A DFT study of the adsorption of glycine in the interlayer space of montmorillonite

Intercalation of the anticancer drug lenalidomide into montmorillonite for bioavailability improvement: a computational study

CONTEXT

Lenalidomide (LEN) is used for the treatment of myeloma blood cancer disease. It has become one of the most efficient drugs to halt this disease. LEN is a low-soluble drug in aqueous media. The search of a pharmaceutical preparation to improve the bioavailability and, therefore, to optimize its efficiency is an important issue for pharmaceutical industries and health care. The use of natural excipients such as montmorillonite (MNT) can provide changes in the physical-chemical properties for improving the bioavailability of this drug. We present the first computational study at the atomic scale of the periodic crystal forms of the polymorphs for this anticancer drug, highly demanded in the pharmacy market. In addition, we propose a pharmaceutical preparation by intercalation of LEN in natural MNT. So, our calculations predict that LEN can be intercalated in the interlayer space of MNT, and be released in aqueous media, and physiological aqueous media in consequence. This release process is a more exothermic reaction than the unpacking energy of any of its polymorphs. Besides, the infrared spectra of the LEN molecule and its crystal polymorphs, and LEN intercalated in the confined space of MNT, have been calculated at different levels of theory. The band frequencies have been assigned, matching with the experimental bands, predicting the use of this technique for experimental studies.

METHOD

In this work, the method is aimed to explore this research at the atomic and molecular level by using computational modelling methods including INTERFACE FF and other FF along with quantum mechanical calculations (Dmol3 and CASTEP) of 3-D periodical systems applying periodical boundary conditions. Models of the isolated molecule and two polymorphs of the crystal structures, with the model of bulk water and LEN intercalated in the MNT model, have been considered. An analysis of the intermolecular interactions is accomplished.

The Use of Organoclays as Excipient for Metformin Delivery: Experimental and Computational Study

This work combines experimental and computational modeling studies for the preparation of a composite of metformin and an organoclay, examining the advantages of a Tunisian clay used for drug delivery applications. The clay mineral studied is a montmorillonite-like smectite (Sm-Na), and the organoclay derivative (HDTMA-Sm) was used as a drug carrier for metformin hydrochloride (MET). In order to assess the MET loading into the clays, these materials were characterized by means of cation exchange capacity assessment, specific surface area measurement, and with the techniques of X-ray diffraction (XRD), differential scanning calorimetry, X-ray fluorescence spectroscopy, and Fourier-transformed infrared spectroscopy. Computational molecular modeling studies showed the surface adsorption process, identifying the clay-drug interactions through hydrogen bonds, and assessing electrostatic interactions for the hybrid MET/Sm-Na and hydrophobic interactions and cation exchange for the hybrid MET/HDTMA-Sm. The results show that the clays (Sm-Na and HDTMA-Sm) are capable of adsorbing MET, reaching a maximum load of 12.42 and 21.97 %, respectively. The adsorption isotherms were fitted by the Freundlich model, indicating heterogeneous adsorption of the studied adsorbate-adsorbent system, and they followed pseudo-second-order kinetics. The calculations of ΔGº indicate the spontaneous and reversible nature of the adsorption. The calculation of ΔH° indicates physical adsorption for the purified clay (Sm-Na) and chemical adsorption for the modified clay (HDTMA-Sm). The release of intercalated MET was studied in media simulating gastric and intestinal fluids, revealing that the purified clay (Sm-Na) and the modified organoclay (HDTMA-Sm) can be used as carriers in controlled drug delivery in future clinical applications. The molecular modeling studies confirmed the experimental phenomena, showing that the main adsorption mechanism is the cation exchange process between proton and MET cations into the interlayer space.

