Interpreting,analysing and modelling COVID-19 mortality data

We present results on the mortality statistics of the COVID-19 epidemic in a number of countries. Our data analysis suggests classifying countries in five groups, (1) Western countries, (2) East Block, (3) developed Southeast Asian countries, (4) Northern Hemisphere developing countries and (5) Southern Hemisphere countries. Comparing the number of deaths per million inhabitants, a pattern emerges in which the Western countries exhibit the largest mortality rate. Furthermore, comparing the running cumulative death tolls as the same level of outbreak progress in different countries reveals several subgroups within the Western countries and further emphasises the difference between the five groups. Analysing the relationship between deaths per million and life expectancy in different countries, taken as a proxy of the preponderance of elderly people in the population, a main reason behind the relatively more severe COVID-19 epidemic in the Western countries is found to be their larger population of elderly people, with exceptions such as Norway and Japan, for which other factors seem to dominate. Our comparison between countries at the same level of outbreak progress allows us to identify and quantify a measure of efficiency of the level of stringency of confinement measures. We find that increasing the stringency from 20 to 60 decreases the death count by about 50 lives per million in a time window of 20  days. Finally, we perform logistic equation analyses of deaths as a means of tracking the dynamics of outbreaks in the “first wave” and estimating the associated ultimate mortality, using four different models to identify model error and robustness of results. This quantitative analysis allows us to assess the outbreak progress in different countries, differentiating between those that are at a quite advanced stage and close to the end of the epidemic from those that are still in the middle of it. This raises many questions in terms of organisation, preparedness, governance structure and so on.

     

An Incremental System To Predict the Effect of Different London Dispersion Donors in All-meta-Substituted Azobenzenes

Predictive models based on incremental systems exist for many chemical phenomena, thus allowing easy estimates. Despite their low magnitude in isolated systems London dispersion interactions are ubiquitous in manifold situations ranging from solvation to catalysis or in biological systems. Based on our azobenzene system, we systematically determined the London dispersion donor strength of the alkyl substituents Me, Et, iPr up to tBu. Based on this data, we were able to implement an incremental system for London dispersion for the azobenzene scheme. We propose an equation that allows the prediction of the effect of change of substituents on London dispersion interactions in azobenzenes, which has to be validated in similar molecular arrangements in the future.     

Surprisingly Long‐Range Surface‐Enhanced Raman Scattering (SERS) on Au–Ni Multisegmented Nanowires

Very long range surface‐enhanced Raman scattering is observed from a nickel nanowire that is separated by 120 nm from a pair of gold nanodisks. The excitation of the surface‐plasmon resonance (SPR) from the gold nanodisk pair generates an enhanced electromagnetic field near the nickel segment (SEM, left), leading to Raman intensity greater than the nickel alone (right).

     

Gold nanoparticle dimer plasmonics: finite element method calculations of the electromagnetic enhancement to surface-enhanced Raman spectroscopy

Finite element method calculations were carried out to determine extinction spectra and the electromagnetic (EM) contributions to surface-enhanced Raman spectroscopy (SERS) for 90-nm Au nanoparticle dimers modeled after experimental nanotags. The calculations revealed that the EM properties depend significantly on the junction region, specifically the distance between the nanoparticles for spacings of less than 1 nm. For extinction spectra, spacings below 1 nm lead to maxima that are strongly red-shifted from the 600-nm plasmon maximum associated with an isolated nanoparticle. This result agrees qualitatively well with experimental transmission electron microscopy images and localized surface plasmon resonance spectra that are also presented. The calculations further revealed that spacings below 0.5 nm, and especially a slight fusing of the nanoparticles to give tiny crevices, leads to EM enhancements of 10¹⁰ or greater. Assuming a uniform coating of SERS molecules around both nanoparticles, we determined that regardless of the separation, the highest EM fields always dominate the SERS signal. In addition, we determined that for small separations less than 3% of the molecules always contribute to greater than 90% of the signal. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Time-dependent density functional calculations of optical rotatory dispersion including resonance wavelengths as a potentially useful tool for determining absolute configurations of chiral molecules

The optical rotations for six organic molecules (verbenone, fenchone, camphor, nopinone, Tr?ger's base, dimethyl-cyclopropane) and the transition metal complex [Co(en)(3)](3+) were calculated as a function of wavelength using time-dependent density functional theory (TDDFT). In the calculations, a realistic behavior of the optical rotation in the vicinity of an electronic transition was obtained by using a phenomenological damping parameter of the order of 0.2 eV (0.007 au). In comparison with experiment, for the molecules studied here the sign and order of magnitude of the optical rotation as well as the excitation energies were reasonably well reproduced in most computations. These findings apply to the investigated wavelength ranges typically between about 200 and 650 nm even when using comparatively small basis sets. Such calculations might therefore routinely be applied to help assigning the absolute configurations of chiral molecules. Supplementary calculations of the circular dichroism (CD) and comparison with experimental CD were used for further assessment of the optical rotation calculations. In particular, a combined study of optical rotation and CD turned out to be useful in cases where the optical rotatory dispersion in a specific energy range exhibits a considerable blue or red shift or where it is difficult to reproduce because of an interplay of several competing Cotton effects. The influence of basis set, density functional, and the damping parameter was also investigated.     

