volume of the structures and the local volumes of fluorine coordinated octahedra around the cations, and we find trends along the series of the 3d transition-metal elements. In the lithiation step from $x$=1 to $x$=2 we find volume changes of about 10 %, and we discuss the discrepancy to the experimentally reported smaller value for Li$_x$CaFeF$\mathrm{_6}$. From $x$=0 to $x$=1 we describe the compensating structural mechanisms that lead to an exceptionally small volume change of Li$_x$CaMnF$\mathrm{_6}$. This compound is therefore a particularly promising zero-strain cathode material.Comment: 13 pages, 9 Figure

Electrostatic treatment of charged interfaces in classical atomistic simulations

Artificial electrostatic potentials can be present in supercells constructed for atomistic simulations of surfaces and interfaces in ionic crystals. Treating the ions as point charges, we systematically derive an electrostatic formalism for model systems of increasing complexity, both neutral and charged, and with either open or periodic boundary conditions. This allows to correctly interpret results of classical atomistic simulations which are directly affected by the appearance of these potentials. We demonstrate our approach at the example of a strontium titanite supercell containing an asymmetric tilt grain boundary. The formation energies of charged oxygen vacancies and the relaxed interface structure are calculated based on an interatomic rigid-ion potential, and the results are analyzed in consideration of the electrostatic effects