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Structural properties of 2-butanol aqueous solutions at different concentrations have been studied using small- and wide-angle X-ray scattering and molecular dynamics simulations. The experimental structure factors have been accurately reproduced by the simulations, allowing one to explain their variation with concentration and to achieve a detailed description of the structural and dynamic properties of the studied systems. The analysis of experimental and computational data has shown that 2-butanol, the simplest aliphatic chiral alcohol, tends to form aggregates at a concentration above 1 M, affecting also both the structural and dynamic properties of the solvent.

Hypothesis The study of Amorphous Calcium Phosphate (ACP) has become a hot topic due to its relevance in living organisms and as a material for biomedical applications. The preparation and characterization of Mg-substituted ACP nanoparticles (AMCP) with tunable Ca/Mg ratio is reported in the present study to address the effect of Mg2+ on their structure and stability. Experiments AMCPs particles were synthesized by precipitation of the precursors from aqueous solutions. The particles were analyzed in terms of morphology, crystallinity, and thermal stability, to get a complete overview of their physico-chemical characteristics. Computational methods were also employed to simulate the structure of ACP clusters at different levels of Mg2+ substitution. Findings Our results demonstrate that AMCP particles with tunable composition and crystallinity can be obtained. The analysis of the heat-induced crystallization of AMCP shows that particles’ stability depends on the degree of Mg2+ substitution in the cluster, as confirmed by computational analyses. The presented results shed light on the effect of Mg2+ on ACP features at different structural levels and may be useful guidelines for the preparation and design of AMCP particles with a specific Ca/Mg ratio.

In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CLpro) of SARS-CoV-2. The core structures of 3CLpro ligands were previously identified using a multimodal structure-based ligand design in combination with docking techniques. The calculated binding free energies for four additional ligands with known activity (either for SARS-CoV or SARS-CoV-2 main protease) are also reported. The nature of binding in the 3CLpro active site and the involved residues besides the CYS-HYS catalytic dyad have been thoroughly characterized by enhanced sampling simulations of the bound state. We have identified several noncongeneric compounds with predicted low micromolar activity for 3CLpro inhibition, which may constitute possible lead compounds for the development of antiviral agents in Covid-19 treatment.

Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S2) of all backbone N-H bond vectors in each system. These data were superimposed to heteronuclear Overhauser effect measurements taken by NMR spectroscopy. This provides a quantitative estimate of the accuracy of the FFs in reproducing protein dynamics, leveraging the information about the protein backbone mobility contained in the NMR data. The correlation between the MD-computed S2 and the experimental data indicated that both tested FFs reproduce well the dynamic behavior of zinc(II)-proteins, with comparable accuracy. Thus, along with ZAFF, NBFF represents a useful tool to simulate metalloproteins with the advantage of being extensible to diverse systems such as those bearing dinuclear metal sites.

Self assembled ordered structures, such as H- or J- type molecular aggregates of organic chromophores, are extremely interesting materials for different optoelectronic applications. In this work we present a novel characterization of light harvesting nanotubes formed by self-assembling of amphiphilic cyanine dyes in water, through a combined ultrafast spectroscopic and theoretical approach. In the condition of low inhomogeneous disorder at low temperature, broadband transient absorption spectroscopy revealed the presence of an unusual ultrafast behavior of the aggregate, manifested through intense and peculiar oscillations of the kinetic traces, lasting tens of picoseconds. Theoretical simulations were performed by adapting a model which grasps vibronically coherent effects in the double wall nanotube system experiencing inter-wall energy transfer. Good agreement between model predictions and experimental observations were obtained under the assumption of coupling between bright and dark electronic states. The model clarified the vibronic origin of the observed oscillations, evidencing new important pieces of information about transport mechanisms and excitonic interactions in these complex molecular systems.

Water has a fundamental role in important processes spanning a wide range of pressure and temperature conditions. Knowledge of structural, dynamic and thermodynamic properties of water at nonstandard conditions is a primary concern since interest in astronomical, geological, and technological processes is continuously growing. Molecular dynamics simulations allow us to study thermodynamic conditions that require sophisticated techniques and instruments, while at the same time offering the interpretation of properties at the atomic level. It is established that the behavior of water is strongly affected by the temperature and pressure conditions, determining the existence of low and high density regimes. For the first time, a thermodynamic property, isothermal compressibility, has been adopted to detect the low-high density turning point at ambient temperature in liquid water due to pressure. Molecular dynamics simulations have been performed with five three-site models, allowing us to characterize the complexity of water nature at these conditions at the atomic level.

