Characterizing Counterion-Dependent Aggregation of Rhodamine B by Classical Molecular Dynamics Simulations

The aggregation in a solution of charged dyes such as Rhodamine B (RB) is significantly affected by the type of counterion, which can determine the self-assembled structure that in turn modulates the optical properties. RB aggregation can be boosted by hydrophobic and bulky fluorinated tetraphenylborate counterions, such as F5TPB, with the formation of nanoparticles whose fluorescence quantum yield (FQY) is affected by the degree of fluorination. Here, we developed a classical force field (FF) based on the standard generalized Amber parameters that allows modeling the self-assembling process of RB/F5TPB systems in water, consistent with experimental evidence. Namely, the classical MD simulations employing the re-parametrized FF reproduce the formation of nanoparticles in the RB/F5TPB system, while in the presence of iodide counterions, only RB dimeric species can be formed. Within the large, self-assembled RB/F5TPB aggregates, the occurrence of an H-type RB-RB dimer can be observed, a species that is expected to quench RB fluorescence, in agreement with the experimental data of FQY. The outcome provides atomistic details on the role of the bulky F5TPB counterion as a spacer, with the developed classical FF representing a step towards reliable modeling of dye aggregation in RB-based materials

Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as “K”. We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics

Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra

Accurate ab initio modeling of spectroscopic signals in nonlinear electronic spectra, such as bidimensional (2D) spectra, requires the computation of the electronic transitions induced by the incoming pump/probe pulses, resulting in a challenging calculation of many electronic excited states. A protocol is thus required to evaluate the variations of spectral properties, like transition energies and dipole moments, with the computational level, and to estimate the sensitivity of the spectra to these variations. Such a protocol is presented here within the framework of complete and restricted active space self-consistent field (CASSCF/RASSCF) theory and its second-order perturbation theory extensions (CASPT2/RASPT2). The electronic excited-state manifolds of pyrimidine nucleobases (thymine, uracil, and cytosine) are carefully characterized in vacuo employing high-level RAS(0,0|10,8|2,12)//SS-RASPT2 calculations. The results provide a reference data set that can be used for optimizing computational efforts and costs, as required for studying computationally more demanding multichromophoric systems (e.g., di- and oligonucleotides). The spectroscopic signatures of the 2D electronic spectrum of a perfectly stacked uracil–cytosine dimer model are characterized, and experimental setups are proposed that can resolve non-covalent interchromophoric interactions in canonical pyrimidine nucleobase-stacked dimers

Simulating Plasmon Resonances of Gold Nanoparticles with Bipyramidal Shapes by Boundary Element Methods

Computational modeling and accurate simulations of localized surface plasmon resonance (LSPR) absorption properties are reported for gold nanobipyramids (GNBs), a class of metal nanoparticle that features highly tunable, geometry-dependent optical properties. GNB bicone models with spherical tips performed best in reproducing experimental LSPR spectra while the comparison with other geometrical models provided a fundamental understanding of base shapes and tip effects on the optical properties of GNBs. Our results demonstrated the importance of averaging all geometrical parameters determined from transmission electron microscopy images to build representative models of GNBs. By assessing the performances of LSPR absorption spectra simulations based on a quasi-static approximation, we provided an applicability range of this approach as a function of the nanoparticle size, paving the way to the theoretical study of the coupling between molecular electron densities and metal nanoparticles in GNB-based nanohybrid systems, with potential applications in the design of nanomaterials for bioimaging, optics and photocatalysis

Influence of stabilisers on the catalytic activity of supported Au colloidal nanoparticles for the liquid phase oxidation of glucose to glucaric acid: understanding the catalyst performance from NMR relaxation and computational studies

Supported Au colloidal nanoparticles have been prepared in the presence of stabilising polymers, such as, PVA, PVP and PEG (polyvinylalcohol, polyvinylpyrrolidone, polyethylene glycol). The effect of the polymer to Au weight ratio was investigated, for the synthesis of Au nanoparticles with varying particle size and particle size distribution. By varying the polymer/Au wt/wt ratio, Au nanoparticles with mean diameters from 3 to 8 nm were synthesised. The synthesised Au catalysts were studied in the liquid phase oxidation of glucose to glucaric acid under alkaline conditions. We demonstrated that the choice of polymer and polymer to Au weight ratio, have an important influence in terms of catalytic activity and yield to glucaric acid. The highest yield to glucaric acid (22%) was obtained using Au–PVA catalysts. A strong deactivation was observed using Au catalysts. Further evaluation of the possible reasons for deactivation were investigated using experimental, computational and NMR relaxation studies

Impact Forecasting to Support Emergency Management of Natural Hazards

Forecasting and early warning systems are important investments to protect lives, properties, and livelihood. While early warning systems are frequently used to predict the magnitude, location, and timing of potentially damaging events, these systems rarely provide impact estimates, such as the expected amount and distribution of physical damage, human consequences, disruption of services, or financial loss. Complementing early warning systems with impact forecasts has a twofold advantage: It would provide decision makers with richer information to take informed decisions about emergency measures and focus the attention of different disciplines on a common target. This would allow capitalizing on synergies between different disciplines and boosting the development of multihazard early warning systems. This review discusses the state of the art in impact forecasting for a wide range of natural hazards. We outline the added value of impact-based warnings compared to hazard forecasting for the emergency phase, indicate challenges and pitfalls, and synthesize the review results across hazard types most relevant for Europe

Allostery in Its Many Disguises: From Theory to Applications.

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts

Long-term vitamin E supplementation fails to reduce lipid peroxidation in people at cardiovascular risk: analysis of underlying factors

BACKGROUND: Antioxidant supplementation with vitamin E had no effect in the prevention of cardiovascular diseases (CVD) in three recent large, randomized clinical trials. In order to reassess critically the role of vitamin E in CVD prevention, it is important to establish whether these results are related to a lack of antioxidant action. METHODS: We examined the in vivo antioxidant effect of vitamin E (300 mg/day for about three years) in 144 participants in the Primary Prevention Project (females and males, aged ≥ 50 y, with at least one major CV risk factor, but no history of CVD). Urinary 8-epi-PGF(2α) (isoprostane F(2α)-III or 15-F(2t)-isoP), a validated biomarker of lipid peroxidation, was measured by mass spectrometry. RESULTS: Urinary excretion of 8-epi-PGF(2α) [pg/mg creatinine, median (range)] was 141 (67–498) in treated and 148 (76–561) in untreated subjects (p = 0.10). Taking into account possible confounding variables, multiple regression analysis confirmed that vitamin E had no significant effect on this biomarker. Levels of 8-epi-PGF(2α) were in the normal range for most subjects, except smokers and those with uncontrolled blood pressure or hyperglycemia. CONCLUSIONS: Prolonged vitamin E supplementation did not reduce lipid peroxidation in subjects with major cardiovascular risk factors. The observation that the rate of lipid peroxidation was near normal in a large proportion of subjects may help explain why vitamin E was not effective as an antioxidant in the PPP study and was ineffective for CVD prevention in large scale trials

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations