Nanocellulose-Bovine Serum Albumin Interactions in an Aqueous Medium: Investigations Using In Situ Nanocolloidal Probe Microscopy and Reactive Molecular Dynamics Simulations.

As a versatile nanomaterial derived from renewable sources, nanocellulose has attracted considerable attention for its potential applications in various sectors, especially those focused on water treatment and remediation. Here, we have combined atomic force microscopy (AFM) and reactive molecular dynamics (RMD) simulations to characterize the interactions between cellulose nanofibers modified with carboxylate or phosphate groups and the protein foulant model bovine serum albumin (BSA) at pH 3.92, which is close to the isoelectric point of BSA. Colloidal probes were prepared by modification of the AFM probes with the nanofibers, and the nanofiber coating on the AFM tip was for the first time confirmed through fluorescence labeling and confocal optical sectioning. We have found that the wet-state normalized adhesion force is approximately 17.87 ± 8.58 pN/nm for the carboxylated cellulose nanofibers (TOCNF) and about 11.70 ± 2.97 pN/nm for the phosphorylated ones (PCNF) at the studied pH. Moreover, the adsorbed protein partially unfolded at the cellulose interface due to the secondary structure's loss of intramolecular hydrogen bonds. We demonstrate that nanocellulose colloidal probes can be used as a sensitive tool to reveal interactions with BSA at nano and molecular scales and under in situ conditions. RMD simulations helped to gain a molecular- and atomistic-level understanding of the differences between these findings. In the case of PCNF, partially solvated metal ions, preferentially bound to the phosphates, reduced the direct protein-cellulose connections. This understanding can lead to significant advancements in the development of cellulose-based antifouling surfaces and provide crucial insights for expanding the pH range of use and suggesting appropriate recalibrations.

Achieving Sub-ppm Sensitivity in SO2 Detection with a Chemically Stable Covalent Organic Framework.

We report the inaugural experimental investigation of covalent organic frameworks (COFs) to address the formidable challenge of SO2 detection. Specifically, an imine-functionalized COF (SonoCOF-9) demonstrated a modest and reversible SO2 sorption of 3.5 mmol g-1 at 1 bar and 298 K. At 0.1 bar (and 298 K), the total SO2 uptake reached 0.91 mmol g-1 with excellent reversibility for at least 50 adsorption-desorption cycles. An isosteric enthalpy of adsorption (ΔHads) for SO2 equaled -42.3 kJ mol-1, indicating a relatively strong interaction of SO2 molecules with the COF material. Also, molecular dynamics simulations and Møller-Plesset perturbation theory calculations showed the interaction of SO2 with π density of the rings and lone pairs of the N atoms of SonoCOF-9. The combination of experimental data and theoretical calculations corroborated the potential use of this COF for the selective detection and sensing of SO2 at the sub-ppm level (0.0064 ppm of SO2).

An Atomically Dispersed Mn-Photocatalyst for Generating Hydrogen Peroxide from Seawater via the Water Oxidation Reaction (WOR).

In this work, we have fabricated an aryl amino-substituted graphitic carbon nitride (g-C3N4) catalyst with atomically dispersed Mn capable of generating hydrogen peroxide (H2O2) directly from seawater. This new catalyst exhibited excellent reactivity, obtaining up to 2230 µM H2O2 in 7 h from alkaline water and up to 1800 µM from seawater under identical conditions. More importantly, the catalyst was quickly recovered for subsequent reuse without appreciable loss in performance. Interestingly, unlike the usual two-electron oxygen reduction reaction pathway, the generation of H2O2 was through a less common two-electron water oxidation reaction (WOR) process in which both the direct and indirect WOR processes occurred; namely, photoinduced h+ directly oxidized H2O to H2O2 via a one-step 2e- WOR, and photoinduced h+ first oxidized a hydroxide (OH-) ion to generate a hydroxy radical (•OH), and H2O2 was formed indirectly by the combination of two •OH. We have characterized the material, at the catalytic sites, at the atomic level using electron paramagnetic resonance, X-ray absorption near edge structure, extended X-ray absorption fine structure, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, magic-angle spinning solid-state NMR spectroscopy, and multiscale molecular modeling, combining classical reactive molecular dynamics simulations and quantum chemistry calculations.

