Blueshift of the CN stretching vibration of acetonitrile in solution: computational and experimental study.

Acetonitrile, a polar molecule that cannot form hydrogen bonds on its own, interacts with solvent molecules mainly through the lone pair of its nitrogen atom and the π electrons of its CN triple bond [Correction added on 17 July 2024, after first online publication: Acetole has been changed to Acetonitrile in the preceeding sentence.]. Interestingly, acetonitrile exhibits an unexpected strengthening of the triple bond's force constant in an aqueous environment, leading to an upshift (blueshift) in the corresponding stretching vibration: this effect contrasts with the usual consequence of hydrogen bonding on the vibrational frequencies of the acceptor groups, that is, frequency redshift. This investigation elucidates this phenomenon using Raman spectroscopy to examine the behavior of acetonitrile in organic solvent, water, and silver ion aqueous solutions, where an even more pronounced upshift is observed. Raman spectroscopy is particularly well suited for analyzing aqueous solutions due to the minimal scattering effect of water molecules across most of the vibrational spectrum. Computational approaches, both static and dynamical, based on Density Functional Theory and hybrid functionals, are employed here to interpret these findings, and accurately reproduce the vibrational frequencies of acetonitrile in different environments. Our calculations also allow an explanation for this unique behavior in terms of electric charge displacements. On the other hand, the study of the interaction of acetonitrile with water molecules and metal ions is relevant for the use of this molecule as a solvent in both chemical and pharmaceutical applications.

Quantum-Chemistry Study of the Hydrolysis Reaction Profile in Borate Networks: A Benchmark.

This investigation involved an ab initio and Density Functional Theory (DFT) analysis of the hydrolysis mechanism and energetics in a borate network. The focus was on understanding how water molecules interact with and disrupt the borate network, an area where the experimental data are scarce and unreliable. The modeled system consisted of two boron atoms, bridging oxygen atoms, and varying numbers of water molecules. This setup allows for an exploration of hydrolysis under different environmental conditions, including the presence of OH- or H+ ions to simulate basic or acidic environments, respectively. Our investigation utilized both ab initio calculations at the MP2 and CCSD(T) levels and DFT with a range of exchange-correlation functionals. The findings indicate that the borate network is significantly more susceptible to hydrolysis in a basic environment, with respect to an acidic or to a neutral pH setting. The inclusion of explicit water molecules in the calculations can significantly affect the results, depending on the nature of the transition state. In fact, some transition states exhibited closed-ring configurations involving water and the boron-oxygen-boron network; in these cases, there were indeed more water molecules corresponding to lower energy barriers for the reaction, suggesting a crucial role of water in stabilizing the transition states. This study provides valuable insights into the hydrolysis process of borate networks, offering a detailed comparison between different computational approaches. The results demonstrate that the functionals B3LYP, PBE0, and wB97Xd closely approximated the reference MP2 and CCSD(T) calculated reaction pathways, both qualitatively in terms of the mechanism, and quantitatively in terms of the differences in the reaction barriers within the 0.1-0.2 eV interval for the most plausible reaction pathways. In addition, CAM-B3LYP also yielded acceptable results in all cases except for the most complicated pathway. These findings are useful for guiding further computational studies, including those employing machine learning approaches, and experimental investigations requiring accurate reference data for hydrolysis reactions in borate networks.

Unraveling the complexity of amyloid polymorphism using gold nanoparticles and cryo-EM.