Resonance Raman scattering of rhodamine 6G as calculated using time-dependent density functional theory

In this work, we present the first calculation of the resonance Raman scattering (RRS) spectrum of rhodamine 6G (R6G) which is a prototype molecule in surface-enhanced Raman scattering (SERS). The calculation is done using a recently developed time-dependent density functional theory (TDDFT) method, which uses a short-time approximation to evaluate the Raman scattering cross section. The normal Raman spectrum calculated with this method is in good agreement with experimental results. The calculated RRS spectrum shows qualitative agreement with SERS results at a wavelength that corresponds to excitation of the S(1) state, but there are significant differences with the measured RRS spectrum at wavelengths that correspond to excitation of the vibronic sideband of S(1). Although the agreement with the experiments is not perfect, the results provide insight into the RRS spectrum of R6G at wavelengths close to the absorption maximum where experiments are hindered due to strong fluorescence. The calculated resonance enhancements are found to be on the order of 10(5). This indicates that a surface enhancement factor of about 10(10) would be required in SERS in order to achieve single-molecule detection of R6G.     

TDDFT studies of absorption and SERS spectra of pyridine interacting with Au20

We present time dependent density functional theory (TDDFT) calculations for a tetrahedral Au20 complex interacting with pyridine for the purpose of modeling absorption and surface enhanced Raman scattering, with emphasis on chemical and electrodynamic enhancement effects. These calculations are done using the ADF code with the BP86 functional, the zeroth-order regular approximation and with the resonant electronic response modeled using a short time approximation expression for the perturbed density matrix, with a damping factor that is empirically chosen. The absorption spectrum of bare Au20 shows strong intraband (sp-sp) and interband (sp-d) coupling with a low-energy peak at 2.89 eV that is mostly intraband and other peaks at 3.94 and 4.70 eV that have mixed intra- and interband character. SERS spectra are calculated for pyridine/Au20 for both vertex (V) and surface (S) configurations at their respective lowest energy absorption maxima (near 2.89 eV), and we find that the V configuration has higher intensities that correspond to SERS enhancements of 10(3)-10(4), whereas S has an enhancement of 10(2)-10(3). These enhancement values are significantly lower than the analogous results for pyridine/Ag20 primarily because of reduced oscillator strength associated with the intraband transition in Au20. Decomposition of the pyridine/Au20 enhancement factor into chemical and electromagnetic contributions (through an analysis of the static SERS intensities) shows enhanced chemical enhancements compared to Ag20 but reduced electromagnetic enhancements.     

Direct dynamics simulations of O(3P) + HCl at hyperthermal collision energies

The dynamics of the O(3P) + HCl reaction at hyperthermal collision energies were investigated using the quasiclassical trajectory method. Stationary points on the OClH 3A" and 3A' potential energy surfaces (PESs) were also examined. The lowest transition state leading to OCl + H on the 3A" surface is 2.26 eV above the reagents at the CCSD(T)/cc-pVTZ level of theory. This saddle point is bent and product-like. Direct dynamics calculations at the MP2/cc-pVTZ level of theory were used to investigate the excitation functions for OH + Cl, OCl + H, and O + H + Cl formation. OCl is formed mainly from small-impact-parameter collisions, and the OCl + H excitation function peaks around 5 eV, where it is similar in magnitude to the OH + Cl excitation function. The shape of the OCl + H excitation function is discussed, and features are identified that should be general to hyperthermal collision dynamics.     

A cooperative beads-on-a-string approach to exceptionally stable DNA triplexes

A poly(dT) oligomer can serve as the string on which synthetic hairpins possessing poly(dA) and poly(dT) arms connected by a hydrophobic perylene diimide linker are assembled like beads on a string. The synthetic hairpins form head-to-head dimers and trimers, respectively, in the absence of the poly(dT) string and in the presence of a string with inverted polarity at mid-strand. However, they assemble in cooperative head-to-tail fashion on normal poly(dT) oligomers.