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We describe a step‐by‐step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows computing with good accuracy the RDFE between small molecules with arbitrary differences in volume, charge, and chemical topology. The procedure is illustrated for the challenging SAMPL9 batch of host–guest pairs. The article is supplemented by a detailed online tutorial, available at https://procacci.github.io/vdssb%5fgromacs/NE-RDFE and by a public Zenodo repository available at https://zenodo.org/record/6982932. [ABSTRACT FROM AUTHOR]

Hydrogen bond interactions strongly affect vibrational properties and frequencies, the most common consequence being a redshift of the stretching vibration involved; there are, however, few exceptions to this general trend. In previous works, we have proved the effectiveness of ab initio simulations combined with wavelet analysis to investigate these effects and put them into relation to structural environment. In this work, we investigate the hydrogen bond effects on the structural and vibrational properties of 1,3-propanediol in acetonitrile by a combined experimental and computational approach. We explain the appearance of two spectral components in the O-H stretching band on the basis of intra- and intermolecular hydrogen bond interactions. We also elucidate the blueshift of the C≡N stretching band as due to a hydrogen bond interaction between the glycol and acetonitrile that modify the electron density distribution inside the CN group. This effect is well reproduced by ab initio molecular dynamics simulations and density functional calculations reported in this work. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The chemical reactions Cl[sup -]+Cl(CH[sub 2])[sub n]CN (n=2–5) have been studied with ab initio molecular dynamics. The effects of the cyano group on the energy profile of the reactions as the length of the alkilic chain increases have been discussed in terms of electrostatics of the systems. The thermal effects have been computed in the Blue Moon Ensemble showing a large influence on the energy barriers. It has been shown that six membered hydrogen-bonded pre-reactive complexes are stable even at room temperature. The results of the simulation allow for an explanation for the increased reactivity of these systems compared to the parent Cl[sup -]+Cl(CH[sub 2])[sub n]CH[sub 3] reactions. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

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. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The thermal effects on the C1CH[sub 2]CN+Cl[sup -]S[sub N]2 reaction at 300 K have been studied by ab initio molecular dynamics. The role of the cyano-substituent is explained by the formation of a hydrogen bond and is discussed by comparison with the reactions of ClCH[sub 3] and Cl[sub 2]CH[sub 2]. It is shown that the interactions occurring in the prereactive complex are sufficiently strong to be effective also at high temperature. It is also shown that the temperature effects on the activation barrier are significant. [ABSTRACT FROM AUTHOR]

The double proton transfer (PT) reaction has been investigated in the [2,2′‐bipyridyl]‐3‐3′‐diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, that is the two protons are exchanged simultaneously, or stepwise, where the two protons are transferred sequentially. To this end, a static exploration of the potential energy surface (PES) was carried together with the analysis of the free‐energy surface (FES), both surfaces being evaluated at density functional theory level and different exchange‐correlation functionals. While the concerted mechanism has been clearly discharged, the characteristics of the stepwise PT significantly depends on the chosen functionals, some suggesting a clear stepwise mechanism characterized by a stable reaction intermediates and two transitions states, whereas other approaches propend for a asynchronous PT, with a single TS. These features appear on both PES and FES, albeit some differences appears due to their different nature. [ABSTRACT FROM AUTHOR]

Abstract: The IR and Raman spectra of alizarin, purpurin, kermesic acid, and carminic acid have been computed performing density functional theory calculations at the B3LYP/6‐31G(d) level of theory. The computational approach adopted has been validated on the basis of a series of calculations with different level of theory on the anthraquinone molecule, the common moiety of these dyes. The computed vibrational frequencies have been adopted as a guideline to propose the vibrational assignment of the dyes and to obtain useful information on the Raman spectra of their aluminum complexes. [ABSTRACT FROM AUTHOR]

