Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates

Computational density-functional approaches on finite-size and guest-lattice effects in CO2@sII clathrate hydrate

We performed first-principles computations to investigate guest-host/host-host effects on the encapsulation of the CO₂ molecule in sII clathrate hydrates from finite-size clusters up to periodic 3D crystal lattice systems. Structural and energetic properties were first computed for the individual and first-neighbors clathrate-like sII cages, where highly accurate ab initio quantum chemical methods are available nowadays, allowing in this way the assessment of the density functional (DFT) theoretical approaches employed. The performance of exchange-correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. On this basis, structural relaxations of the CO₂-filled and empty sII unit cells yield lattice and compressibility parameters comparable to experimental and previous theoretical values available for sII hydrates. According to these data, the CO₂ enclathration in the sII clathrate cages is a stabilizing process, either by considering both guest-host and host-host interactions in the complete unit cell or only the guest-water energies for the individual clathrate-like sII cages. CO₂@sII clathrates are predicted to be stable whatever the dispersion correction applied and in the case of single cage occupancy are found to be more stable than the CO₂@sI structures. Our results reveal that DFT approaches could provide a good reasonable description of the underlying interactions, enabling the investigation of formation and transformation processes as a function of temperature and pressure.

Modeling of the adsorption of a protein-fragment on kaolinite with potential antiviral activity

This work aimed at studying the potentiality of interactions between kaolinite surfaces and a protein-fragment (350-370 amino acid units) extracted from the glycoprotein E1 in the transmembrane domain (TMD) of hepatitis C virus capsid. A computational work was performed for locating the potential electrostatic interaction sites between kaolinite aluminol and siloxane surfaces and the residues of this protein-fragment ligand, monitoring the possible conformational changes. This hydrated neutralized kaolinite/protein-fragment system was simulated by means of molecular modeling based on atomistic force fields based on empirical interatomic potentials and molecular dynamic (MD) simulations. The MD calculations indicated that the studied protein-fragment interacted with the kaolinite surfaces with an exothermic process and structural distortions were observed, particularly with the hydrophilic aluminol surface by favorable adsorption energy. The viral units isolation or trapping by the adsorption on the kaolinite nanoparticles producing structural distortion of the peptide ligands could lead to the blockage of the entry on the receptor and hence a lack of viral activity would be produced. Therefore, these findings with the proposed insights could be an useful information for the next experimental and development studies in the area of discovering inhibitors of the global challenged hepatitis and other pathogenic viruses based on the phyllosilicate surface activity. These MD studies can be extended to other viruses like the COVID-19 interacting with silicate minerals surfaces.

Molecular Insights into Cage Occupancy of Hydrogen Hydrate: A Computational Study

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases?

The subject of this Perspective is quantum approaches, beyond the harmonic approximation, to vibrational dynamics and IR spectroscopy.

Conformational polymorphic changes in the crystal structure of the chiral antiparasitic drug praziquantel and interactions with calcium carbonate

Praziquantel is an antiparasitic drug used for decades. Currently, the praziquantel commercial preparation is a racemic mixture, in which only the levo-enantiomer possesses anthelmintic activity. The knowledge of its properties in the solid state and other chemical-physical properties is necessary for improving its efficacy and applications. Drug solid dispersions were prepared with calcium carbonate at 1:5 drug to excipient weight ratio by solvent evaporation method. Then, the modification of the crystal structure of the racemic polymorph of praziquantel in presence of calcium carbonate has been studied by means of several analytical techniques (DSC, TGA, XRD, SEM, FTIR, Raman spectroscopy and chiral liquid chromatography). This study has been completed with atomistic calculations based on empirical interatomic force fields and quantum mechanics methods applied to the crystal structure of praziquantel and of intermolecular interactions. The results evidenced that calcium carbonate provoked a conformational change in the praziquantel molecule yielding the formation of different polymorphs of praziquantel crystal. These alterations were not observed replacing calcium carbonate with colloidal silica as excipient in the solid dispersion.