Lignin-Supported Heterogeneous Photocatalyst for the Direct Generation of H2O2 from Seawater.

The development of smart and sustainable photocatalysts is in high priority for the synthesis of H2O2 because the global demand for H2O2 is sharply rising. Currently, the global market share for H2O2 is around 4 billion US$ and is expected to grow by about 5.2 billion US$ by 2026. Traditional synthesis of H2O2 via the anthraquinone method is associated with the generation of substantial chemical waste as well as the requirement of a high energy input. In this respect, the oxidative transformation of pure water is a sustainable solution to meet the global demand. In fact, several photocatalysts have been developed to achieve this chemistry. However, 97% of the water on our planet is seawater, and it contains 3.0-5.0% of salts. The presence of salts in water deactivates the existing photocatalysts, and therefore, the existing photocatalysts have rarely shown reactivity toward seawater. Considering this, a sustainable heterogeneous photocatalyst, derived from hydrolysis lignin, has been developed, showing an excellent reactivity toward generating H2O2 directly from seawater under air. In fact, in the presence of this catalyst, we have been able to achieve 4085 µM of H2O2. Expediently, the catalyst has shown longer durability and can be recycled more than five times to generate H2O2 from seawater. Finally, full characterizations of this smart photocatalyst and a detailed mechanism have been proposed on the basis of the experimental evidence and multiscale/level calculations.

Π-Π Stacking Complex Induces Three-Component Coupling Reactions To Synthesize Functionalized Amines.

π-π stacking and ion-pairing interactions induced the generation of α-amino radicals under the irradiation of visible light without the requirement of an expensive photocatalyst. This strategy enabled the construction of functionalized amines via three-component coupling reactions with broad scope (we report >50 examples with an up to 90 % yield). This synthetic pathway also delivered complex functionalized amines with a very high yield. Quantum chemistry Density Functional Theory (DFT) calculations identified π-π stacked ionic complexes; time-dependent DFT was employed to simulate the absorption spectra, and nudged elastic band (NEB) methodology provided a possible interaction/reaction picture of the selected species.

A close view of the organic linker in a MOF: structural insights from a combined 1H NMR relaxometry and computational investigation.

The organic linker in a metal organic framework (MOF) affects its adsorption behavior and performance, and its structure and dynamics play a role in the modulation of the adsorption properties. In this work, the combination of 1H nuclear magnetic resonance (NMR) longitudinal relaxometry and theoretical calculations allowed details of the structure and dynamics of the organic linker in the NH2-MIL-125 MOF to be obtained. In particular, fast field cycling (FFC) NMR, applied here for the first time on MOFs, was used to disclose the dynamics of the amino group and its electronic environment through the analysis of the 14N quadrupole relaxation peaks, observed in the frequency interval 0.5-5 MHz, at different temperatures from 25 to 110 °C. The line width of the peaks allowed a lower boundary on the rotational correlation time of the N-H bonds to be set, whereas relevant changes in the amplitudes were interpreted in terms of a change in the orientation of the 14N averaged electric field gradient tensor. The experimental findings were complemented by quantum chemistry calculations and classical molecular dynamics simulations.

Structure and dynamics of gold nanoparticles decorated with chitosan-gentamicin conjugates: ReaxFF molecular dynamics simulations to disclose drug delivery.

