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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.

A water-soluble ruthenium(II) complex (L), capable of producing singlet oxygen (

A detailed understanding and interpretation of absorption spectra of molecular systems, especially in condensed phases, requires computational models that allow their structural and electronic features to be connected to the observed macroscopic spectra. This work is focused on modeling the electronic absorption spectrum of a fluorescent probe, namely, the 9-(4-((bis(2-((2-(ethylthio)ethyl)thio)ethyl)amino)methyl)phenyl)-6-(pyrrolidin-1-yl)-3

We describe a step-by-step protocol for the computation of relative dissociation free energy with GROMACS, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows to compute with good accuracy the RBFE between small molecules with arbitrary differences in volume, charge and Tanimoto index. The procedure is illustrated for the challenging SAMPL9 batch on the tutorial https://procacci.github.io/vdssb_gromacs/NE-RDFE/

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.

Grimme's dispersion-corrected density functional theory (DFT-D) methods have emerged among the most practical approaches to perform accurate quantum mechanical calculations on molecular systems ranging from small clusters to microscopic and mesoscopic samples, i.e., including hundreds or thousands of molecules. Moreover, DFT-D functionals can be easily integrated into popular ab initio molecular dynamics (MD) software packages to carry out first-principles condensed-phase simulations at an affordable computational cost. Here, starting from the well-established D3 version of the dispersion-correction term, we present a simple protocol to improve the accurate description of the intermolecular interactions of molecular clusters of growing size, considering acetonitrile as a test case. Optimization of the interaction energy was performed with reference to diffusion quantum Monte Carlo calculations, successfully reaching the same inherent accuracy of the latter (statistical error of ∼0.1 kcal/mol per molecule). The refined DFT-D3 model was then used to perform ab initio MD simulations of liquid acetonitrile, again showing significant improvements toward available experimental data with respect to the default correction.

5-Nitroimidazole (5NIMH), chosen as a molecular model of nitroimidazole derivatives, which represent a broad-spectrum class of antimicrobials, was incorporated into the ruthenium complexes [Ru(tpy)(phen)(5NIM)]PF6 (1) and [Ru(tpy)(dmp)(5NIM)]PF6 (2) (tpy = terpyridine, phen = phenanthroline, dmp = 2,9-dimethyl-1,10-phenanthroline). Besides the uncommon metal coordination of 5-nitroimidazole in its imidazolate form (5NIM), the different architectures of the spectator ligands (phen and dmp) were exploited to tune the "mode of action" of the resulting complexes, passing from a photostable compound where the redox properties of 5NIMH are preserved (1) to one suitable for the nitroimidazole phototriggered release (2) and whose antibacterial activity against B. subtilis, chosen as cellular model, is effectively improved upon light exposure. This study may provide a fundamental knowledge on the use of Ru(II)-polypyridyl complexes to incorporate and/or photorelease biologically relevant nitroimidazole derivatives in the design of a novel class of antimicrobials.

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.

The structural and vibrational properties of the molecular units of sulfur hexafluoride crystal as a function of pressure have been studied by the Extreme Pressure Polarizable Continuum Model (XP-PCM) method. Within the XP-PCM model, single molecule calculations allow a consistent interpretation of the experimental measurements when considering the effect of pressure on both the molecular structure and the vibrational normal modes. This peculiar aspect of XP-PCM provides a detailed description of the electronic origin of normal modes variations with pressure, via the curvature of the potential energy surface and via the anharmonicity of the normal modes. When applied to the vibrational properties of the sulfur hexafluoride crystal, the XP-PCM method reveals a hitherto unknown interpretation of the effects of the pressure on the vibrational normal modes of the molecular units of this crystal.