The complete path of the Brandi-Guarna rearrangement of 5-spirocyclopropane isoxazolidines has been investigated by means of density functional theory calculations to rationalize the competing formation of tetrahydropyridones and enaminones by the determination of the minimum energy reaction paths. Our calculations confirm that the rearrangement is triggered by the homolysis of the isoxazolidine N-O bond followed by cleavage of one of the two C-CH2 cyclopropane bonds as previously proposed by the Fabian group [ Eur. J. Org. Chem. 2001, 2001, 4223]. In addition, the results of this work suggest that in the presence of a stereogenic center at isoxazolidine C-4', the formation of a piperidinone or an enaminone as the final product depends on which of the two diastereotopic C-CH2 bonds of cyclopropane is cleaved in the second step of the process. The result can be of great interest for the understanding of other processes involving the opening of a cyclopropane ring.

Underwater vehicle propulsion performed by exploiting electrical motor is in general the most flexible solution and it is growing in popularity because of its high efficiency both at high and at low advance speed, quick and simple deployment, low costs, and encumbrance. In the present work, permanent magnet synchronous motors for underwater propulsion are proposed. In particular, advanced sensorless control techniques of permanent magnet synchronous motors permit reduced costs, high reliability, and performances. When dealing with small autonomous underwater vehicle propulsion, such devices are hard to find in the market. Hence, the authors focused the research in the development of a system able to perform a reliable rotational speed and torque sensorless estimation. The design and implementation of a complete solution for underwater propulsion are presented as well as a novel rotor polarity identification technique exploiting a high-frequency injection control. Pool tests for the identification of the performances and of the dynamic parameters of the propulsion system are presented. Finally, the possibility of operating a sensorless estimation of the thrust and torque exerted by the propeller and pool test measurements are presented. These features could be exploited to improve navigation accuracy and involves obvious benefits in terms of cost reduction and reliability of the system.

We have applied a computational strategy, using a combination of virtual screening, docking and molecular dynamics techniques, aimed at identifying possible lead compounds for the non-covalent inhibition of the main protease 3CLpro of the SARS-CoV2 Coronavirus. Based on the X-ray structure (PDB code: 6LU7), ligands were generated using a multimodal structure-based design and then docked to the monomer in the active state. Docking calculations show that ligand-binding is strikingly similar in SARS-CoV and SARS-CoV2 main proteases. The most potent docked ligands are found to share a common binding pattern with aromatic moieties connected by rotatable bonds in a pseudo-linear arrangement.

The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.

The spectroscopic properties of As4S4 with pressure have been computed by the quantum mechanical XP-PCM method and by density functional theory periodic calculations. The comparison has allowed the interpretation of the available experimental data. By comparison of the two methods and with experiments, we show that the XP-PCM method is able to reproduce the same behavior of the periodic calculations with much lower computational cost allowing to be adopted as a first choice computational tool for a qualitative interpretation of molecular crystals properties under pressure.

A correct description of electrostatic contributions in force fields for classical simulations is mandatory for an accurate modeling of molecular interactions in pure liquids or solutions. Here, we propose a new protocol for point charge fitting, aimed to take into the proper account different polarization effects due to the environment employing virtual sites and tuning the point charge within the polarizable continuum model framework. The protocol has been validated by means of molecular dynamics simulations on pure pyridine liquid and on pyridine aqueous solution, reproducing a series of experimental observables and providing the information for their correct interpretation at atomic level. A correct description of electrostatic contributions in force fields for classical simulations is mandatory for an accurate modeling of molecular interactions in pure liquids or solutions. Here, we propose a new protocol for point charge fitting, aimed to take into the proper account different polarization effects due to the environment employing virtual sites and tuning the point charge within the polarizable continuum model framework. The protocol has been validated by means of molecular dynamics simulations on pure pyridine liquid and on pyridine aqueous solution, reproducing a series of experimental observables and providing the information for their correct interpretation at atomic level.