With the aim of designing an efficient procedure for producing biocompatible drug delivery systems based on nanoparticle carriers for in situ controlled antibiotic release, we have defined a novel computational approach resorting to a reactive force field capable of realistically describing hybrid systems. The modeling procedure was focused on well-known components, namely gold nanoparticles, citrate, chitosan and gentamicin, and the experiments tuned on purpose. On the one hand, gold nanoparticles were synthesized, fuctionalized with chitosan, loaded with gentamicin and characterized by means of transmission electron microscopy (TEM), scanning electron microscopy (SEM), dynamic light scattering (DLS), UV-visible (UV-vis) spectroscopy, and Fourier transform infrared spectroscopy (FTIR). On the other hand, an effective model of a functionalized gold nanoparticle was created and its structure and dynamics were explored by classical reactive molecular dynamics simulations in solution based on the ReaxFF atomistic description. The structure, dynamics and drug release were reproduced realistically disclosing the motion of all the molecular components, their adsorption on the metal support, desorption, intermolecular interactions and self-assembly. The system size was very close to the experimental conditions and all the calculations could efficiently identify the most probable binding modes, the locations of the adsorbed molecules, the characteristic arrangements of the chains and the effects due to the surrounding environment. The role played by the substrate and water molecules in the releasing process was described in detail. In line with the literature it was found that the antibiotic activity was preserved and the drug release from the carrier could be tuned by changing the chitosan/getamicin weight ratio and the deposition pattern of the adsorbed layers.

Experimental and theoretical elucidation of catalytic pathways in TiO2-initiated prebiotic polymerization.

The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.

Molecular dynamics simulations of melting and sintering of Si nanoparticles: a comparison of different force fields and computational models.

Melting and sintering of silicon nanoparticles are investigated by means of classical molecular dynamics simulations to disclose the dependence of modelling on the system type, the simulation procedure and interaction potential. The capability of our parametrization of a reactive force field ReaxFF to describe such processes is assessed through a comparison with formally simpler Stillinger-Weber and Tersoff potentials, which are frequently used for simulating silicon-based materials. A substantial dependence of both the predicted melting point and its variation as a function of the nanoparticle size on the simulation model is also highlighted. The outcomes of the molecular dynamics simulations suggest that the trend of the nanoparticulate sintering/coalescence time vs. temperature could provide a valid tool to determine the melting points of nanoparticles theoretically/experimentally.

Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution.

The adsorption and dynamics of cystine, which is the oxidized dimer of cysteine where the monomers are connected through a disulfide bond, on the Au(110) surface, in water solution, is characterized by means of classical molecular dynamics simulations based on a recently developed reactive force field (ReaxFF). The adopted computational procedure and the force field description are able to give a complete and reliable picture, in line with experiments, of the molecule behavior in solution and in close contact with the metal support. Many different aspects, which have never been explored computationally at this level of theory, are disclosed, namely, physisorption, chemisorption, disulfide bridge breaking/creation, and formation of staples. It is demonstrated that all these events are connected with the specific orientation and location of cystine on the substrate. Simulations in pure water reveal that the disulfide bridge is stable, whereas dissociation is observed on gold. This is favored at low coverage, whereas at high coverage both intact and dissociated forms can be observed depending on local arrangements. The computed photoemission spectra at different K-edges for the predicted adsorbate structures satisfactorily agree with the experimental measurements extracted from literature.

Experimental and theoretical XPS and NEXAFS studies of N-methylacetamide and N-methyltrifluoroacetamide.

Experimental Near-Edge X-ray Absorption Fine-Structure (NEXAFS) spectra of N-methyltrifluoroacetamide (FNMA), which is a peptide model system, measured at the C, N, O and F K-edges are reported. The features in the spectra have been assigned by Static-Exchange (STEX) calculations. Using the same method, we have also assigned previously measured NEXAFS spectra of another peptide model system, N-methylacetamide (NMA). To facilitate the NEXAFS feature assignments, X-ray Photoelectron Spectroscopy (XPS) measurements for NMA and FNMA have been carried out with the aim of obtaining the 1s electron ionization potentials, which are compared with the values predicted by our Hartree-Fock (ΔHF) and Multi Configuration Self Consistent Field (ΔMCSCF) calculations. We also demonstrate an approach to compensate for screening effects that are neglected in the STEX method. Ion yield measurements of FNMA associated with the excitation of several C, N, O, and F K-shell pre-edge resonances have revealed site-specific fragmentation in some cases which we interpret with the aid of our theoretical calculations.

Computational Study of Acidic and Basic Functionalized Crystalline Silica Surfaces as a Model for Biomaterial Interfaces.

