Fast vibrational calculation of anharmonic OH-stretch frequencies for two low-energy noradrenaline conformers

We introduce a new reduced-coupling technique to accelerate direct calculations of a selected number of vibrational frequencies in large molecular systems. Our method combines the advantages of the single-to-all correlation-corrected vibrational self-consistent field (STA-CC-VSCF) approach [D. M. Benoit, J. Chem. Phys. 125, 244110 (2006)] with those of the fast-CC-VSCF technique [D. M. Benoit, J. Chem. Phys. 120, 562 (2004)] and allows the ab initio calculation of only the relevant parts of the required potential energy surface (PES). We demonstrate, using a set of five aliphatic alcohol molecules, that the new fast-STA-CC-VSCF method is accurate and leads to very substantial time gains for the computations of the PES. We then use the fast-STA-CC-VSCF method to accelerate the computation of the OH-stretch and NH-stretch frequencies of the two lowest-energy conformers of noradrenaline, namely, AG1a and GG1a. Our new approach enables us to run the calculation 89 times faster than the standard CC-VSCF technique and makes it possible to use a high-level MP2/TZP description of the PES. We demonstrate that the influence of the strong mode-mode couplings is crucial for a realistic description of the particular OH-stretch vibrational signature of each conformer. Finally, of the two possible low-energy conformers, we identify AG1a as the one most likely to have been observed in the experiments of Snoek [Mol. Phys. 101, 1239 (2003)]

Vibrational signature of a single water molecule adsorbed on Pt(111): toward a reliable anharmonic description

In this study, we present a thorough benchmarking of our direct anharmonic vibrational variation-perturbation approach for adsorbed molecules on surfaces. We then use our method to describe the vibrational structure of a water molecule adsorbed on a Pt(111) surface and compare our results with the available experimental data. By using an explicitly correlated hybrid method to describe the molecule-surface interaction, we improve on the initial periodic PBE/DZP potential energy landscape and obtain vibrational frequencies that are of near-experimental accuracy. We introduce an implementation of anharmonic z-polarized IR intensity calculation and explain the absence of antisymmetric O-H stretch in the experimental data for the adsorbed water molecule, while the symmetric O-H stretch is predicted to be visible

The nature and role of the gold-krypton interactions in small neutral gold clusters

© 2015 American Chemical Society. We investigate the nature and role of krypton embedding in small neutral gold clusters. For some of these clusters, we observe a particular site-dependent character of the Kr binding that does not completely follow the criterion of binding at low-coordinated sites, widely accepted for interaction of a noble gas with closed-shell metal systems such as metal surfaces. We aim at understanding the effect of low dimensionality and open-shell electronic structure of the odd-numbered clusters on the noble gas-metal cluster interaction. First, we investigate the role of attractive and repulsive forces, and the frontier molecular orbitals. Second, we investigate the Au-Kr interaction in terms of reactivity and bonding character. We use a reactivity index derived from Fukui formalism, and criteria provided by the electron localization function (ELF), in order to classify the type of bonding. We carry out this study on the minimum energy structures of neutral gold clusters, as obtained using pseudo potential plane-wave density functional theory (DFT). A model is proposed that includes the effect of attractive electrostatic, van der Waals and repulsive forces, together with effects originating from orbital overlap. This satisfactorily explains minimum configurations of the noble gas-gold cluster systems, the site preference of the noble gas atoms, and changes in electronic properties

Vibrational anharmonicity of small gold and silver clusters using the VSCF method

We study the vibrational spectra of small neutral gold (Au2–Au10) and silver (Ag2–Au5) clusters using the vibrational self-consistent field method (VSCF) in order to account for anharmonicity. We report harmonic, VSCF, and correlation-corrected VSCF calculations obtained using a vibrational configuration interaction approach (VSCF/VCI). Our implementation of the method is based on an efficient calculation of the potential energy surfaces (PES), using periodic density functional theory (DFT) with a plane-wave pseudopotential basis. In some cases, we use an efficient technique (fast-VSCF) assisted by the Voter–Chen potential in order to get an efficient reduction of the number of pair-couplings between modes. This allows us to efficiently reduce the computing time of 2D-PES without degrading the accuracy. We found that anharmonicity of the gold clusters is very small with maximum rms deviations of about 1 cm−1, although for some particular modes anharmonicity reaches values slightly larger than 2 cm−1. Silver clusters show slightly larger anharmonicity. In both cases, large differences between calculated and experimental vibrational frequencies (when available) stem more likely from the quality of the electronic structure method used than from vibrational anharmonicity. We show that noble gas embedding often affects the vibrational properties of these clusters more than anharmonicity, and discuss our results in the context of experimental studies

Adsorption of imidazole on Au(111) surface: Dispersion corrected density functional study

