*Sci Rep ; 10(1): 7742, 2020 May 08.*

##### RESUMO

X-ray diffraction, Amorphous silicon, Multi-objective optimization, Monte Carlo methods. This paper addresses a difficult inverse problem that involves the reconstruction of a three-dimensional model of tetrahedral amorphous semiconductors via inversion of diffraction data. By posing the material-structure determination as a multiobjective optimization program, it has been shown that the problem can be solved accurately using a few structural constraints, but no total-energy functionals/forces, which describe the local chemistry of amorphous networks. The approach yields highly realistic models of amorphous silicon, with no or only a few coordination defects (≤1%), a narrow bond-angle distribution of width 9-11.5°, and an electronic gap of 0.8-1.4 eV. These data-driven information-based models have been found to produce electronic and vibrational properties of a-Si that match accurately with experimental data and rival that of the Wooten-Winer-Weaire models. The study confirms the effectiveness of a multiobjective optimization approach to the structural determination of complex materials, and resolves a long-standing dispute concerning the uniqueness of a model of tetrahedral amorphous semiconductors obtained via inversion of diffraction data.

*Nanoscale ; 12(3): 1464-1477, 2020 Jan 23.*

##### RESUMO

The paper presents an ab initio study of temperature-induced nanostructural evolution of hydrogen-rich voids in amorphous silicon. By using large a-Si models, obtained from classical molecular-dynamics simulations, with a realistic void-volume density of 0.2%, the dynamics of Si and H atoms on the surface of the nanometer-size cavities were studied and their effects on the shape and size of the voids were examined using first-principles density-functional simulations. The results from ab initio calculations were compared with those obtained from using the modified Stillinger-Weber potential. The temperature-induced nanostructural evolution of the voids was examined by analyzing the three-dimensional distribution of Si and H atoms on/near void surfaces using the convex-hull approximation, and computing the radius of gyration of the corresponding convex hulls. A comparison of the results with those from the simulated values of the intensity in small-angle X-ray scattering of a-Si/a-Si:H in the Guinier approximation is also provided, along with a discussion on the dynamics of bonded and non-bonded hydrogen in the vicinity of voids.

*Phys Chem Chem Phys ; 20(29): 19546-19551, 2018 Jul 25.*

##### RESUMO

In this paper, we provide evidence that low density nano-porous amorphous carbon (a-C) consists of interconnected regions of amorphous graphene (a-G). We include experimental information in producing models, while retaining the power and accuracy of ab initio methods with no biasing assumptions. Our models are highly disordered with predominant sp2 bonding and ring connectivity mainly of sizes 5-8. The structural, dynamical and electronic signatures of our 3-D amorphous graphene are similar to those of monolayer amorphous graphene. We predict an extended x-ray absorption fine structure (EXAFS) signature of amorphous graphene. Electronic density of states calculations for 3-D amorphous graphene reveal similarity to monolayer amorphous graphene and the system is non conducting.

*J Chem Phys ; 148(20): 204503, 2018 May 28.*

##### RESUMO

It is widely accepted in the materials modeling community that defect-free realistic networks of amorphous silicon cannot be prepared by quenching from a molten state of silicon using classical or ab initio molecular-dynamics (MD) simulations. In this work, we address this long-standing problem by producing nearly defect-free ultra-large models of amorphous silicon, consisting of up to half a million atoms, using classical MD simulations. The structural, topological, electronic, and vibrational properties of the models are presented and compared with experimental data. A comparison of the models with those obtained from using the modified Wooten-Winer-Weaire bond-switching algorithm shows that the models are on par with the latter, which were generated via event-based total-energy relaxations of atomistic networks in the configuration space. The MD models produced in this work represent the highest quality of amorphous-silicon networks so far reported in the literature using MD simulations.

*J Phys Chem A ; 120(51): 10216-10222, 2016 Dec 29.*

##### RESUMO

The presence of counterions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent re-formation, and ligand exchanges. In this work, it is shown how halide (Cl-, Br-) and perchlorate (ClO4-) anions affect the strength of the primary solvent coordination shells around Th4+ using explicit-solvent and finite-temperature ab initio molecular dynamics modeling methods. The 9-fold solvent geometry was found to be the most stable hydration structure in each aqueous solution. Relative to the dilute aqueous solution, the presence of the counterions did not significantly alter the geometry of the primary hydration shell. However, the free energy analyses indicated that the 10-fold hydrated states were thermodynamically accessible in dilute and bromide aqueous solutions within 1 kcal/mol. Analysis of the results showed that the hydrogen bond lifetimes were longer and solvent exchange energy barriers were larger in solutions with counterions in comparison with the solution with no counterions. This implies that the presence of the counterions induces a strengthening of the Th4+ hydration shell.

*Inorg Chem ; 51(5): 3016-24, 2012 Mar 05.*

##### RESUMO

Ab initio molecular dynamics simulations at 300 K, based on density functional theory, are performed to study the hydration shell geometries, solvent dipole, and first hydrolysis reaction of the uranium(IV) (U(4+)) and uranyl(V) (UO(2)(+)) ions in aqueous solution. The solvent dipole and first hydrolysis reaction of aqueous uranyl(VI) (UO(2)(2+)) are also probed. The first shell of U(4+) is coordinated by 8-9 water ligands, with an average U-O distance of 2.42 Å. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 Å, respectively. The simulated EXAFS of U(4+) matches well with recent experimental data. The first shell of UO(2)(+) is coordinated by five water ligands in the equatorial plane, with the average UâO(ax) and U-O distances being 1.85 Å and 2.54 Å, respectively. Overall, the hydration shell structure of UO(2)(+) closely matches that of UO(2)(2+), except for small expansions in the average UâO(ax) and U-O distances. Each ion strongly polarizes their respective first-shell water ligands. The computed acidity constants (pK(a)) of U(4+) and UO(2)(2+) are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24, respectively. The predicted pK(a) value of UO(2)(+) is 8.5.

*J Phys Chem A ; 115(18): 4665-77, 2011 May 12.*

##### RESUMO

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 Å and 4.67-4.75 Å respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 Å. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.

##### Assuntos

Cúrio/química , Simulação de Dinâmica Molecular , Teoria Quântica , Termodinâmica , Modelos Moleculares , Estrutura Molecular , Soluções , Água/química*J Phys Condens Matter ; 21(26): 265801, 2009 Jul 01.*

##### RESUMO

Localized basis ab initio molecular dynamics simulation within the density functional framework has been used to generate realistic configurations of amorphous silicon carbide (a-SiC). Our approach consists of constructing a set of smart initial configurations that conform to essential geometrical and structural aspects of the materials obtained from experimental data, which is subsequently driven via a first-principles force field to obtain the best solution in a reduced solution space. A combination of a priori information (primarily structural and topological) along with the ab initio optimization of the total energy makes it possible to model a large system size (1000 atoms) without compromising the quantum mechanical accuracy of the force field to describe the complex bonding chemistry of Si and C. The structural, electronic and vibrational properties of the models have been studied and compared to existing theoretical models and available data from experiments. We demonstrate that the approach is capable of producing large, realistic configurations of a-SiC from first-principles simulation that display its excellent structural and electronic properties. Our study reveals the presence of predominant short range order in the material originating from heteronuclear Si-C bonds with a coordination defect concentration as small as 5% and a chemical disorder parameter of about 8%.