We have studied the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease at the atomic level using a computational approach based on extensive molecular dynamics simulations with explicit solvent. PF-07321332, whose chemical structure has been recently disclosed, is a promising oral antiviral clinical candidate with well-established anti-SARS-CoV-2 activity in vitro. The drug, currently in phase III clinical trials in combination with ritonavir, relies on the electrophilic attack of a nitrile warhead to the catalytic cysteine of the protease. Nonbonded interaction between the inhibitor and the residues of the binding pocket, as well as with water molecules on the protein surface, have been characterized using two different force fields and the two possible protonation states of the main protease catalytic dyad HIS41-CYS145. When the catalytic dyad is in the neutral state, the non-covalent binding is likely to be stronger. Molecular dynamics simulations seems to lend support for an inhibitory mechanism in two steps: a first non-covalent addition with the dyad in neutral form and then the formation of the thiolate-imidazolium ion pair and the ligand relocation for finalising the electrophilic attack., Graphical abstract Image 1

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 MgAMCPs 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 MgOur 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 Mg

The regioselectivity in the 1,3-dipolar cycloaddition (1,3-DC) between five-membered cyclic nitrone and methylenecyclopropane (MCP) has been studied through density functional theory (DFT) calculations. The computational study of 1,3-DC with different 1-alkyl- (or 1,1-dialkyl)-substituted alkenes and the comparison with MCP have evidenced that the electrostatic interaction has a central role in the regioselectivity of the reactions. It has been observed that the electronic effect of the substituent (donor or attractor groups) determines the polarization of the alkene double bond and the reaction mechanism, consequently determining the interaction with nitrones and favoring an orientation between this moiety and the dipolarophile.

With the world plagued by the coronavirus pandemic, efficient automated protocols for a reliable in silico estimate of the binding strength of compounds vs SARS-CoV2-related biological targets are urgently needed. The consensus computational pipeline in drug development starts from triaging via docking tools of data-driven generated libraries of compounds followed by Molecular Dynamics (MD) techniques on a subset of the best scoring ligands. In this context, absolute binding free energy determination via MD is a crucial and challenging intermediate step, preceding the drug optimization process, using efficient alchemical MD techniques on strictly congeneric series. Here we describe an alchemical MD technique based on nonequilibrium thermodynamics capable of delivering in few hours on a modern HPC platform reliable estimates of the absolute binding free energies in drug–receptor systems. The methodology can be combined with well established alchemical relative binding free energy calculations providing an automatable workflow for drug optimization starting from a set of chemically distant ligands.

Robotics for Medicine and Healthcare is undoubtedly an important emerging sector of the newborn third millennium. There are many aspects in which this branch of robotics already operates; in this article, the focus will be on the so-called “Robotic assistive technology”. In particular, a novel electromechanical design for an assistive Hand Exoskeleton System is presented here. Since freedom of movement plays a crucial role in making actually usable an assistive device, the main point of innovation of the proposed solution lies in the complete wearability of the resulting system: including mechanics, control electronics, and power supply. From the combination of the authors’ previous experience with the improvements presented in this article comes a fully standalone tailor-made assistive device, https://youtu.be/MiF5Hn1Q3fA https://www.youtube.com/watch?v=KfjOP6QuUnk

Since the development of the first autonomous underwater vehicles, the demanded tasks for subsea operations have become more and more challenging as, for instance, intervention, maintenance and repair of seabed installations, in addition to surveys. As a result of these considerations, the development of Autonomous Underwater Re-configurable Vehicles (AURVs) with the capability of interacting with the surrounding environment and autonomously changing the configuration, according to the task at hand, can represent a real breakthrough in underwater system technologies. A novel formulation for the dynamic maneuverability analysis of an AURV, adapting Yoshikawa’s manipulability theory for robotic arms, is proposed., https://youtu.be/huq45_AmoAM

In recent years, seabed inspection has become one of the most sought-after tasks for Autonomous Underwater Vehicles (AUVs) in various applications. Forward-Looking Sonars (FLS) are commonly favored over optical cameras, which are not-negligibly affected by environmental conditions, to carry out inspection and exploration tasks. Indeed, sonars are not influenced by illumination conditions and can provide high-range data at the cost of lower-resolution images compared to optical sensors. However, due to the lack of features, sonar images are often hard to interpret by using conventional image processing techniques, leading to the necessity of human operators analyzing thousands of images acquired during the AUV mission to identify the potential targets of interest. This paper reports the development of an Automatic Target Recognition (ATR) methodology to identify and localize potential targets in FLS imagery, which could help human operators in this challenging, demanding task. The Mask R-CNN (Region-based Convolutional Neural Network), which constitutes the core of the proposed solution, has been trained with a dataset acquired in May 2019 at the Naval Support and Experimentation Centre (Centro di Supporto e Sperimentazione Navale - CSSN) basin, in La Spezia (Italy). The ATR strategy was then successfully validated online in the same site in October 2019, where the targets were replaced and relocated on the seabed.

