Shape and Morphology Effects on the Electronic Structure of TiO2 Nanostructures: From Nanocrystals to Nanorods

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Chemical bond analysis for the entire periodic table: Energy Decomposition and Natural Orbitals for Chemical Valence in the Four-Component Relativistic Framework

Chemical bonding is a ubiquitous concept in chemistry and it provides a common basis for experimental and theoretical chemists to explain and predict the structure, stability and reactivity of chemical species. Among others, the Energy Decomposition Analysis (EDA, also known as the Extended Transition State method) in combination with Natural Orbitals for Chemical Valence (EDA-NOCV) is a very powerful tool for the analysis of the chemical bonds based on a charge and energy decomposition scheme within a common theoretical framework. While the approach has been applied in a variety of chemical contexts, the current implementations of the EDA-NOCV scheme include relativistic effects only at scalar level, so simply neglecting the spin-orbit coupling effects and de facto limiting its applicability. In this work, we extend the EDA-NOCV method to the relativistic four-component Dirac-Kohn-Sham theory that variationally accounts for spin-orbit coupling. Its correctness and numerical stability have been demonstrated in the case of simple molecular systems, where the relativistic effects play a negligible role, by comparison with the implementation available in the ADF modelling suite (using the non-relativistic Hamiltonian and the scalar ZORA approximation). As an illustrative example we analyse the metal-ethylene coordination bond in the group 6-element series (CO)$_5$TM-C$_2$H$_4$, with TM =Cr, Mo, W, Sg, where relativistic effects are likely to play an increasingly important role as one moves down the group. The method provides a clear measure (also in combination with the CD analysis) of the donation and back-donation components in coordination bonds, even when relativistic effects, including spin-orbit coupling, are crucial for understanding the chemical bond involving heavy and superheavy atoms.Comment: 49 pages, 2 figure

Environmental effects with Frozen Density Embedding in Real-Time Time-Dependent Density Functional Theory using localized basis functions

Frozen Density Embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on the electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane-waves and periodic boundary conditions (Pavanello et al. J. Chem. Phys. 142, 154116, 2015). In the current paper, we extend our recent formulation of real-time time-dependent Kohn-Sham method based on localized basis set functions and developed within the Psi4NumPy framework (De Santis et al. J. Chem. Theory Comput. 2020, 16, 2410) to the FDE scheme. The latter has been implemented in its "uncoupled" flavor (in which the time evolution is only carried out for the active subsystem, while the environment subsystems remain at their ground state), using and adapting the FDE implementation already available in the PyEmbed module of the scripting framework PyADF. The implementation was facilitated by the fact that both Psi4NumPy and PyADF, being native Python API, provided an ideal framework of development using the Python advantages in terms of code readability and reusability. We demonstrate that the inclusion of the FDE potential does not introduce any numerical instability in time propagation of the density matrix of the active subsystem and in the limit of weak external field, the numerical results for low-lying transition energies are consistent with those obtained using the reference FDE calculations based on the linear response TDDFT. The method is found to give stable numerical results also in the presence of strong external field inducing non-linear effects

Implementation and Use of a Direct, Partially Integral-Driven Non-Dyson Propagator Method for Molecular Ionization

Abstract: The Green's function ADC(3) scheme has been for many years a successful method to predict theoretically the ionization (and electron affinity) spectrum of molecules. However, a dramatic enhancement of the method's power has come only recently, with the development of an approximation method to the one-particle Green's function which does not make direct use of the Dyson equation. In the present work, we present an efficient computer implementation of this novel approach, with first comparative tests demonstrating its enormous computational advantage over the conventional approach

Gold-superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study

The chemistry of superheavy elements (Z \ue2\u89\ua5 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis

A Continuous-Time Inequality Measure Applied to Financial Risk: The Case of the European Union