Structure and Intercalation of Cysteine-Asparagine-Serine Peptide into Montmorillonite as an Anti-Inflammatory Agent Preparation-A DFT Study

Peptides are receiving significant attention in pharmaceutical sciences due to their applications as anti-inflammatory drugs; however, many aspects of their interactions and mechanisms at the molecular level are not well-known. This work explores the molecular structure of two peptides-(i) cysteine (Cys)-asparagine (Asn)-serine (Ser) (CNS) as a molecule in the gas phase and solvated in water in zwitterion form, and (ii) the crystal structure of the dipeptide serine-asparagine (SN), a reliable peptide indication whose experimental cell parameters are well known. A search was performed by means of atomistic calculations based on density functional theory (DFT). These calculations matched the experimental crystal structure of SN, validating the CNS results and useful for assignments of our experimental spectroscopic IR bands. Our calculations also explore the intercalation of CNS into the interlayer space of montmorillonite (MNT). Our quantum mechanical calculations show that the conformations of these peptides change significantly during intercalation into the confined interlayer space of MNT. This intercalation is energetically favorable, indicating that this process can be a useful preparation for therapeutic anti-inflammatory applications and showing high stability and controlled release processes.

Formation of cation bridges and its promoting mechanism for sorption of sulfamethoxazole by montmorillonite

The coexistence of metal cations is often accompanied by organic pollution and could affect the environmental fate of organics by mediating the formation of cation bridges. However, the environmental fate and risk of organics in cation co-existing environments are poorly understood due to the lack of accurate identification of cation bridge formation and stability. In this study, the sorption of sulfamethoxazole (SMX) on montmorillonite (MT) with the coexistence of three different valence metal cations (Na+, Ca2+, and Cr3+) was investigated. Ca2+ and Cr3+ can significantly promote the sorption of SMX on MT for about 5∼10 times promotion, respectively, while Na+ bridges displayed little effect on the sorption of SMX. The sorption binding energy of SMX with MT-Ca (-44.01 kcal/mol) and MT-Cr (-64.57 kcal/mol) bridges was significantly lower than that with MT-Na (-38.45 kcal/mol) and MT (-39.39 kcal/mol), indicating that the sorption affinity of SMX on Cr and Ca bridges was much stronger. The higher valence of the cations also resulted in a more stable adsorbed SMX with less desorption fluctuation. In addition, the relatively higher initial concentration of SMX and the valence of cations increased the bonding density of the cation bridges, thus promoting the apparent sorption of SMX on MT to a certain extent. This work reveals the formation and function of cation bridges in the sorption of SMX on MT. It lays a theoretical foundation for further understanding the environmental fate and risk of organics.

Adsorption of Ciprofloxacin on Clay Minerals in Argentinian Santa Rosa-Corrientes Soils

The presence of antibiotics in soils is increasing drastically in last decades due to the intensive farming industry and excessive human consumption. Clay minerals are one of the soil components with great adsorption capacity for organic pollutants. The study of interactions between antibiotics and mineral surfaces will give us scientific knowledge of these pollutants through soils. In this work, we study the adsorption of the antibiotic ciprofloxacin in the clay mineral fraction of soils from the Argentinian zone of Santa Rosa (Corrientes), in a collaborative research of experiments and atomistic modelling calculations of the intercalation of ciprofloxacin in the interlayer space of montmorillonite. Adsorption and desorption isotherms were performed and compared with different isotherm models. Additionally, enthalpy, entropy, and free energy were determined from equilibrium constants at a function of temperature. All these experiments and calculations lead to the conclusions that two adsorption types of ciprofloxacin are found on clay minerals: one weakly sorbed that is released during the desorption experiments, and other one strongly joined that remains in the soil.