Increasing evidence suggests that amyloid polymorphism gives rise to different strains of amyloids with distinct toxicities and pathology-spreading properties. Validating this hypothesis is challenging due to a lack of tools and methods that allow for the direct characterization of amyloid polymorphism in hydrated and complex biological samples. Here, we report on the development of 11-mercapto-1-undecanesulfonate-coated gold nanoparticles (NPs) that efficiently label the edges of synthetic, recombinant, and native amyloid fibrils derived from different amyloidogenic proteins. We demonstrate that these NPs represent powerful tools for assessing amyloid morphological polymorphism, using cryogenic transmission electron microscopy (cryo-EM). The NPs allowed for the visualization of morphological features that are not directly observed using standard imaging techniques, including transmission electron microscopy with use of the negative stain or cryo-EM imaging. The use of these NPs to label native paired helical filaments (PHFs) from the postmortem brain of a patient with Alzheimer's disease, as well as amyloid fibrils extracted from the heart tissue of a patient suffering from systemic amyloid light-chain amyloidosis, revealed a high degree of homogeneity across the fibrils derived from human tissue in comparison with fibrils aggregated in vitro. These findings are consistent with, and strongly support, the emerging view that the physiologic milieu is a key determinant of amyloid fibril strains. Together, these advances should not only facilitate the profiling and characterization of amyloids for structural studies by cryo-EM, but also pave the way to elucidate the structural basis of amyloid strains and toxicity, and possibly the correlation between the pathological and clinical heterogeneity of amyloid diseases.

Alginate Beads Containing Cerium-Doped Mesoporous Glass and Curcumin: Delivery and Stabilization of Therapeutics.

Cancer is a leading cause of death worldwide, its genesis and progression are caused by homeostatic errors, and reactive oxygen species play a major role in promoting aberrant cancer homeostasis. In this scenario, curcumin could be an interesting candidate due to its versatile antioxidant, anti-inflammatory, anti-tumor, anti-HIV, and anti-infection properties. Nonetheless, the major problem related to its use is its poor oral bioavailability, which can be overcome by encapsulating it into small particles, such as hydrogel beads containing mesoporous silica. In this work, various systems have been synthesized: starting from mesoporous silica glasses (MGs), cerium-containing MGs have been produced; then, these systems have been loaded with 4 to 6% of curcumin. Finally, various MGs at different compositions have been included in alginate beads. In vitro studies showed that these hybrid materials enable the stabilization and effective delivery of curcumin and that a synergic effect can be achieved if Ce3+/Ce4+ and curcumin are both part of the beads. From swelling tests, it is possible to confirm a controlled curcumin release compartmentalized into the gastrointestinal tract. For all beads obtained, a curcumin release sufficient to achieve the antioxidant threshold has been reached, and a synergic effect of cerium and curcumin is observed. Moreover, from catalase mimetic activity tests, we confirm the well-known catalytic activity of the couple Ce3+/Ce4+. In addition, an extremely good radical scavenging effect of curcumin has been demonstrated. In conclusion, these systems, able to promote an enzymatic-like activity, can be used as drug delivery systems for curcumin-targeted dosing.

Can DFT Calculations Provide Useful Information for SERS Applications?

Density functional theory (DFT) calculations allow us to reproduce the SERS (surface-enhanced Raman scattering) spectra of molecules adsorbed on nanostructured metal surfaces and extract the most information this spectroscopy is potentially able to provide. The latter point mainly concerns the anchoring mechanism and the bond strength between molecule and metal as well as the structural and electronic modifications of the adsorbed molecule. These findings are of fundamental importance for the application of this spectroscopic technique. This review presents and discusses some SERS-DFT studies carried out in Italy as a collaboration between the universities of Modena and Reggio-Emilia and of Florence, giving an overview of the information that we can extract with a combination of experimental SERS spectra and DFT modeling. In addition, a selection of the most recent studies and advancements on the DFT approach to SERS spectroscopy is reported with commentary.

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters.

Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems. As a prototype system, we used fused silica, which easily crystallizes to ß-cristobalite through MetaD simulations, owing to its simple microstructure. We investigated the influence of the height, width, and bias factor used to define the biasing Gaussian potential, as well as the effects of the temperature and system size on the results. Among these parameters, the bias factor and temperature seem to be most effective in sampling the free energy landscape of melt to crystal transition and reaching convergence more quickly. We also demonstrate that the temperature rescaling from T > Tm is a reliable approach to recover free energy surfaces below Tm, provided that the temperature gap is below 600 K and the configurational space has been properly sampled. Finally, albeit a complete crystallization is hard to achieve with large simulation boxes, these can be reliably and effectively exploited to study the first stages of nucleation.