1,6-Methano[10]annulene solutions in cyclohexane have been subjected to continuous and pulsed UV irradiation. Photolysis occurs in both cases, giving naphthalene as a minor and major product, respectively. The wavelength dependence of the reaction in solution indicates that the photochemical process occurs, exciting 1,6-methano[10]annulene in the second and third singlet electronic excited states. The reaction kinetics has been determined under pulsed irradiation. From the time dependence of concentrations, along with support of density functional theory calculations and early published data, two mechanisms are proposed for naphthalene production. Reaction steps such as direct migration of the bridging methylene of 1,6-methano[10]annulene to cyclohexane and 1,6-methano[10]annulene isomerization to benzotropilidene have been identified. The calculated energy diagrams relative to the ground and lowest excited states allow one to relate these steps to processes such as electrocyclic closure and sigmatropic shift. The norcaradienic form of 1,6-methano[10]annulene results in the critical species for methylene migration and the sigmatropic [1,5] shift. The present results and those arising from photolysis in the gas phase are good examples of the photochemical reactivity of 1,6-methano[10]annulene. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The structure and the vibrational properties of the P4S3 crystal at high pressures are discussed by application of the XP-PCM method. The vibrational assignment has been clarified. The structure and the electron distribution changes as a function of pressure are analyzed. The pressure effect on the vibrational frequencies is satisfactorily reproduced and discussed in terms of confinement and structure relaxation contributions. [ABSTRACT FROM AUTHOR]

The structural, electronic, and spectroscopicproperties of methanediolin aqueous solutions have been studied by a combined approach basedon Car–Parrinello molecular dynamics simulations and ab initiocalculations. The hydrogen bond interactions between the solute andwater have been characterized, showing the important role of the solventin the stabilization of the methanediol conformers in solution. Firstinsights on the experimental vibrational spectra have been obtainedby the analysis of the simulation results, with particular regardto the most prominent band at 1050 cm–1that hasbeen attributed to both the symmetric and antisymmetric CO stretchingmodes. The assignment has been completed adopting both electric andmechanical anharmonic calculations considering the interactions withthe solvent using a polarizable continuum model. [ABSTRACT FROM AUTHOR]

Theequilibrium geometry structural and vibrational spectroscopic propertiesof fullerenes C60and C70under high pressurehave been studied with a quantum-chemical computational approach inwhich ab initiocalculations on a single fullerenemolecule have been carried out within the polarizable continuum modelframework to mimic pressure effects. The adopted approach has beenrevealed effective to explain the geometry variations and the frequencyshifts observed experimentally. [ABSTRACT FROM AUTHOR]

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. [Display omitted] • Study of the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease using a computational approach. • The catalytic dyad HIS41-CYS145 has been characterized using two different force fields (AMBER and OPLS-AA) and the two possible protonation states. • Molecular dynamics simulations seem to lend support for an inhibitory mechanism in two steps. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Simple Summary: Preventing possible pain caused by functional asymmetry of both rider and horse needs an investigation of the rider-related variables that could affect the distribution of mass on the stirrups. Using digital load cells applied to the stirrup leathers of a wooden horseback model, we measured the directional force exerted by both legs of 147 riders on stirrup straps determining possible asymmetries. Furthermore, we investigated the possible associations between the asymmetry and eight variables related to the riders: gender, age, level of riding ability, years of riding experience, riding style, motivation of riding, primary discipline, and handedness. The preliminary findings confirmed that the majority of the riders are asymmetrical while riding on wooden horseback. Riding style seems to be a risk factor for asymmetry. Further studies using larger sample groups controlled for leg dominance and riding experience are required. Riders' asymmetry may cause back pain in both human and equine athletes. This pilot study aimed at documenting in a simple and quick way asymmetry in riders during a simulation of three different riding positions on wooden horseback using load cells applied on the stirrup leathers and identifying possible associations between riders' asymmetry and their gender, age, level of riding ability, years of riding experience, riding style, motivation of riding, primary discipline and handedness. After completing an interview to obtain the previously mentioned information, 147 riders performed a standardized test on a saddle fixed on a wooden horseback-shaped model. The riding simulation was split into three phases of 1 min each: (1) sit in the saddle, (2) standing in the stirrups and (3) rising trot. The directional force on the left and the right stirrup leathers was recorded every 0.2 s. A paired t-test was performed on the recorded data to test the difference (i.e., asymmetry) in each phase. In phases 1, 2 and 3, 99.3% (53.4% heavier on the right (R)), 98% (52.8% heavier on the left (L)) and 46.3% (51.5% heavier on the left (L)) of the riders were asymmetrical, respectively. Chi-square tests showed a significant association between riding ability and riding experience, but no significant association between reported handedness and calculated leg-sidedness (p > 0.05). Univariate logistic (1: asymmetry, 0: symmetry) regression analysis was performed only on the phase 3 data. One-hand riders were found twice more likely to be asymmetrical than two-hand riders (Odds Ratio (OR): 2.18, Confidence Interval (CI): 1.1–4.29; p = 0.024). This preliminary study confirmed that the majority of the riders are asymmetrical in load distribution on stirrups and suggested the riding style as a possible risk factor for asymmetry. [ABSTRACT FROM AUTHOR]