Exploring the biointerfaces: ab initio investigation of nano-montmorillonite clay, and its interaction with unnatural amino acids

We investigated the interaction between biomimetic Fe and Mg co-doped montmorillonite nanoclay and eleven unnatural amino acids. Employing three different functionals (PBE-GGA, PBE-GGA + U, and HSE06), we examined the clay's structural, electronic, and magnetic properties. Our results revealed the necessity of using PBE-GGA + U with U ≥ 4 eV to accurately describe key clay properties. We identified amino acids that strongly interacted with the clay surface, with steric orientation playing a crucial role in facilitating binding. Our DFT calculations highlighted significant electrostatic interactions between the amino acids and the clay slab, with the amino group's predominant role in this interaction. These findings hold promise for designing amino acids for clay-amino acid systems, leading to innovative bio-material composites for various applications. Additionally, our ab-initio molecular dynamics simulations confirmed the stability of clay-amino acid systems under ambient conditions, and the introduction of an implicit water solvent enhanced the binding energy of amino acids on the clay surface.

Electronic band structure and density of state modulation of amphetamine and ABW type-zeolite adsorption system: DFT-CASTEP analysis

The structured abstract is combined from two parts: CONTEXT: The adsorption behavior of amphetamine (AMP) on the surface of ABW-aluminum silicate zeolite was implemented with a computational depiction. Studies of the electronic band structure (EBS) and density of states (DOS) were conducted to demonstrate transition behavior attributed to aggregate-adsorption interaction. Thermodynamic illustration of the studied adsorbate was studied to investigate the structural behavior of the adsorbate on the surface of the zeolite adsorbent. The best investigated models were assessed with adsorption annealing calculations related to adsorption energy surface. The periodic adsorption-annealing calculation model predicted a highly stable energetic adsorption system based on total energy, adsorption energy, rigid adsorption energy, deformation energy, and dE_ad/d_Ni ratio. METHODS: Cambridge sequential total energy package (CASTEP) based on density functional theory (DFT), under Perdew-Burke-Ernzerhof (PBE) basis set, was used to depict the energetic levels of the adsorption mechanism between AMP and ABW-aluminum silicate zeolite surface. DFT-D dispersion correction function was postulated for weakly interacted systems. Structural and electronic elucidations were described with geometrical optimization, FMOs, and MEP analyses. Thermodynamic parameters such as entropy, enthalpy, Gibbs free energy, and heat capacity over temperature dependence studied the conductivity behavior over localized energetic states based on Fermi level and described the disorder degree of the system.

Adsorption of Capsaicin into the Nanoconfined Interlayer Space of Montmorillonite by DFT Calculations

Capsaicin is the main compound responsible of the hot sense of the chili fruits. This compound has interesting therapeutic properties including anticancer, anti-inflammatory effects, and analgesic. However, its use has several secondary effects, such as skin irritation and allergies. Then, new therapeutic strategies are searched in order to overcome these problems. Montmorillonite has proved to be an excellent excipient for the release of pharmaceutical drugs. In this work, the molecular structure and crystal structure of capsaicin, and the adsorption of this molecule into the interlayer space of montmorillonite have been studied using quantum mechanical calculations based on Density Functional Theory (DFT) level of theory and molecular dynamics simulations. The crystal structure has been predicted with these calculations and the intermolecular interactions have been determined with a higher resolution than the previous experimental data. The adsorption of capsaicin into the confined interlayer space of montmorillonite is energetically favourable with low and high octahedral charge. This adsorption can be monitored by IR spectroscopy observing frequency shifts in some bands during the adsorption. This enhances the use of these clay minerals for capsaicin therapeutic formulations.

Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations

Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.