Novel Pet-Degrading Enzymes: Structure-Function from a Computational Perspective.

The bacterium strain Ideonella sakaiensis 201-F6 is able to hydrolyze low-crystallinity PET films at 30 °C due to two enzymes named PETase and MHETase. Since its discovery, many efforts have been dedicated to elucidating the structure and features of those two enzymes, and various authors have highlighted the necessity to optimize both the substrate binding site and the global structure in order to enhance the stability and catalytic activity of these PET biocatalysts so as to make them more suitable for industrial applications. In this review, the strategies adopted by different research groups to investigate the structure and functionality of both PETase and MHETase in depth are described, emphasizing the advantages provided by the use of computational methods to complement and drive experiments. Subsequently, the modifications implemented with protein engineering are discussed. The versatility of the enzymes secreted by I. sakaiensis enables the prediction that they will find several applications in the disposal of PET debris, encouraging a prioritization of efforts in this prolific research field.

Development and Application of a ReaxFF Reactive Force Field for Cerium Oxide/Water Interfaces.

Ceria (CeO2) is a well-known catalytic oxide with many environmental, energy production, and industrial applications, most of them involving water as a reactant, byproduct, solvent, or simple spectator. In this work, we parameterized a Ce/O/H ReaxFF for the study of ceria and ceria/water interfaces. The parameters were fitted to an ab initio training set obtained at the DFT/PBE0 level, including the structures, cohesive energies, and elastic properties of the crystalline phases Ce, CeO2, and Ce2O3; the O-defective structures and energies of vacancy formation on CeO2 bulk and CeO2 (111) surface, as well as the absorption and reaction energies of H2 and H2O molecules on CeO2 (111). The new potential reproduced reasonably well all the fitted properties as well as the relative stabilities of the different ceria surfaces, the oxygen vacancies formation, and the energies and structures of associative and dissociative water molecules on them. Molecular dynamics simulations of the liquid water on the CeO2 (111) and CeO2 (100) surfaces were carried out to study the coverage and the mechanism of water dissociation. After equilibration, on average, 35% of surface sites of CeO2 (111) are hydroxylated whereas 15% of them are saturated with molecular water associatively adsorbed. As for the CeO2 (100) surface, we observed that water preferentially dissociates covering 90% of the available surface sites in excellent agreement with recent experimental findings.

Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles.

Protein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse-grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS-capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems.

Disclosing the Interaction of Gold Nanoparticles with Aß(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations.

Amyloid-ß aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-ß monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming ß-sheets secondary structures that are characteristics of mature amyloid fibrils.

Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aß(1-40) Monomers by Means of Molecular Dynamics.

In this study, we compared the effects of two well-known natural compounds on the early step of the fibrillation process of amyloid-ß (1-40), responsible for the formation of plaques in the brains of patients affected by Alzheimer's disease (AD). The use of extensive replica exchange simulations up to the µs scale allowed us to characterize the inhibition activity of (-)-epigallocatechin-3-gallate (EGCG) and curcumin (CUR) on unfolded amyloid fibrils. A reduced number of ß-strands, characteristic of amyloid fibrils, and an increased distance between the amino acids that are responsible for the intra- and interprotein aggregations are observed. The central core region of the amyloid-ß (Aß(1-40)) fibril is found to have a high affinity to EGCG and CUR due to the presence of hydrophobic residues. Lastly, the free binding energy computed using the Poisson Boltzmann Surface Ares suggests that EGCG is more likely to bind to unfolded Aß(1-40) fibrils and that this molecule can be a good candidate to develop new and more effective congeners to treat AD.

Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles.

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration.

