Correction: Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra

Correction for 'Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra' by Silvio Pipolo et al., Org. Biomol. Chem., 2011, 9, 5149–5155

Equation of Motion for the Solvent Polarization Apparent Charges in the Polarizable Continuum Model: Application to Time-Dependent CI

The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion (EOM) for the apparent solvent polarization charges that generate the reaction field in the Polarizable Continuum Model (PCM) for solvation and we have coupled them to a real-time time-dependent density functional theory (RT TDDFT) description of the solute [Corni et al. J. Phys. Chem. A 119, 5405 (2014)]. Here we present an extension of the EOM-PCM approach to a Time-Dependent Configuration Interaction (TD CI) description of the solute dynamics, which is free from the qualitative artifacts of RT TDDFT in the adiabatic approximation. As tests of the developed approach, we investigate the solvent Debye relaxation after an electronic excitation of the solute obtained either by a $\pi$ pulse of light or by assuming the idealized sudden promotion to the excited state. Moreover, we present EOM for the Onsager solvation model and we compare the results with PCM. The developed approach provides qualitatively correct real-time evolutions and is promising as a general tool to investigate the electron dynamics elicited by external electromagnetic fields for molecules in solution.Comment: This is the final peer-reviewed manuscript accepted for publication in The Journal of Chemical Physics. Copyright by AIP, the final published version can be found at http://scitation.aip.org/content/aip/journal/jcp/146/6/10.1063/1.497562

Real-Time Description of the Electronic Dynamics for a Molecule close to a Plasmonic Nanoparticle

The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems in a Quantum Chemistry perspective, one has to take into account that the plasmonic nanostructure (e.g., a metal nanoparticle - NP) is often too large to be treated atomistically. Therefore, a multiscale description, where the molecule is treated by an ab initio approach and the metal NP by a lower level description, is needed. Here we present an extension of one such multiscale model [Corni, S.; Tomasi, J. {\it J. Chem. Phys.} {\bf 2001}, {\it 114}, 3739] originally inspired by the Polarizable Continuum Model, to a real-time description of the electronic dynamics of the molecule and of the NP. In particular, we adopt a Time-Dependent Configuration Interaction (TD CI) approach for the molecule, the metal NP is described as a continuous dielectric of complex shape characterized by a Drude-Lorentz dielectric function and the molecule- NP electromagnetic coupling is treated by an equation-of-motion (EOM) extension of the quasi-static Boundary Element Method (BEM). The model includes the effects of both the mutual molecule- NP time-dependent polarization and the modification of the probing electromagnetic field due to the plasmonic resonances of the NP. Finally, such an approach is applied to the investigation of the light absorption of a model chromophore, LiCN, in the presence of a metal NP of complex shape.Comment: This is the final peer-reviewed manuscript accepted for publication of an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. Link to the original article: http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.6b1108

Power Flow Management by Active Nodes: A Case Study in Real Operating Conditions

The role of distributor system operators is experiencing a gradual but relevant change to include enhanced ancillary and energy dispatch services needed to manage the increased power provided by intermittent distributed generations in medium voltage networks. In this context, the paper proposes the insertion, in strategic points of the network, of specific power electronic systems, denoted as active nodes, which permit the remote controllability of the active and reactive power flow. Such capabilities, as a further benefit, enable the distributor system operators to provide ancillary network services without requiring any procurement with distributed generation systems owners. In particular, the paper highlights the benefits of active nodes, demonstrating their capabilities in reducing the inverse power flow issues from medium to high voltage lines focusing on a network cluster including renewable energy resources. As a further novelty, this study has accounted for a real cluster operated by the Italian distributor system operator Areti. A specific simulation model of the electrical lines has been implemented in DigSilent PowerFactory (DIgSILENT GmbH–Germany) software using real operating data obtained during a 1-year measurement campaign. A detailed cost-benefit analysis has been provided, accounting for different load flow scenarios. The results have demonstrated that the inclusion of active nodes can significantly reduce the drawbacks related to the reverse power flow

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light–matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).This work was supported by the European Research Council (Grant No. ERC-2015-AdG694097), the Cluster of Excellence “Advanced Imaging of Matter” (AIM), Grupos Consolidados (IT1249-19), and SFB925. The Flatiron Institute is a division of the Simons Foundation. X.A., A.W., and A.C. acknowledge that part of this work was performed under the auspices of the U.S. Department of Energy at Lawrence Livermore National Laboratory under Contract No. DE-AC52-07A27344. J.J.-S. gratefully acknowledges the funding from the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie Grant Agreement No. 795246-StrongLights. J.F. acknowledges financial support from the Deutsche Forschungsgemeinschaft (DFG Forschungsstipendium FL 997/1-1). D.A.S. acknowledges University of California, Merced start-up funding.Peer reviewe

Simulating complex transformation in condensed matter

International audienc

On the Binding Free Energy and Molecular Origin of Sickle Cell Hemoglobin Aggregation

International audienceProtein aggregation is associated with various diseases, including Alzheimer and Parkinson as well as sickle cell disease (SCD). From a molecular point of view, protein aggregation depends on a complex balance of electrostatic and hydrophobic interactions mediated by water. An impressive manifestation of the importance of this balance concerns the human hemoglobin (HbA) mutant, HbS (sickle cell Hb), where a single substitution at the 6th position of HbA β-chains, from glutamic acid to valine, causes the polymerization of deoxygenated HbS (deoxy-HbS), responsible for SCD. HbS polymerization is believed to occur via a double nucleation mechanism initiated by the formation of HbS fibers (homogeneous nucleation), followed by fiber growth. Furthermore, it was proposed that homogeneous nucleation proceeds through a two-step mechanism, where metastable dense clusters play the role of nucleation precursors. Thus, hindering or delaying the formation of such precursors could represent a potential SCD therapeutic route. Here, we study, through molecular dynamics, the binding free energy and protein–protein contacts involved in the deoxy-HbS dimer aggregation and stabilization process. A binding free energy of ∼−14.0 ± 1 kcal/mol is estimated from a one-dimensional potential of mean force. Analysis of protein–protein interactions shows that both electrostatic and van der Waals interactions play an important role on the aggregation of HbS. With respect to the former, our results indicate that aggregation is largely favored by the formation of salt bridges (SB), mostly, Lys–Glu, Lys–Asp, and Heme-Lys SB, which outweigh electrostatic repulsions involving similar residues. Thus, our results suggest that a potential antisickling drug could be one with the ability to weaken or hinder the formation of a few SB between carboxylate and ammonium groups