The hydrogen-bond dynamics of lithium nitrate trihydratehas beenstudied by a combined approach based on ab initio molecular dynamicssimulations and wavelet analysis. The simultaneous bifurcated interactionbetween one hydrogen atom of water molecules and two oxygen atomsof nitrate ions is the pivotal feature of the crystal structure: thisbifurcated interaction has deep effects on the O–H stretchingregion of the vibrational spectrum. The structural, dynamic, spectroscopic,and electronic properties of the bifurcated hydrogen bond have beeninvestigated computationally, elucidating at the molecular level thedifferences with weak and strong hydrogen bonds present in the crystal.These studies corroborate the very recent IR experiments performedon the lithium nitrate trihydrate crystal, offering new perspectivesto interpreting the vibrational spectra. In fact, this approach allowsobtaining two-dimensional plots, which summarize the essential featuresof both the hydrogen-bond network and IR spectra, resulting in a peculiar“signature” of the bifurcated interaction. [ABSTRACT FROM AUTHOR]

Alacranite, As8S9, has been studied by a combined approach based on micro-Raman measurements and ab initio molecular dynamics simulations, with the Car -Parrinello method. The structure of this arsenic sulfide mineral consists of an ordered packing of As4S4) and As4S5 cagelike molecules, with a topology closely resembling that found in the β-As4S4. The presence in the crystal structure of molecular clusters with permanent dipole moment induces stronger intermolecular interactions than those observed in other arsenic sultides, making the adoption ot ab initio computational methods particularly important for a complete characterization of the spectroscopic properties. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

The interactions between oxazole and water or silver nanoparticles in aqueous dispersions have been studied with a computational approach based on ab initio molecular dynamics simulations, with the Car−Parrinello method, and density functional calculations in combination with Raman and surface enhanced Raman scattering (SERS) experiments. The solvation dynamics of oxazole in water allowed for the characterization of the hydrogen bond between water and solute, which has been shown to occur essentially through the nitrogen atom of the heterocyclic molecule. To mimic the solvation process or the adsorption on silver and interpreting the corresponding Raman and SERS spectra in aqueous solution or in Ag hydrosols, density functional calculations have been carried out on model systems made up by oxazole bound to water molecules or to positively charged silver clusters. Also, the chemisorption on Ag nanoparticles is found to occur by means of the nitrogen atom of oxazole interacting with the metal substrate. [ABSTRACT FROM AUTHOR]

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O 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. [ABSTRACT FROM AUTHOR]

The structure of the solvation shell of Na+ and K+ in fully deuterated liquid methanol has been studied by ab initio Car-Parrinello molecular dynamics simulations. The solvent cage has been found relatively stable and this property has been explained by means of charge transfer and electrostatic interactions as was previously done for Li+ in the same solvent. The differences with Li+ such as the increase of the coordination number going from Li+ to K+ and the reduced stability of the cage have been ascribed to the increase in the ionic radius. [ABSTRACT FROM AUTHOR]

The results of the analysis of ab initio molecular dynamics simulations of the transition state of a bimolecular nuclear substitution reaction in water are discussed and a lower limit for the life-time of the hydrogen bonded interactions between the halogens and the surrounding water molecules is estimated. A new function is introduced to compute a lower estimate of the H-bond life-time and compared with the results of the traditional one. [Copyright &y& Elsevier]