In silico modeling of acidic (CH2COOH) or basic (CH2NH2) functionalized silica surfaces has been carried out by means of a density functional approach based on a gradient-corrected functional to provide insight into the characterization of experimentally functionalized surfaces via a plasma method. Hydroxylated surfaces of crystalline cristobalite (sporting 4.8 OH/nm(2)) mimic an amorphous silica interface as unsubstituted material. To functionalize the silica surface we transformed the surface Si-OH groups into Si-CH2COOH and Si-CH2NH2 moieties to represent acidic/basic chemical character for the substitution. Structures, energetics, electronic, and vibrational properties were computed and compared as a function of the increasing loading of the functional groups (from 1 to 4 per surface unit cell). Classical molecular dynamics simulations of selected cases have been performed through a Reax-FF reactive force field to assess the mobility of the surface added chains. Both DFT and force field calculations identify the CH2NH2 moderate surface loading (1 group per unit cell) as the most stable functionalization, at variance with the case of the CH2COOH group, where higher loadings are preferred (2 groups per unit cell). The vibrational fingerprints of the surface functionalities, which are the ν(C═O) stretching and δ(NH2) bending modes for acidic/basic cases, have been characterized as a function of substitution percentage in order to guide the assignment of the experimental data. The final results highlighted the different behavior of the two types of functionalization. On the one hand, the frequency associated with the ν(C═O) mode shifts to lower wavenumbers as a function of the H-bond strength between the surface functionalities (both COOH and SiOH groups), and on the other hand, the δ(NH2) frequency shift seems to be caused by a subtle balance between the H-bond donor and acceptor abilities of the NH2 moiety. Both sets of data are in general agreement with experimental measurements on the corresponding silica-functionalized materials and provide finer details for a deeper interpretation of experimental spectra.

NEXAFS and XPS studies of nitrosyl chloride.

The electronic structure of nitrosyl chloride (ClNO) has been investigated in the gas phase by X-ray Photoelectron (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy at the Cl 2p, Cl 2s, N 1s and O 1s edges in a combined experimental and theoretical study. The theoretical calculations at different levels of approximation predict ionization potential values in good agreement with the experimental data and allow us to assign the main features of the absorption spectra. An unexpected failure of the density functional model is, however, observed in the calculation of the Cl 2s binding energy, which is related to a large self-interaction error. Largely different photoabsorption cross-section patterns are experimentally observed in core excitations from the investigated quantum shells (n = 1, 2). This finding is confirmed by the oscillator strength distributions calculated at different absorption edges; in the case of the n = 2 shell the bands below the threshold are extremely weak and most of the absorption intensity is due to excitations in the continuum.

The effects of ferulic acid on ß-amyloid fibrillar structures investigated through experimental and computational techniques.

BACKGROUND: Current research has indicated that small natural compounds could interfere with ß-amyloid fibril growth and have the ability to disassemble preformed folded structures. Ferulic acid (FA), which possesses both hydrophilic and hydrophobic moieties and binds to peptides/proteins, is a potential candidate against amyloidogenesis. The molecular mechanisms connected to this action have not been elucidated in detail yet. METHODS: Here the effects of FA on preformed fibrils are investigated by means of a concerted experimental-computational approach. Spectroscopic techniques, such as FTIR, fluorescence, size exclusion chromatography and confocal microscopy in combination with molecular dynamics simulations are used to identify those features which play a key role in the destabilization of the aggregates. RESULTS: Experimental findings highlight that FA has disruptive effects on the fibrils. The computational analysis suggests that dissociation of peptides from the amyloid superstructures could take place along the fibril axis and be primarily determined by the cooperative rupture of the backbone hydrogen bonds and of the Asp-Lys salt bridges. CONCLUSION: FA clusters could induce a sort of stabilization and tightening of the fibril structure in the short term and its disruption in the long term, inhibiting further fibril re-assembly through FA screening effects. GENERAL SIGNIFICANCE: The combination of experimental and computational techniques could be successfully used to identify the disrupting action of FA on preformed Aß fibrils in water solution.