Robotics for Medicine and Healthcare is undoubtedly an important emerging sector of the newborn third millennium. There are many aspects in which this branch of robotics already operates; in this article, the focus will be on the so-called “Robotic assistive technology”. In particular, a novel electromechanical design for an assistive Hand Exoskeleton System is presented here. Since freedom of movement plays a crucial role in making actually usable an assistive device, the main point of innovation of the proposed solution lies in the complete wearability of the resulting system: including mechanics, control electronics, and power supply. From the combination of the authors’ previous experience with the improvements presented in this article comes a fully standalone tailor-made assistive device.

The paper presents an accurate in silico measurement of the dissociation constant of HCQ on three important SARS-Cov2 protein targets, namely the main protease (3CLpro) and the Papain-like protease (PLpro) and the RNA dependent RNA polimerase (RdRp), using the recently the released PDB stuructures of these protein. Calculations are done using state-of-the art force fields and advanced simulation methodologies combining enhanced sampling and nonequilibrium techniques amenable to massive parallelization on a dedicated HPC cluster.We have shown that HCQ may act as a mild inhibitor for all the three viral proteins, with potency increasing in the series PLpro, 3CLpro, RdRp. By analyzing the bound state configurations, we were able to improve the potency for the 3CLpro target, designing a novel HCQ-inspired compound, named PMP329, with predicted nanomolar activity. If confirmed in vitro, our results provide a convincing molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19.

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 3CL

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.

In the companion article (Giovannelli et al., 10.1021/acs.jctc.7b00594), we presented an alchemical approach, based on nonequilibrium molecular dynamics simulations, to compute absolute binding free energies of a generic host-guest system. Two alternative computational routes, called binded-domain and single-point alchemical-path schemes, have been proposed. This study is addressed to furnish numerical validation and illustrative examples of the above-mentioned alchemical schemes. Validation is provided by comparing binding free-energy data relative to two poses of a Zn(II)·anion complex with those recovered from an alternative approach, based on steered molecular dynamics simulations. We illustrate important technical and theoretical aspects for a good practice in applying both alchemical schemes, not only through the calculations on the Zn(II)·anion complex, but also estimating absolute binding free energies of 1:1 complexes of β-cyclodextrin with aromatic compounds (benzene and naphthalene). Comparison with experimental data and previous molecular dynamics simulation studies further confirms the validity of the present nonequilibrium-alchemical methodology.

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.

Nowadays, underwater acoustic communication is an interesting topic of research. This is especially true in the case of Autonomous Underwater Vehicles (AUVs): due to the limitations of underwater environment, where wireless and radio communications are not possible, it is very important to possess efficient and reliable tools for acoustic data exchange. Indeed, an underwater network of acoustic nodes can enhance the navigation and localization capabilities of one or more vehicles. In this paper, the authors investigate the use of an AUV as a mobile bridging node within a network of fixed heterogeneous acoustic modems. In particular, MARTA AUV, developed and built by the Department of Industrial Engineering (DIEF) of the University of Florence is employed in order to enable data transmission between modems of different manufacturers. Suitable bridging tests, whose results are proposed in this paper, were executed in order to evaluate the feasibility of such approach, showing that AUVs can efficiently accomplish the role of gateway between the nodes of the network.

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.

Design of autonomous underwater vehicles is deeply influenced by required mission specifications. In particular, some activities like inspection of offshore plants or harsh marine environments require underwater vehicle with high autonomy, good propulsion performances and manoeuvrability. These features are deeply influenced by design and performances of the propulsion system. In particular, performances of underwater vehicles (both remotely operated and autonomous) are deeply influenced by four quadrants performances of propellers and by complex fluid dynamics interactions that are difficult to be, even roughly, evaluated. In this work, a study of a reconfigurable propulsion layout and its comparison with a conventional one is introduced. In particular, this study is also focused on modelling techniques that should really represent a reasonable trade-off in terms of accuracy and involved computational resources for fast prototyping and simulation of this kind of mechatronic systems.