Curcumin derivatives and Aß-fibrillar aggregates: An interactions' study for diagnostic/therapeutic purposes in neurodegenerative diseases.

Several neurodegenerative diseases, like Alzheimer's (AD), are characterized by amyloid fibrillar deposition of misfolded proteins, and this feature can be exploited for both diagnosis and therapy design. In this paper, structural modifications of curcumin scaffold were examined in order to improve its bioavailability and stability in physiological conditions, as well as its ability to interfere with ß-amyloid fibrils and aggregates. The acid-base behaviour of curcumin derivatives, their pharmacokinetic stability in physiological conditions, and in vitro ability to interfere with Aß fibrils at different incubation time were investigated. The mechanisms governing these phenomena have been studied at atomic level by means of molecular docking and dynamic simulations. Finally, biological activity of selected curcuminoids has been investigated in vitro to evaluate their safety and efficiency in oxidative stress protection on hippocampal HT-22 mouse cells. Two aromatic rings, π-conjugated structure and H-donor/acceptor substituents on the aromatic rings showed to be the sine qua non structural features to provide interaction and disaggregation activity even at very low incubation time (2h). Computational simulations proved that upon binding the ligands modify the conformational dynamics and/or interact with the amyloidogenic region of the protofibril facilitating disaggregation. Significantly, in vitro results on hippocampal cells pointed out protection against glutamate toxicity and safety when administered at low concentrations (1 µM). On the overall, in view of its higher stability in physiological conditions with respect to curcumin, of his rapid binding to fibrillar aggregates and strong depolymerizing activity, phtalimmide derivative K2F21 appeared a good candidate for both AD diagnostic and therapeutic purposes.

Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-ß(1⁻40) Fibrils.

One of the principal hallmarks of Alzheimer's disease (AD) is related to the aggregation of amyloid-ß fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists of either blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-epigallocatechin-3-gallate, quercetin, and rosmarinic acid) with amyloid-ß(1⁻40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulates the double-layered structure stability.

Synthesis, Characterization, and Selective Delivery of DARPin-Gold Nanoparticle Conjugates to Cancer Cells.

We demonstrate that the designed ankyrin repeat protein (DARPin)_9-29, which specifically targets human epidermal growth factor receptor 2 (HER 2), binds tightly to gold nanoparticles (GNPs). Binding of the protein strongly increases the colloidal stability of the particles. The results of experimental analysis and molecular dynamics simulations show that approximately 35 DARPin_9-29 molecules are bound to the surface of a 5 nm GNP and that the binding does not involve the receptor-binding domain of the protein. The confocal fluorescent microscopy studies show that the DARPin-coated GNP conjugate specifically interacts with the surface of human cancer cells overexpressing epidermal growth factor receptor 2 (HER2) and enters the cells by endocytosis. The high stability under physiological conditions and high affinity to the receptors overexpressed by cancer cells make conjugates of plasmonic gold nanostructures with DARPin molecules promising candidates for cancer therapy.

Phenylindenone isomers as divergent modulators of p38α MAP kinase.

Two new fluorophenylindenone derivatives were designed as potential p38α MAPK modulators by preserving the key interactions of the vicinal pyridine/fluorophenyl pharmacophore with the enzyme protein. Interestingly, these two fluorophenylindenone isomers showed divergent activities, with compound 6 behaving as an inhibitor and 5 as a putative activator. These results were rationalized by docking studies and molecular dynamics simulations in terms of stabilization of DFG loop, by compound 5 in a conformation more accessible to phosphorylation.

DFT and TD-DFT assessment of the structural and optoelectronic properties of an organic-Ag14 nanocluster.