A Systematic Protocol for Benchmarking Guest-Host Interactions by First-Principles Computations: Capturing CO2 in Clathrate Hydrates

Clathrate hydrates of CO₂ have been proposed as potential molecular materials in tackling important environmental problems related to greenhouse gases capture and storage. Despite the increasing interest in such hydrates and their technological applications, a molecular-level understanding of their formation and properties is still far from complete. Modeling interactions is a challenging and computationally demanding task, essential to reliably determine molecular properties. First-principles calculations for the CO₂ guest in all sI, sII, and sH clathrate cages were performed, and the nature of the guest-host interactions, dominated by both hydrogen-bond and van der Waals forces, was systematically investigated. Different families of density functionals, as well as pairwise CO₂ @H₂ O model potentials versus wavefunction-based quantum approaches were studied for CO₂ clathrate-like systems. Benchmark energies for new distance-dependent datasets, consisting of potential energy curves sampling representative configurations of the systems at the repulsive, near-equilibrium, and asymptotic/long-range regions of the full-dimensional surface, were generated, and a general protocol was proposed to assess the accuracy of such conventional and modern approaches at minimum and non-minimum orientations. Our results show that dispersion interactions are important in the guest-host stabilization energies of such clathrate cages, and the encapsulation of the CO₂ into guest-free clathrate cages is always energetically favorable. In addition, the orientation of CO₂ inside each cage was explored, and the ability of current promising approaches to accurately describe non-covalent CO₂ @H₂ O guest-host interactions in sI, sII, and sH clathrates was discussed, providing information for their applicability to future multiscale computer simulations.

DFT calculation of the potential energy landscape topology and Raman spectra of type I CH4and CO2hydrates

Type I methane and carbon dioxide hydrates analyzed using DFT calculations: Raman spectra and potential energy landscape.

Indigo adsorption on a silicate surface: a theoretical density functional study

The applicability of naturally available low-cost and eco-friendly adsorbent materials for the removal of hazardous dyes from aqueous waste is of increasing environmental interest. Among the adsorption treatments available, clays seem to be economically attractive due to their abundance and adsorption capabilities. Indeed, many ancient coloring materials utilized clays mixed with natural dyes (e.g., indigo in Maya Blue). In this work, we performed a quantum-mechanical theoretical study of the adsorption of the indigo molecule onto the (001) surface of a phyllosilicate. Different methods and approaches were applied and compared. We found that the presence of a tetrahedral charge and a sodium counterion significantly increased the adsorption energy of the indigo molecule. The vibrational spectrum of the dye-surface system was also studied, and some interesting shifts in the frequencies of the main vibrational modes of indigo due to its interaction with the surface of the clay mineral were identified.

Characterization of CO2 and mixed methane/CO2 hydrates intercalated in smectites by means of atomistic calculations

The recent increase in anthropogenic CO2 gas released to the atmosphere and its contribution to global warming make necessary to investigate new ways of CO2 storage. Injecting CO2 into subsurface CH4 hydrate reservoirs would displace some of the CH4 in the hydrate crystal lattice, converting simple CH4 hydrates into either simple CO2 hydrates or mixed CH4CO2 hydrates. Molecular simulations were performed to determine the structure and behavior of CO2 and mixed hydrate complexes in the interlayer of Na-rich montmorillonite and beidellite smectite. Molecular Dynamics (MD) simulations used NPT ensembles in a 4×4×1 supercell comprised of montmorillonite or beidellite with CO2 or mixed CH4/CO2 hydrate complexes in the interlayer. The smectite 2:1 layer surface helps provide a stabilizing influence on the formation of gas hydrate complexes. The type of smectite affects the stability of the smectite-hydrate complexes, where high charge located on the tetrahedral layer of the smectites disfavor the formation of hydrate complexes.