Carbon dioxide (CO2) is widespread in astrochemically relevant environments, often coexisting with water (H2O) ices and thus triggering a great interest regarding the possible formation of their adducts under various thermodynamic conditions. Amongst them, solid carbonic acid (H2CO3) remains elusive, yet being widely studied. Synthetic routes followed for its production have always been characterised by drastic irradiation on solid ice mixtures or complex procedures on fluid samples (such as laser heating at moderate to high pressures). Here we report about a simpler yet effective synthetic route to obtain two diverse carbonic acid crystal structures from the fast, cold compression of pristine clathrate hydrate samples. The two distinct polymorphs we obtained, differing in the water content, have been deeply characterised via spectroscopic and structural techniques to assess their composition and their astonishing pressure stability, checked up to half a megabar, also highlighting the complex correlations between them so to compile a detailed phase diagram of this system. These results may have a profound impact on the prediction and modelisation of the complex chemistry which characterises many icy bodies of our Solar System. [ABSTRACT FROM AUTHOR]

Carbon dioxide (CO2) is widespread in astrochemically relevant environments, often coexisting with water (H2O) ices and thus triggering a great interest regarding the possible formation of their adducts under various thermodynamic conditions. Amongst them, solid carbonic acid (H2CO3) remains elusive, yet being widely studied. Synthetic routes followed for its production have always been characterised by drastic irradiation on solid ice mixtures or complex procedures on fluid samples (such as laser heating at moderate to high pressures). Here we report about a simpler yet effective synthetic route to obtain two diverse carbonic acid crystal structures from the fast, cold compression of pristine clathrate hydrate samples. The two distinct polymorphs we obtained, differing in the water content, have been deeply characterised via spectroscopic and structural techniques to assess their composition and their astonishing pressure stability, checked up to half a megabar, also highlighting the complex correlations between them so to compile a detailed phase diagram of this system. These results may have a profound impact on the prediction and modelisation of the complex chemistry which characterises many icy bodies of our Solar System. [ABSTRACT FROM AUTHOR]

Several organisms are able to polycondensate tetraoxosilicic(IV) acid to form silicon(IV) dioxide using polycationic molecules. According to an earlier mechanistic proposal, these molecules undergo a phase separation and recent experimental evidence appears to confirm this model. At the same time, polycationic proteins like lysozyme can also promote polycondensation of silicon(IV) dioxide, and they do so under conditions that are not compatible with liquid‐liquid phase separation. In this manuscript we investigate this conundrum by molecular simulations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] 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. 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. 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. [ABSTRACT FROM AUTHOR]

A SERS investigation combined with ab initiocomputational analysis involving Car–Parrinello molecular dynamics simulations and Density Functional Theory approach allows fundamental information to be obtained on the behaviour of thiazole in silver aqueous suspension where solvation and chemisorption processes competitively occur. [ABSTRACT FROM AUTHOR]

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. Analysis of unique micro-samples from Leonardo da Vinci's Last Supper (left) and other Old Master paintings by Masolino, Tintoretto and Veronese are presented and demonstrate the identification of hexavalent Al-based pigment complexes: kermes by Leonardo and Masolino (right) and carmine by Tintoretto and Veronese. Unlabelled Image • Raman spectra from red lake particles in Old Master Paintings are assigned. • Differences in spectra are ascribed to Kermes and Cochineal pigments. • Red lakes in Leonardo's Last Supper and Masolino's paintings share Raman signatures. • Similar Raman spectra are found in cochineal in works by Veronese and Tintoretto. [ABSTRACT FROM AUTHOR]