An extensive benchmark of exchange-correlation functionals on the structure of the X-ray resolved phosphine and thiolate-protected Ag14-based nanocluster, named XMC1, is reported. Calculations were performed both on simplified model systems, with the complexity of the ligands greatly reduced, and on the complete XMC1 particle. Most of the density functionals that yielded good relaxed structures on analogous calculations on gold nanoclusters (viz. those employing the generalized gradient approximation) significantly deform the structure of XMC1. On the contrary, some of the exchange-correlation functionals including part of the exact Hartree-Fock exchange (hybrid functionals) reproduce the experimental geometry with minimal errors. In particular, the widely adopted B3LYP yields fairly accurate structures for XMC1, whereas it is outperformed by many other functionals (both hybrids and generalized gradient corrected) in similar calculations on analogous gold-based systems. Time-dependent density functional calculations have been employed to recover the experimental UV-vis spectrum. The present investigation shows that to correctly reproduce the optical feature of XMC1 the ligands cannot be omitted, because they interact with the metal core at energies much closer to the optical gap than in the case of gold-based nanoclusters of similar sizes. Due to this fact, a functional that accurately describes charge-transfer electronic transitions (such as the long-range corrected CAM-B3LYP) has to be adopted.

Calcium environment in silicate and aluminosilicate glasses probed by 4³Ca MQMAS NMR experiments and MD-GIPAW calculations.

4³Ca MQMAS NMR spectra of three silica-based glasses in which Ca²âº ions play different structural roles have been collected and processed in order to extract the underlying NMR parameter distributions. The NMR parameters have been interpreted with the help of molecular dynamics simulations and DFT-GIPAW calculations. This synergetic experimental-computational approach has allowed us to investigate the Ca environment, to estimate Ca coordination numbers from MD-derived models, and to push further the discussion about 4³Ca NMR sensitivity to the first and second coordination spheres: 4³Ca δiso and Ca-O distance can be successfully correlated as a function of Ca coordination number.

Unraveling the polymorphism of [(p-cymene)Ru(κN-INA)Cl2] through dispersion-corrected DFT and NMR GIPAW calculations.

The structural and (13)C/(1)H NMR parameters of the four crystal forms (1α, 1·H2O, 1ß, and 1γ) of the solid wheel-and-axle (WAA) metal-organic compound [(p-cymene)Ru(κN-INA)Cl2] have been studied by means of periodic DFT calculations. The quality of the results obtained strongly depends on a correct description of long-range interactions; thus, in the geometry refinement protocol used, the pure DFT functionals need to be coupled with a dispersion-correction term (B3LYP-D2, B3LYP-D*). The solid-state (13)C/(1)H NMR δ(iso) parameters and (13)C MAS NMR spectra, calculated by means of the PBE-GIPAW method, agree well with the experimental data for the four crystal forms (mean absolute deviations of the (13)C and (1)H δ(iso) data values lie in the ranges 1.3-2.9 and 0.3-1.0 ppm, respectively). In this context, some revisions in the experimental assignment of the (13)C/(1)H NMR δ(iso) parameters of the 1·H2O, 1ß, and 1γ crystal forms can be suggested. The mismatch in the assignment seems to be due to the rotation of the -COOH moiety, which occurs at the 1α-1·H2O transition and was not considered in the experiments. Finally, the results obtained suggest the presence of two COOH···Cl hydrogen bonds of comparable strength established by the two molecules in the asymmetric unit of the 1γ polymorph, in partial disagreement with previous findings.

On the opto-electronic properties of phosphine and thiolate-protected undecagold nanoclusters.

We present here a detailed time-dependent density-functional theory investigation aimed at systematically dissecting the electronic spectra of two thiolate and phosphine protected undecagold nanoclusters. Calculations performed on the experimental structures of Au11(PPh3)7Cl3 and Au11(PPh3)7(SPyr)3 show that ligands have negligible contributions in the visible region. Metal → ligand charge transfer transitions appear at energies well above the visible threshold, while transitions with some small ligand → metal and ligand → ligand character occur sporadically at even higher energies. Thus, the conjugation effect between the π-electrons of the ligand and electrons of gold, recently hypothesized to interpret the spectra of phosphine and thiolate-protected nanoclusters, is not confirmed by the results of this study.