We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.

The paper presents the electromechanical design of an Autonomous Surface Vehicle (ASV) developed by the Department of Industrial Engineering (DIEF) of the University of Florence (UNIFI), Italy. One of the main functions of this autonomous moving buoy is to localize underwater targets, such as Autonomous Underwater Vehicles (AUVs), through an Ultra Short BaseLine (USBL) and to enable the communication with them; furthermore, it is possible to equip the buoy with sensors or payloads, for instance cameras to detect the seabed. The buoy specifications and its navigation devices are described. The main features of the developed floating device are given, starting from its system architecture to its structural design. The buoy will be assembled during Summer 2019 and tested together with the UNIFI DIEF underwater vehicles.

The structural and dynamic properties of imidazole in aqueous solution have been studied by means of classical and ab initio molecular dynamics simulations. We developed a new force field for the imidazole molecule with improved modeling of the electrostatic interactions, specifically tailored to address the well-known drawbacks of existing force fields based on the atomic fractional charge approach. To this end, we reparametrized the charge distribution on the heterocyclic ring, introducing an extra site accounting for the lone pair on the deprotonated nitrogen. The accuracy of the model in describing the hydrogen bond pattern in the aqueous solvent has been confirmed by comparing the classical results on imidazole-water interactions to accurate Car-Parrinello molecular dynamics simulations. It reproduces satisfactorily the experimental water/octanol partition coefficient of imidazole, as well as the structure of the imidazole molecular crystal. The force field has been finally applied to simulate aqueous solutions at various imidazole concentrations to obtain information on both imidazole-water and imidazole-imidazole interactions, providing a description of the different molecular arrangements in solution.

Since the development of the first autonomous underwater vehicles, the demanded tasks for subsea operations have become more and more challenging as, for instance, intervention, maintenance and repair of seabed installations, in addition to surveys. As a result, the development of autonomous underwater reconfigurable vehicles (AURVs) with the capability of interacting with the surrounding environment and autonomously changing the configuration, according to the task at hand, can represent a real breakthrough in underwater system technologies. Driven by these considerations, an innovative AURV has been designed by the Department of Industrial Engineering of the University of Florence (named as UNIFI DIEF AURV), capable of efficiently reconfiguring its shape according to the task at hand. In particular, the UNIFI DIEF AURV has been provided with two extreme configurations: a slender (“survey”) configuration for long navigation tasks, and a stocky (“hovering”) configuration designed for challenging goals as intervention operations. In order to observe the several dynamic features for the two different configurations, a novel formulation for the dynamic maneuverability analysis (DMA) of an AURV, adapting Yoshikawa’s well-known manipulability theory for robotic arms, is proposed in this work. More specifically, we introduce a novel analysis which relates the vehicle body-fixed accelerations with the rotational speed of each thruster, taking into account also the AURV dynamic model for each configuration and the propulsion system.

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

In this paper we report on the Raman scattering of antimalarial artesunate, as a neutral species and as an anion in sodium salt, and on the surface-enhanced Raman scattering (SERS) of the anion adsorbed on silver nanoparticles. The vibrational assignment of the strongest Raman peaks of artesunate has been made with reference to the Raman data on artemisinin and by identifying peaks due to modes largely localized on the succinic side chain of artesunate. The structure of artesunate, as well as that of the anion, has been optimized by means of ab-initio calculations at the DFT/B3LYP/cc-pVDZ calculation level and found in good agreement with the experimental molecular geometry. The conformational minima of the flexible side chain both in the anion and in the anion complexed with Ag+ have been characterized by ab-initio methods at the same level of accuracy and eight pairs of conformers have been predicted. From these data the vibrational frequencies and Raman intensities have been obtained. This has allowed to assign the SERS spectrum of chemisorbed artesunate to conformers with nearly all-trans side chain. For these conformers the artemisinin core lies as far as ≈ 9 A from the silver ion and the active SERS modes are localized on the succinic fragment. Minor contributions to the SERS intensity are due to the di-silver complex and a more sterically hindered mono complex. It is a major conclusion of this study that the interaction of artesunate with the silver surface is exclusively through the side chain, leaving untouched the peroxide group responsible of the antimalarial activity.