The study of marine Lagrangian transport holds significant importance from a scientific perspective as well as for practical applications such as environmental-pollution responses and prevention (e.g., oil spills, dispersion/accumulation of plastic debris, etc.). In this regard, this concept paper introduces the Smart Drifter Cluster: an innovative approach that leverages modern "consumer" IoT technologies and notions. This approach enables the remote acquisition of information on Lagrangian transport and important ocean variables, similar to standard drifters. However, it offers potential benefits such as reduced hardware costs, minimal maintenance expenses, and significantly lower power consumption compared to systems relying on independent drifters with satellite communication. By combining low power consumption with an optimized, compact integrated marine photovoltaic system, the drifters achieve unlimited operational autonomy. With the introduction of these new characteristics, the Smart Drifter Cluster goes beyond its primary function of mesoscale monitoring of marine currents. It becomes readily applicable to numerous civil applications, including recovering individuals and materials at sea, addressing pollutant spills, and tracking the dispersion of marine litter. An additional advantage of this remote monitoring and sensing system is its open-source hardware and software architecture. This fosters a citizen-science approach, enabling citizens to replicate, utilize, and contribute to the improvement of the system. Thus, within certain constraints of procedures and protocols, citizens can actively contribute to the generation of valuable data in this critical field. [ABSTRACT FROM AUTHOR]

Using a combination of enhanced sampling molecular dynamics techniques and non-equilibrium alchemical transformations with full atomistic details, we have shown that hydroxychloroquine (HCQ) may act as a mild inhibitor of important functional proteins for SARS-CoV2 replication, 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 molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19. [ABSTRACT FROM AUTHOR]

Abstract: Structural characterization of liquid pyrrole has been obtained by performing classical molecular dynamics simulations with a new parameterization of electrostatic interactions. Despite the relatively simple molecular structure of pyrrole, a correct and accurate representation of its intermolecular interactions in bulk phase is a challenging task, since these are affected at short range by the quadrupole–quadrupole term. This new parameterization permits not only to correctly describe the liquid structure but also to obtain macroscopic properties in excellent agreement with experiments. [ABSTRACT FROM AUTHOR]

Inspection of offshore plants or harsh marine environments, requires underwater vehicles with high autonomy, performances and maneuverability. These features are deeply affected by the design of propulsion system. An accurate design of the propulsion system, involves the modelling of the response of propellers. In this work a reconfigurable propulsion layout for an inspection vehicle is presented. Performances of the proposed solution are evaluated and compared respect to the conventional one which is currently installed on benchmark test vehicle (the MARTA AUV from University of Florence). Proposed layout exhibit superior maneuvering performances that should be useful for the inspection of offshore plants and more generally for harsh operational conditions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] • 2-Hydroxyethyl methacrylate (HEMA) and acrylic acid (AA) were investigated through MD simulations and DFT calculations. • Properties derived from simulations were compared to experimental electronic and vibrational spectra. • Different solvation models were used in theoretical spectra calculation. 2-hydroxyethyl methacrylate (HEMA) and acrylic acid (AA) are monomers widely used in the production of hydrogels with medium-high water content. The structural and spectroscopic properties of HEMA and AA were studied using a combination of computational strategies based on both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT calculations have confirmed the co-existence of two stable HEMA conformers, while solute-solvent interactions between HEMA and AA with water were characterized by the analysis of MD simulations carried out by employing four different water models and different simulation conditions. The carbonyl and hydroxyl oxygen atoms of HEMA are involved in hydrogen bonding, whereas the ester oxygen atom does not appreciably interacts with the solvent. No significant differences in solute-solvent interactions are found between the two HEMA conformers. Their spectroscopic properties were calculated and the results were compared to experimental data. Although electronic spectra do not really allow a differentiation of the conformers, IR spectra present some peculiar bands to discriminate the presence and obtain information on the ratio of the conformers in solution. To verify the influence of a solvent with higher dipole moment on chemical properties, acetonitrile has been considered as an alternative solvent. [ABSTRACT FROM AUTHOR]

The effect of binding pyridine to silver clusters has been studied by density functional calculations by adopting a hybrid functional. The calculations allow proposing an explanation for the different SERS spectra of the ligand observed on Ag colloids in the presence and in the absence of coadsorbed chloride anions. In the latter case, a better agreement is obtained modeling the system by adsorption of pyridine on a $$(Ag_{4})^{+2}$$ surface cluster. [ABSTRACT FROM AUTHOR]

Abstract: A conclusive study on the SERS band of pyridine occurring at about 1025cm−1 was performed by a density functional theory (DFT) approach, by considering the ligand molecules bound to silver adclusters. The existence of (Ag3)+2 surface active-sites, ascertained in Ag/SiO2 colloids as metal adclusters stabilised by the interaction with the silica nanoparticles, was confirmed by DFT calculations, which satisfactorily account for the experimental findings. [Copyright &y& Elsevier]