The analysis of red particles in paint cross-sections from Leonardo da Vinci's Last Supper, Masolino da Panicale's wall painting Beheading of St. John the Baptist in Castiglione Olona, Tintoretto's The Discovery of the Body of Saint Mark and Paolo Veronese's Supper in the House of Simon has been carried out with micro-Raman measurements. Subtracted shifted Raman spectroscopy methods have been employed to resolve the signals in the presence of fluorescence. Taking advantage of the vibrational assignments based on recent ab initio calculations of aluminum-complexes of anthraquinones, the approach allowed the discriminate between anthraquinone dyes and lakes based on kermesic and carminic acids present in the studied samples for the first time without heavy sample treatment.

– The identification of adenine by surface enhanced Raman scattering (SERS) on different mineral phases of a Martian meteorite Dar al Gani (DaG) 670 has been adopted as a test to verify the capability of this technique to detect trace amounts of organic or biological substances deposited over, or contained in, extraterrestrial materials. Raman spectra of different phases of meteorite (olivine, pyroxene, and ilmenite), representative of Martian basaltic rocks, have been measured by three laser sources with wavelengths at 785, 632.8, and 514.5 nm, coupled to a confocal micro-Raman apparatus. Adenine deposited on the Martian meteorite cannot be observed in the normal Raman spectra; when, instead, meteorite is treated with silver colloidal nanoparticles, the SERS bands of adenine are strongly enhanced, allowing an easy and simple identification of this nucleobase at subpicogram level.

The hydrogen-bond dynamics of lithium nitrate trihydrate has been studied by a combined approach based on ab initio molecular dynamics simulations and wavelet analysis. The simultaneous bifurcated interaction between one hydrogen atom of water molecules and two oxygen atoms of nitrate ions is the pivotal feature of the crystal structure: this bifurcated interaction has deep effects on the O-H stretching region of the vibrational spectrum. The structural, dynamic, spectroscopic, and electronic properties of the bifurcated hydrogen bond have been investigated computationally, elucidating at the molecular level the differences with weak and strong hydrogen bonds present in the crystal. These studies corroborate the very recent IR experiments performed on the lithium nitrate trihydrate crystal, offering new perspectives to interpreting the vibrational spectra. In fact, this approach allows obtaining two-dimensional plots, which summarize the essential features of both the hydrogen-bond network and IR spectra, resulting in a peculiar "signature" of the bifurcated interaction.

The identification of two nucleobases (adenine and hypoxanthine) by Surface-Enhanced Raman Scattering (SERS) on different mineral substrates was adopted as a test case to verify the capability of this analytical technique to detect trace amounts of organic or biological substances deposited over, or contained in, Martian regolith. Raman spectra were collected on polished samples of calcite, dolomite, magnesite, siderite, anhydrite, and gypsum, onto which traces of nucleobases were added. While spectroscopic features of the two nucleobases could not be observed in normal Raman spectrum, the addition of silver nanoparticles allowed easy identification of the vibrational bands characteristic of the two nucleobases.

Four nanostructured Ag substrates have been fabricated with different surface morphologies and tested with surface-enhanced Raman scattering (SERS) experiments by adsorption of adenine. Their SERS efficiency has been compared and related to the surface roughness resulting from atomic force microscopy measurements. Chemical etching of silver by thiourea/Fe(III)nitrate produces homogeneously roughened plates, exhibiting the largest three-dimensional surface and the best SERS enhancement. They mostly exhibit surface protrusions with sizes around 200 nm, thus matching the best condition for obtaining SERS enhancement by laser excitation at 785 nm. This is quite important in the case of biomolecules, whose samples often present strong fluorescence bands, which usually are not observed with red-shifted exciting lines. Moreover, these Ag platforms, owing to their uniform nanostructured surfaces, are suitable for obtaining reproducible results from microRaman investigation. In conclusion, the present nanofabrication of Ag surfaces allows obtaining SERS-active substrates, which combine high reproducibility and sensitivity and can be successfully employed in the molecular recognition of different organic ligands or biomolecules like nucleic acids and proteins.

In order to extract spectroscopic information from trajectories obtained by classical or ab initio molecular dynamics simulations, usually Fourier transforms are employed. In recent years wavelet transforms have been shown to be a valid alternative tool to analyze time-series, due to their capability of localizing a signal both in time and frequency. In this article wavelet transforms are applied for the analysis of Car-Parrinello molecular dynamics simulations to the purpose of time-correlating structural and spectroscopic properties of methyl acetate dissolved in water and methanol. The results demonstrate the possibility of obtaining information that may be of valuable help in the interpretation of time-resolved spectroscopic data.

Ab initio molecular dynamics simulations with the Car–Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.