Molecular dynamics simulations have been performed to compute the solvation free energy and the octanol/water partition coefficients for a challenging set of selected organic molecules, characterized by the simultaneous presence of functional groups coarsely spanning a large portion of the chemical space in druglike compounds and, in many cases, by a complex conformational landscape (2-propoxyethanol, acetylsalicylic acid, cyclohexanamine, dialifor, ketoprofen, nitralin, profluralin, terbacil). OPLS-AA and GAFF2 parametrizations of the organic molecules and of 1-octanol have been done via the Web-based automatic parameter generators, LigParGen [ Dodda et al. Nucl. Acids Res. 2017 , 121 , 3864 ] and PrimaDORAC [ Procacci J. Chem. Inf. Model. 2017 , 57 , 1240 ], respectively. For the water solvent, three popular three-point site models, TIP3P, SPCE, and OPC3, were tested. Solvation free energies in water and 1-octanol are evaluated using a recently developed nonequilibrium alchemical technology [ Procacci et al. J. Chem. Theory Comput. 2014 , 10 , 2813 ]. Extensive and accurate simulations, including all possible combinations of organic molecule, solvent, and solvent model, are allowed to assess the accuracy with regard to solvation free energies of the latest release of two widespread force fields, OPLS and GAFF. The collected data are relevant in the evaluation of the predictive power of these classical force fields (and of the related support software for automated parametrization) with regard to binding free energies in a drug-receptor system for industrial applications.

Zeno (Zeno Environment Nautical Operator) is a compact AUV (Autonomous Underwater Vehicle) designed by the Department of Industrial Engineering of the University of Florence (UNIFI) and MDM Team S.r.l., an official spin-off company of UNIFI, within the ARCHEOSUb (Autonomous underwater Robotic and sensing systems for Cultural HEritage discovery cOnservation and in SitU valorization) European project and tailored for archaeological missions. One of the main purposes of this project is to develop low-cost AUVs, both used as a tool for services supporting the identification of new Underwater Cultural Heritage (UCH) sites and for the conservation, protection and enhancement of new and discovered ones (covering the first two phases of an archaeological campaign: search and inspection). The paper deals with the design, realization and testing of the vehicle. Its main features, payloads and implementation details are given. The official demos have already started and will be completed in autumn 2018; the different archaeological sites involved are in Italy and in Israel.

A new type of vehicle has been designed by the Department of Industrial Engineering of the University of Florence (DIEF); it is an AUV (Autonomous Underwater Vehicle) capable of switching its shape according to mission needs matching the best UUVs (Unmanned Underwater Vehicles) features: it is compact and near torpedo-shaped in case of long distance missions, such as surveillance and monitoring (closed configuration, typical of AUVs), on the other end it becomes isotropic for site inspection and on-site manipulation (open configuration, emblem of ROVs - Remotely Operated Vehicles). The main goal of the work is adding to the hydrodynamic vehicle the capability of changing its structure and its thruster configuration. The paper deals with the study and the design of the vehicle. Its main features, design choices and payloads, that can be equipped with, are described.

The problem of recovering the free energy difference between two electronic states has been investigated by Frezzato [Chem. Phys. Lett. 533, 106 (2012)], exploring the equivalence between light-absorption spectra and work distribution, hence opening to the application of a spectroscopic version of the Jarzynski equality (JE) [Phys. Rev. Lett. 78, 2690 (1997)]. Here, assuming the validity of the time-dependent perturbation theory, we demonstrate that such equivalence does not lead to the known form of the JE. This is ascribed to the fact that light-absorption processes cannot be described as stochastic processes. To emphasize such an aspect, we devise a stochastic model for the UV-vis (ultraviolet and visible) absorption, suitable for determining the free energy difference between two generic quantum manifolds in a JE-like fashion. However, the model would require explicit knowledge of the transition dipole moments, which are in general not available. Nonetheless, we derive a spectroscopic version of the JE that allows us to recover the free energy difference between the ground and an excited electronic state when the latter state is the only one observed in the spectrum.