The knowledge of the adsorption geometry of an analyte on a metal substrate employed in surface enhanced Raman scattering (SERS) spectroscopy is important information for the correct interpretation of experimental data. The adsorption geometry of alizarin on silver nanoparticles was studied through ab initio calculations in the framework of density functional theory (DFT) by modeling alizarin taking into account all the different charged species present in solution as a function of pH. The calculations allowed a faithful reproduction of the measured SERS spectra and to elucidate the adsorption geometry of this dye on the silver substrate. [ABSTRACT FROM AUTHOR]

• Antimalarial artesunate has been studied by means of Raman spectroscopy as a neutral species, as an anion in sodium salt, and by means of SERS as anion adsorbed on silver nanoparticles. • 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. • The SERS spectrum of chemisorbed species is due to conformers with nearly all-trans side chain, where the artemisinin core lies as far as ≈ 9 Å from the silver ion. • The interaction of artesunate with the silver surface is exclusively through the side chain, leaving untouched the peroxide group responsible of the antimalarial activity. 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 Å 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. The SERS spectra of artesunate, one of the most appealing derivatives of the antimalarial drug artemisinin, adsorbed on silver nanoparticles have been measured and reproduced by means of high level ab-initio calculations. The comparison allowed to state that the interaction of artesunate with the silver surface is due exclusively to the succinic side chain, leaving untouched the peroxide bridge, responsible for the antimalarial activity. Image, graphical abstract [ABSTRACT FROM AUTHOR]

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). • Sonar (FLS)-aided navigation strategy for AUVs. • AUV dynamic modelling for navigation. • Offline validation of underwater navigation algorithms by means of experimental data collected at sea. [ABSTRACT FROM AUTHOR]

A simple and efficient method for C‐2 deuterium labeling of 3,4‐di‐tert‐butoxypyrroline N‐oxide, a useful chiral building block in azaheterocycles syntheses, is presented. Selective and quantitative deuterium incorporation (> 99 %) was achieved by base‐catalyzed H/D exchange in D2O under mild reaction conditions. A mechanistic pathway based on kinetic and computational data was proposed. The labeled nitrone was used in the synthesis of C‐8a deuterated (1R,2R,8aR)‐lentiginosine. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: The advantages of the use of optical spectroscopy methods (infrared and Raman spectroscopy, electronic spectroscopy) in the study of high pressure transformation and chemical reactions are illustrated considering several examples. In particular, the efficiency of the spectroscopic methods in the analysis of phase transitions at high pressure, of pressure induced changes of the electronic structure and of the elucidation of the reaction mechanisms at very high pressures are considered. [Copyright &y& Elsevier]

[Display omitted] • Local and collective Water dynamics in solution vs pressure and concentration. • Ultrafast spectroscopy as a powerful tool to investigate water dynamics. • Pressure and concentration similarly affect water dynamics. • Experimental evidence of the second and first solvation shell merging. The presence of ions induces perturbations in the water network, these structural and dynamic modifications can extent over space scales overcoming the local solvation shell: aqueous solutions of sodium perchlorate (NaClO 4) are characterized by extended phenomena of structure breaking of the solvent network. The aim of the present work is the experimental investigation of the interplay between the local structural modifications induced by the perchlorate ions and the collective dynamical properties of the solvent. Ultrafast Optical Kerr Effect (OKE) and time resolved infrared absorption are the experimental techniques adopted: OKE is mostly sensitive to the collective properties of the sample, while transient IR provides access to local properties of the solvent. Classical Molecular Dynamics (MD) simulations support the analysis of the experimental results. All experiments and simulations are performed at room temperature, varying the concentrations (0–6 M) and varying the applied pressure (10−4–1.3 GPa). Experiments and computer simulations confirm that pressure and concentration have convergent effects on the water dynamics, due to the analogous modification of the short-range liquid structure that cancel some dynamical anomalies typical of pure water. Both local and collective dynamic observables point to structural properties as responsible for their peculiar pressure and concentration dependence. [ABSTRACT FROM AUTHOR]