We use density functional theory in the generalized gradient approximation to study the adsorption of imidazole on the Au(111) surface and account for dispersion effect using Grimme's empirical dispersion correction technique. Our results show that the adsorption energy of imidazole depends on the slab size and on the adsorption site. In agreement with other studies, we find the largest adsorption energy for imidazole on a top site of Au(111). However, we also note that the adsorption energy at other sites is substantial

An alternative methodology to assess the quality of empirical potentials for small gold clusters

We present a methodology based on local comparisons of potential energy surfaces (PES) in order to assess the quality of empirical potentials. We compare five typical empirical potentials using a criterion that shows which of these potentials resembles better a PES obtained with a high-level electronic structure method. The methodology relies on a many-body expansion in terms of normal coordinates of both the empirical and high-level theory PES. Then we investigate in a systematical way, how the features of the reference high-level theory PES are reproduced by each empirical potential in the vicinity of a given minimum energy structure. We use plane-wave density functional theory (DFT) as a reference, in particular the Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional and an ultrasoft Vanderbilt pseudo potential. This study is carried out on neutral gold clusters with up to five atoms

Ultra-shallow-marine anoxia in an Early Triassic shallow-marine clastic ramp (Spitsbergen) and the suppression of benthic radiation

Lower Triassic marine strata in Spitsbergen accumulated on a mid-to-high latitude ramp in which high-energy foreshore and shoreface facies passed offshore into sheet sandstones of probable hyperpycnite origin. More distal facies include siltstones, shales and dolomitic limestones. Carbon isotope chemostratigraphy comparison allows improved age dating of the Boreal sections and shows a significant hiatus in the upper Spathian. Two major deepening events, in earliest Griesbachian and late Smithian time, are separated by shallowing-upwards trends that culminated in the Dienerian and Spathian substages. The redox record, revealed by changes in bioturbation, palaeoecology, pyrite framboid content and trace metal concentrations, shows anoxic phases alternating with intervals of better ventilation. Only Dienerian–early Smithian time witnessed persistent oxygenation that was sufficient to support a diverse benthic community. The most intensely anoxic, usually euxinic, conditions are best developed in offshore settings, but at times euxinia also developed in upper offshore settings where it is even recorded in hyperpycnite and storm-origin sandstone beds: an extraordinary facet of Spitsbergen's record. The euxinic phases do not track relative water depth changes. For example, the continuous shallowing upwards from the Griesbachian to lower Dienerian was witness to several euxinic phases separated by intervals of more oxic, bioturbated sediments. It is likely that the euxinia was controlled by climatic oscillations rather than intra-basinal factors. It remains to be seen if all the anoxic phases found in Spitsbergen are seen elsewhere, although the wide spread of anoxic facies in the Smithian/Spathian boundary interval is clearly a global event

An abrupt extinction in the Middle Permian (Capitanian) of the Boreal Realm (Spitsbergen) and its link to anoxia and acidification

The controversial Capitanian (Middle Permian, 262 Ma) extinction event is only known from equatorial latitudes, and consequently its global extent is poorly resolved. We demonstrate that there were two, severe extinctions amongst brachiopods in northern Boreal latitudes (Spitsbergen) in the Middle to Late Permian, separated by a recovery phase. New age dating of the Spitsbergen strata (belonging to the Kapp Starostin Formation), using strontium isotopes and d13C trends and comparison with better-dated sections in Greenland, suggests that the first crisis occurred in the Capitanian. This age assignment indicates that this Middle Permian extinction is manifested at higher latitudes. Redox proxies (pyrite framboids and trace metals) show that the Boreal crisis coincided with an intensification of oxygen depletion, implicating anoxia in the extinction scenario. The widespread and near-total loss of carbonates across the Boreal Realm also suggests a role for acidification in the crisis. The recovery interval saw the appearance of new brachiopod and bivalve taxa alongside survivors, and an increased mollusk dominance, resulting in an assemblage reminiscent of younger Mesozoic assemblages. The subsequent end-Permian mass extinction terminated this Late Permian radiation

Adenosine-mono-phosphate-activated protein kinase-independent effects of metformin in T cells

The anti-diabetic drug metformin regulates T-cell responses to immune activation and is proposed to function by regulating the energy-stress-sensing adenosine-monophosphate-activated protein kinase (AMPK). However, the molecular details of how metformin controls T cell immune responses have not been studied nor is there any direct evidence that metformin acts on T cells via AMPK. Here, we report that metformin regulates cell growth and proliferation of antigen-activated T cells by modulating the metabolic reprogramming that is required for effector T cell differentiation. Metformin thus inhibits the mammalian target of rapamycin complex I signalling pathway and prevents the expression of the transcription factors c-Myc and hypoxia-inducible factor 1 alpha. However, the inhibitory effects of metformin on T cells did not depend on the expression of AMPK in T cells. Accordingly, experiments with metformin inform about the importance of metabolic reprogramming for T cell immune responses but do not inform about the importance of AMPK