A5043968534- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
- Molecular spectroscopy and chirality
- Photochemistry and Electron Transfer Studies
- Cancer therapeutics and mechanisms
- Genetic and phenotypic traits in livestock
- Protein Structure and Dynamics
- Chemical and Physical Properties in Aqueous Solutions
- Animal Genetics and Reproduction
- Trace Elements in Health
- DNA and Nucleic Acid Chemistry
- Supramolecular Chemistry and Complexes
- X-ray Spectroscopy and Fluorescence Analysis
- Neurological diseases and metabolism
- Hemoglobin structure and function
- Electron Spin Resonance Studies
- Prion Diseases and Protein Misfolding
- Antibiotics Pharmacokinetics and Efficacy
- Machine Learning in Materials Science
- Molecular Spectroscopy and Structure
- Genetic Mapping and Diversity in Plants and Animals
- Ionic liquids properties and applications
- Crystallography and molecular interactions
- Porphyrin and Phthalocyanine Chemistry
- Electrochemical Analysis and Applications
Università degli Studi della Tuscia
2010-2025
Scuola Normale Superiore
2014-2023
Istituto Nazionale di Fisica Nucleare, Sezione di Pisa
2010-2022
Istituto Nazionale di Fisica Nucleare
2015-2021
University of Pisa
2016-2018
Consortium GARR
2009-2012
Centro Interuniversitario di Ricerca Per lo Sviluppo sostenibile
2009-2011
University of Rome Tor Vergata
2005-2009
Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari
2009
Sapienza University of Rome
2008
The accurate characterization of prototypical bricks life can strongly benefit from the integration high resolution spectroscopy and quantum mechanical computations. We have selected a number representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid asparagine) to validate new computational setup rooted in quantum-chemical computations increasing accuracy guided by machine learning tools. Together with low-lying energy minima, barriers ruling their...
X-ray absorption near-edge structure (XANES) spectroscopy has been used to determine the of hydrated strontium in aqueous solution. The XANES analysis carried out using solid [Sr(H2O)8](OH)2 as reference model. Classical and Car–Parrinello molecular dynamics (MD) simulations have former case two different sets Lennard-Jones parameters for Sr2+ ion. best performing theoretical approach chosen on basis experimental results. spectra calculated starting from MD trajectories, without carrying any...
Abstract The role of Virtual Reality (VR) tools in molecular sciences is analyzed this contribution through the presentation Caffeine software to quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, specifically tailored for representation and data visualization with VR systems, such as theaters helmets. Usefulness advantages that can be gained by exploiting are here reported, considering few examples selected illustrate different level theory representation.
A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter fact, generally accepted octahedral solvation ion cannot be reconciled with XAS results. Next, refined QM computations point out remarkable stability heptacoordinated structure C 2 symmetry, long-time MD simulations new interaction potentials...
Calving in cattle is affected by calf morphology and dam characteristics. It described two different traits: maternal calving ease, which the ability to generate dams with good physiological predisposition calving, direct calves that are easily born. The aim of this study was identify regions genome harboring genes possibly affecting ease Piedmontese breed. A population 323 bulls scored for (EBV) analyzed a medium-density SNP marker panel (54,001 SNPs) perform genome-wide scan. strongest...
Abstract Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence the water an prerequisite studying biology of this species, necessary to manage genetic diversity use modern breeding genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 domestic buffalo, river (2n = 50) swamp 48) buffalo. Here we describe draft quality created from Illumina GA Roche 454 short...
A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of methyl group significantly increases conformational complexity with respect to parent acid threonine. The landscape characterized in great detail, special attention given inter-conversion pathways between different conformers. This led identification 13 stable low-energy minima. equilibrium population so many conformers produces a very...
Urbanization poses significant challenges to ecosystems, resources, and human well-being, necessitating sustainable planning. Urban vegetation, particularly trees, provides critical ecosystem services such as carbon sequestration, air quality improvement, biodiversity conservation. Traditional tree assessments are resource-intensive time-consuming. Recent advances in remote sensing, especially high-resolution multispectral imagery object-based image analysis (OBIA), offer efficient...
A novel statistical procedure has been developed to optimize the parameters of nonbonded force fields metal ions in soft matter. The criterion for optimization is minimization deviations from ab initio forces and energies calculated model systems. method exploits combination linear ridge regression cross-validation techniques with differential evolution algorithm. Wide freedom choice functional form allowed since both nonlinear can be optimized. In order maximize information content data...
The Zn<sup>2+</sup>coordination structure changes when the Zn(Tf<sub>2</sub>N)<sub>2</sub>salt is dissolved in ionic liquids resulting more favorable interactions among solvent cations and anions.
Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure of water molecules on kaolinite surfaces confined in interlayer a halloysite model nanometric dimension. The first technique allowed us accurately describe tetrahedral-octahedral slab vacuum interaction with assess performance two widely employed empirical force fields water/clay interfaces. Classical were study hydrogen bond network adsorbed interlayer. results are...
The conversion of the prion protein (PrP(C)) into prions plays a key role in transmissible spongiform encephalopathies. Despite importance for pathogenesis, mechanism formation has escaped detailed characterization due to insoluble nature prions. PrP(C) interacts with copper through octarepeat and non-octarepeat binding sites. Copper coordination region garnered interest possibility that this interaction may impact conversion. We used X-ray absorption spectroscopy study at pH 5.5 7.0 human...
The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. computational protocol consists studying the solute solvation with accurate molecular dynamics simulations, characterizing hydrogen bond interactions, calculating transitions for series configurations extracted from trajectories polarizable QM/MM scheme based on fluctuating charge model. Molecular simulations transition calculations performed both nicotine....
X-ray absorption spectroscopy (XAS) has been employed to study the coordination of Ag+ ion in aqueous solution. The conjunction extended fine structure (EXAFS) and near-edge (XANES) data analysis provided results suggesting preference for a first shell linear with mean Ag–O bond distance 2.34(2) Å, different from generally accepted tetrahedral model longer distance. Ab initio molecular dynamics simulations Car–Parrinello approach (CPMD) were also performed able describe hydrated solution...
The fruitful interplay of high-resolution spectroscopy and quantum chemistry has a long history, especially in the field small, semi-rigid molecules. However, recent years, targets spectroscopic studies are shifting toward flexible molecules, characterized by large number closely spaced energy minima, all contributing to overall spectrum. Here, artificial intelligence comes into play since it is at basis powerful unsupervised techniques for exploration soft degrees freedom. Integration such...
The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration potential-energy landscapes is presented. based on modern consumer-grade technology and builds two key concepts: (a) reduction dimensionality surface process-tailored, physically meaningful generalized coordinates, (b) analogy between evolution a chemical process pathway through valleys (potential wells) mountain passes (saddle points) associated potential...
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective accurate strategies for investigation spectroscopic properties medium-to-large size chromophores in condensed phases. In this context we are developing a novel workflow aimed at improving generality, reliability, ease use available computational tools. paper report our latest developments with specific reference to unsupervised atomistic simulations...
This is the first systematic study exploring potentiality of X-ray absorption near edge structure (XANES) technique as a structural tool for systems containing lanthanoid(III) ions. A quantitative analysis XANES spectra at K- and L3-edges has been carried out three hydrated ions, namely, Yb, Nd, Gd, in aqueous solution isostructural trifluoromethanesulfonate salts. The dynamic properties ions have investigated by combined experimental-theoretical approach employing spectroscopy molecular...
The flexible nature of the first hydration shell cadmium(II) ion has been definitively assessed through an extensive study, combining X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations. structural dynamic properties have determined from long-time MD simulations, influence water-water interactions evaluated using SPC/E TIP5P water models. Comparison theoretical results with EXAFS data suggests that simulation provides a better description...
Molecular dynamics simulations of the Hg2+ ion in aqueous solution have been carried out using an effective two-body potential derived from quantum mechanical calculations. A stable heptacoordinated structure first hydration shell has observed and confirmed by extended X-ray absorption fine (EXAFS) experimental data. The structural properties shells investigated radial angular distribution functions, while dynamical behavior discussed terms reorientational correlation mean residence times...
The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy molecular dynamics (MD) simulations. This method allows one to perform quantitative analysis near-edge structure (XANES) spectra ionic solutions using proper description thermal fluctuations. XANES computed starting from MD trajectory, without carrying out any minimization parameter space....
The structure and dynamics of water in ionic solutions at high pressure have been investigated using a combined approach based on extended X-ray absorption fine (EXAFS) spectroscopy Molecular Dynamics (MD) simulations. Modification the hydration properties Zn2+ ion induced by increase from ambient condition up to ∼6.4 GPa has revealed accurately analyzed. With increasing first shell found retain an octahedral symmetry with shortening Zn–O distance 0.09 Å increased width associated thermal...
A number of methods are available to scan a genome for selection signatures by evaluating patterns diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is reliable approach detect regions under recent selective pressure. The objective this study was use identify that positive shared the most representative Italian dairy beef cattle total 3220 animals from Holstein (2179), Brown (775), Simmental (493), Marchigiana (485) Piedmontese (379) breeds were...
In this contribution we show that it is possible to build accurate force fields for small organic molecules allowing the reliable reproduction of a large panel bulk properties, which are seldom addressed in same context. Starting from results obtained recent studies, developed protocol charge estimation and virtual site generation amide class molecules. The parametrization electrostatic properties based on population analysis orbital localization quantum mechanical computations rooted...