Clays and the Origin of Life: The Experiments

There are three groups of scientists dominating the search for the origin of life: the organic chemists (the Soup), the molecular biologists (RNA world), and the inorganic chemists (metabolism and transient-state metal ions), all of which have experimental adjuncts. It is time for Clays and the Origin of Life to have its experimental adjunct. The clay data coming from Mars and carbonaceous chondrites have necessitated a review of the role that clays played in the origin of life on Earth. The data from Mars have suggested that Fe-clays such as nontronite, ferrous saponites, and several other clays were formed on early Mars when it had sufficient water. This raised the question of the possible role that these clays may have played in the origin of life on Mars. This has put clays front and center in the studies on the origin of life not only on Mars but also here on Earth. One of the major questions is: What was the catalytic role of Fe-clays in the origin and development of metabolism here on Earth? First, there is the recent finding of a chiral amino acid (isovaline) that formed on the surface of a clay mineral on several carbonaceous chondrites. This points to the formation of amino acids on the surface of clay minerals on carbonaceous chondrites from simpler molecules, e.g., CO2, NH3, and HCN. Additionally, there is the catalytic role of small organic molecules, such as dicarboxylic acids and amino acids found on carbonaceous chondrites, in the formation of Fe-clays themselves. Amino acids and nucleotides adsorb on clay surfaces on Earth and subsequently polymerize. All of these observations and more must be subjected to strict experimental analysis. This review provides an overview of what has happened and is now happening in the experimental clay world related to the origin of life. The emphasis is on smectite-group clay minerals, such as montmorillonite and nontronite.

Structural Refinement and Density Functional Theory Study of Synthetic Ge-Akaganéite (β-FeOOH)

In this study, we propose a revised structural model for highly ordered synthetic Ge-akaganéite, a stable analogue of tunnel-type Fe-oxyhydroxide, based on the Rietveld refinement of synchrotron X-ray diffraction data and density functional theory with dispersion correction (DFT-D) calculations. In the proposed crystal structure of Ge-akaganéite, Ge is found not only in the tunnel sites as GeO(OH)3− tetrahedra, but also 4/5 of total Ge atoms are in the octahedral sites substituting 1/10 of Fe. In addition, the tunnel structures are stabilized by the presence of hydrogen bonds between the framework OH and Cl− species, forming a twisted cube structure and the GeO(OH)3− tetrahedra corner oxygen, forming a conjugation bond. The chemical formula of the synthetic Ge-akaganéite was determined to be (Fe7.2Ge0.8)O8.8(OH)7.2Cl0.8(Ge(OH)4)0.2.

Compressibility of 2M1 muscovite-phlogopite series minerals

Muscovite (Ms) and phlogopite (Phl) belong to the 2:1 dioctahedral and trioctahedral layer silicates, respectively, and are the end members of Ms-Phl series minerals. This series was studied in the 2M₁ polytype and modeled by the substitution of three Mg²⁺ cations in the Phl octahedral sites by two Al³⁺ and one vacancy, increasing the substitution up to reach the Ms. The series was computationally examined at DFT level as a function of pressure to 9 GPa. Cell parameters as a function of pressure and composition, and bulk moduli as a function of the composition agrees with the existing experimental results. The mixing Gibbs free energy was calculated as a function of composition. From these data, approximated solvi were calculated at increasing pressure. A gap of solubility is found, decreasing the gap of solubility at high pressure.

Structural and Electronic Properties of Iron-Doped Sodium Montmorillonite Clays: A First-Principles DFT Study

First-principles calculations done via density functional theory were used to study the structural and electronic properties of sodium montmorillonite clay (Mt-Na+) of general formula M x Al3Si8O24H4Na·nH2O (M x : Mg or Fe). The final position of the interlamellar sodium atom is found to be close to the oxygen atoms located on the upper surface of silica. Following Fe-Mt-Na+ system relaxation, with subsequent analysis of magnetic moment and magnetic states, the electroneutrality of the system established that both Fe2+ and Fe3+ oxidation states are possible to occur. The Mg2+-Mt-Na+ material shows a band gap energy greater than that of Fe2+-Mt-Na+ when iron is in the octahedral site. It is found that the valence-band maximum and the conduction-band minimum of iron-doped montmorillonite are both at the Γ-point, while it is at V → Γ for magnesium-doped montmorillonite. The calculated band gap from hybrid functional (HSE06) of Fe2+-Mt-Na+ is equal to 4.3 eV, exhibiting good agreement with experimental results obtained from ultraviolet-visible spectroscopy of the natural Mt-Na+ (Cloisite-Na+).

Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies

There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.