In this paper, we apply information theory measures and Markov processes in order to analyse the inequality in the distribution of the financial risk in a pool of countries. The considered financial variables are sovereign credit ratings and interest rates of sovereign government bonds of European countries. This paper extends the methodology proposed in our previous work, by allowing the possibility to consider a continuous time process for the credit rating evolution so that complete observations of rating histories and credit spreads can be considered in the analysis. Obtained results suggest that the continuous time model fits real data better than the discrete one and confirm the existence of a different risk perception among the three main rating agencies: Fitch, Moody’s and Standard & Poor’s. The application of the model has been performed by a software we developed, the full code is available on-line allowing the replication of all results

The Effects of Ca²⁺ Concentration and E200K Mutation on the Aggregation Propensity of PrP^C: A Computational Study

<div><p>The propensity of cellular prion protein to aggregation is reputed essential for the initiation of the amyloid cascade that ultimately lead to the accumulation of neurotoxic aggregates. In this paper, we extended and applied an already reported computational workflow [Proteins 2015; 83: 1751–1765] to elucidate in details the aggregation propensity of PrP protein systems including wild type, wild type treated at different [Ca²⁺] and E200K mutant. The application of the computational procedure to two segments of PrP^C, i.e. 125–228 and 120–231, allowed to emphasize how the inclusion of complete C-terminus and last portion (120–126) of the neurotoxic segment 106–126 may be crucial to unveil significant and unexpected interaction properties. Indeed, the anchoring of N-terminus on H2 domain detected in the wild type resulted to be disrupted upon either E200K mutation or Ca²⁺ binding, and to unbury hydrophobic spots on the PrP^C surface. A peculiar dinuclear Ca²⁺ binding motif formed by the C-terminus and the S2-H2 loop was detected for [Ca²⁺] > 5 mM and showed similarities with binding motifs retraced in other protein systems, thus suggesting a possible functional meaning for its formation. Therefore, we potentiated the computational procedure by including a tool that clusterize the minima of molecular interaction fields of a proteinand delimit the regions of space with higher hydrophobic or higher hydrophilic character, hence, more likely involved in the self-assembly process. Plausible models for the self-assembly of either the E200K mutated or Ca²⁺-bound PrP^C were sketched and discussed. The present investigation provides for structure-based information and new prompts that may represent a starting point for future experimental or computational works on the PrP^C aggregation.</p></div

Structural Reshaping of the Zinc-Finger Domain of the SARS-CoV‑2 nsp13 Protein Using Bismuth(III) Ions: A Multilevel Computational Study

The identification of novel therapeutics against the pandemic SARS-CoV-2 infection is an indispensable new address of current scientific research. In the search for anti-SARS-CoV-2 agents as alternatives to the vaccine or immune therapeutics whose efficacy naturally degrades with the occurrence of new variants, the salts of Bi3+ have been found to decrease the activity of the Zn2+-dependent non-structural protein 13 (nsp13) helicase, a key component of the SARS-CoV-2 molecular tool kit. Here, we present a multilevel computational investigation based on the articulation of DFT calculations, classical MD simulations, and MIF analyses, focused on the examination of the effects of Bi3+/Zn2+ exchange on the structure and molecular interaction features of the nsp13 protein. Our calculations confirmed that Bi3+ ions can replace Zn2+ in the zinc-finger metal centers and cause slight but appreciable structural modifications in the zinc-binding domain of nsp13. Nevertheless, by employing an in-house-developed ATOMIF tool, we evidenced that such a Bi3+/Zn2+ exchange may decrease the extension of a specific hydrophobic portion of nsp13, responsible for the interaction with the nsp12 protein. The present study provides for a detailed, atomistic insight into the potential anti-SARS-CoV-2 activity of Bi3+ and, more generally, evidences the hampering of the nsp13–nsp12 interaction as a plausible therapeutic strategy

Simplified scheme of the formation of PrP aggregates.

<p>Simplified scheme of the formation of PrP aggregates.</p