A conclusive study on the SERS band of pyridine occurring at about 1025 cm −1 was performed by a density functional theory (DFT) approach, by considering the ligand molecules bound to silver adclusters. The existence of (Ag 3 ) +2 surface active-sites, ascertained in Ag/SiO 2 colloids as metal adclusters stabilised by the interaction with the silica nanoparticles, was confirmed by DFT calculations, which satisfactorily account for the experimental findings.

A review of the recent theoretical and computational activity at the Chemistry Department of the University of Firenze in the field of molecular simulations of condensed phases is reported. The topics considered include quantitative methods for accurate free energy calculations, molecular dynamics of liquids and ionic solutions, chemical reactions in solutions, phase transformations and polymerization reactions at high pressures.

A Car-Parrinello molecular dynamics simulation has been performed on a solution of Br- in liquid methanol analyzing with particular attention charge transfer and polarization effects. The first solvation shell has been characterized in terms of H-bonds, and it has been found that the high polarization of the bromide gives rise to a stable solvent cage. The differences in the coordination number with the chloride can be ascribed to the ionic radius and to the stronger perturbations brought by the solvent to the bromide ion.

When the free energy surface of the lithium hydroxide monohydrate crystal was explored, the high-pressure solid-state phase transition was determined. The high-pressure phase has been obtained through ab initio Car-Parrinello molecular dynamics simulation in the isothermic-isobaric ensemble. The recent metadynamics method has been applied to overcome the high activation energy barriers typical of rare events, like solid-state phase transition at high pressures. In the LiOH x H2O system, there are two kinds of H bonds: water-water and hydroxyl-water. The effect of the pressure has been investigated, to give further insight into the high-pressure phase. The strengthening of the H bonds of the system produces modifications in the water and the hydroxyl ion dipole electronic environment. The infrared spectra of both phases have been calculated and compared with experiments, and the assignment of the external modes has been discussed.

A Car–Parrinello molecular dynamics simulation has been performed on fully deuterated liquid methanol. The results are compared with the latest available experimental and theoretical data. It is shown that the liquid is aggregated in chains of hydrogen bonded molecules. The structure of the aggregates is characterized and it is found that the dynamics includes a fast and a slow regime. The weak H bond formed by the methyl group hydrogens and oxygen atom of surrounding molecules has been characterized. The importance of inductive effects is shown and discussed in terms of maximally localized Wannier function centers. Special attention is devoted to clarify how the molecular dipole moment depends on the number of H bonds formed by each molecule. The IR spectrum is computed and analyzed in terms of H-bond interactions. Insights on the short time dynamics and on the H-bond network are illustrated.

The solvation dynamics of methyl acetate in heavy water are analyzed by means of two-dimensional infrared spectroscopy, in conjunction with Car-Parrinello molecular dynamics simulations. The C horizontal lineO stretching infrared band of methyl acetate in water splits into a doublet as a consequence of the hydrogen bond interaction with the solvent, which leads to the equilibrium between two solvated species, consisting of one methyl acetate molecule bonded to one and two water molecules. The structure and dynamics of the water molecules bound to methyl acetate are characterized by means of experiments and simulations, allowing an accurate description of the kinetics of the exchange process and the lifetime of the hydrogen bond.

The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.

Electronic polarization response in hydrogen-bond clusters and liquid configurations of water and methanol has been studied by density functional theory (DFT) and by a polarizable force field based on the chemical potential equalization (CPE) principle. It has been shown that an accurate CPE parametrization based on isolated molecular properties is not completely transferable to strongly interacting hydrogen-bond clusters with discrepancies between CPE and DFT overall dipole moments as large as 15%. This is due to the lack of intermolecular charge transfer in the standard CPE implementation. A CPE scheme for evaluating the amount of transferred charge has been developed. The charge transfer parameters are determined with the aid of accurate DFT calculations using only hydrogen-bond dimer configurations. The amount of transferred charge is found to be of the order of few hundredths of electrons, as already found in recent studies on hydrogen-bond systems. The parameters of the model are then used, without further adjustment, to different hydrogen-bond clustered forms of water and methanol (oligomer and liquid configurations). In agreement with different approaches proposed in literature for studying charge transfer effects, the transferred charge in hydrogen-bond dimers is found to decrease exponentially with the hydrogen-bond distance. When allowance is made for charge transfer according to the proposed scheme, the CPE dipole moments are found to reproduce satisfactorily the DFT data.