Cysteine on TiO2(110): a theoretical study by reactive dynamics and photoemission spectra simulation.

Owing to the importance of bioinorganic interface properties for the biocompatibility of implants and for biosensing technology, it has become indispensable to gain understanding of their crucial structure-property relations at the atomistic level. Motivated by this fact, we use cysteine amino acid on perfect and defective TiO2(110) surfaces as model systems and study adsorption by means of classical all-atom reactive molecular dynamics and ab initio O 1s, N 1s, and S 2p photoemission spectra (XPS) simulations of the most relevant adsorbate structures. By analysis of the dynamics results and a detailed comparison with spectra recently collected for this adsorbate, we obtain conclusions of both general and particular character. It is shown that the interaction of cysteine with the TiO2(110) surface has multipoint character involving the carboxylic group as well as the amino and sulfur groups. The proton-transfer reactivity of cysteine is enhanced by the presence of the surface, and different forms of cysteines are confirmed to be present in the adsorbate. A general conclusion is that reactive force field dynamics combined with selected spectroscopy provides a viable path to understanding bioinorganic surfaces with ramifications for the design of such surfaces for future technological applications.

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers.

Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

Functionalized Amorphous Carbon Materials via Reactive Molecular Dynamics Simulations.

We derive a database of atomistic structural models of amorphous carbon materials endowed with exohedral functional groups. We start from phases previously derived using the DynReaxMas method for reactive molecular dynamics simulations, which exhibit atomistic and medium-length-scale features in excellent agreement with available experimental data. Given a generic input structure/phase, we develop postprocessing simulation algorithms mimicking experimental preparation protocols aimed at: (1) "curing" the phase to decrease the defect concentration; (2) automatically selecting the most reactive carbon atoms via interaction with a probe molecular species, and (3) stabilizing the phase by saturating the valence of carbon atoms with single-bond functional groups. Although we focus on oxygen-bearing functionalities, they can be replaced with other monovalent groups, such as -H, -COOH, -CHO, so that the protocol is quite general. We finally classify reactive sites in terms of their location within the structural framework and coordination environment (edges, tunnels, rings, aromatic carbons becoming aliphatic) and try to single out descriptors that correlate with tendency to functionalization.

A robust Fe-based heterogeneous photocatalyst for the visible-light-mediated selective reduction of an impure CO2 stream.

The transformation of CO2 into value-added products from an impure CO2 stream, such as flue gas or exhaust gas, directly contributes to the principle of carbon capture and utilization (CCU). Thus, we have developed a robust iron-based heterogeneous photocatalyst that can convert the exhaust gas from the car into CO with an exceptional production rate of 145 µmol g-1 h-1. We characterized this photocatalyst by PXRD, XPS, ssNMR, EXAFS, XANES, HR-TEM, and further provided mechanistic experiments, and multi-scale/level computational studies. We have reached a clear understanding of its properties and performance that indicates that this highly robust photocatalyst could be used to design an efficient visible-light-mediated reduction strategy for the transformation of impure CO2 streams into value-added products.

Theoretical simulations of structure and X-ray photoelectron spectra of glycine and diglycine adsorbed on Cu(110).

The study of adsorption of glycine and glycylglycine (or diglycine) on a copper surface is an important step for the comprehension of mechanisms that determine the stability of biological functionalizers on metal substrates. These two molecules can be considered as prototypes and essential models to investigate, theoretically and experimentally, the adaptability of flexible short peptide chains to a definite interface. In this work, we have improved and updated earlier molecular dynamics simulations by including reactivity of the various species and the comparison of ab initio calculated C, N, and O core photoelectron chemical shifts with the ones found in previous studies. New diglycine-copper bonding is predicted, and the results of the chemical shift analysis are, in all cases, fully compatible with structural information obtained through experimental measurements. Moreover, we have found that the process of proton transfer, which is fundamental in the dynamics of amino acids and peptides, occurs mainly by intermolecular interaction between the first and second layer of the adsorbate.

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.