Autonomy, performances and manoeuvrability of underwater vehicles are deeply influenced by the features of their propulsion layouts. In particular, the manoeuvrability and the reliability are very important requirements for ROV (Remotely Operated Vehicle) and AUV (Autonomous Underwater Vehicle), for this reason it is necessary to improve these features for underwater vehicles especially if they are emploied in shallow water or potentially dangerous environments. In this work are introduced an application of reconfigurable and redundant propulsion system.

The pressure-induced transformation of molecular crystals can give rise to new materials characterized by intriguing hardness or energetic properties. Mechanisms regulating these reactions at the molecular level result from a complex interplay among crystal structure, lattice dynamics, and electronic properties. Here, we show that the formation of a three-dimensional amorphous carbon nitride by compressing phase II s-triazine is controlled by the competition between two different mechanisms, one entirely structural and the other electronic, representing the first example where such occurrence is demonstrated. Temperature drives the reactivity below 8 GPa by ruling the lattice dynamics, whereas above 8 GPa the electronic modifications, uniquely governed by pressure, trigger the chemical transformation. The amorphous material synthesized has a bonding structure characterized by a bulk typical of a strongly conjugated three-dimensional carbon nitride with hydrogen atoms migrated to saturate C and N terminations.

The fast-switching decoupling method is a powerful nonequilibrium technique to compute absolute binding free energies of ligand-receptor complexes (Sandberg et al., J. Chem. Theory Comput. 2014, 11, 423-435). Inspired by the theory of noncovalent binding association of Gilson and co-workers (Biophys. J. 1997, 72, 1047-1069), we develop two approaches, termed binded-domain and single-point alchemical-path schemes (BiD-AP and SiP-AP), based on the possibility of performing alchemical trajectories during which the ligand is constrained to fixed positions relative to the receptor. The BiD-AP scheme exploits a recent generalization of nonequilibrium work theorems to estimate the free energy difference between the coupled and uncoupled states of the ligand-receptor complex. With respect to the fast-switching decoupling method without constraints, BiD-AP prevents the ligand from leaving the binding site, but still requires an estimate of the positional binding-site volume, which may not be a simple task. On the other side, the SiP-AP scheme allows avoidance of the calculation of the binding-site volume by introducing an additional equilibrium simulation of ligand and receptor in the bound state. In the companion article (DOI: 10.1021/acs.jctc.7b00595), we show that the extra computational effort required by SiP-AP leads to a significant improvement of accuracy in the free energy estimates.

Reliable navigation systems are fundamental for Autonomous Underwater Vehicles (AUVs) to perform complex tasks and missions. It is well known that the Global Positioning System (GPS) cannot be employed in underwater scenarios; thus, during missions below the sea's surface the real-time position is usually obtained with expensive sensors, such as the Doppler Velocity Log (DVL), integrated within a navigation filter such as an Extended Kalman Filter (EKF), Unscented Kalman Filter (UKF), or Dead Reckoning (DR) strategies. The goal of this work is to develop an underwater navigation system that does not rely on a DVL and where linear speed estimations are obtained exploiting data from a Forward-Looking SONAR (FLS) or, in its absence, taking advantage of a dynamic model that presents a reduced set of parameters. The proposed solution is validated through the use of navigation data obtained during sea trials undertaken in July 2018 with FeelHippo AUV at La Spezia (Italy), at the NATO Science and Technology Organization Center for Maritime Research and Experimentation (CMRE).

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 adsorption of isothiazole on silver colloids was studied by surface-enhanced Raman scattering (SERS) spectroscopy in comparison with other five-membered heterocycles. The experimental results coupled with those obtained by density functional theory calculations for molecule/metal complexes evidenced the presence of positively charged active sites on the surface of the silver nanoparticles, along with a close relation between ligand basicity and strong SERS effect.