Does Dispersion Dominate over H-Bonds in Drug-Surface Interactions? The Case of Silica-Based Materials As Excipients and Drug-Delivery Agents

Study of Disordered Mesoporous Silica Regarding Intrinsic Compound Affinity to the Carrier and Drug-Accessible Surface Area

There is increasing research interest in using mesoporous silica for the delivery of poorly water-soluble drugs that are stabilized in a noncrystalline form. Most research has been done on ordered silica, whereas far fewer studies have been published on using nonordered mesoporous silica, and little is known about intrinsic drug affinity to the silica surface. The present mechanistic study uses inverse gas chromatography (IGC) to analyze the surface energies of three different commercially available disordered mesoporous silica grades in the gas phase. Using the more drug-like probe molecule octane instead of nitrogen, the concept of a "drug-accessible surface area" is hereby introduced, and the effect on drug monolayer capacity is addressed. In addition, enthalpic interactions of molecules with the silica surface were calculated based on molecular mechanics, and entropic energy contributions of volatiles were estimated considering molecular flexibility. These free energy contributions were used in a regression model, giving a successful comparison with experimental desorption energies from IGC. It is proposed that a simplified model for drugs based only on the enthalpic interactions can provide an affinity ranking to the silica surface. Following this preformulation research on mesoporous silica, future studies may harness the presented concepts to guide formulation scientists.

Unravelling dispersion forces in liquid-phase enantioseparation. Part I: Impact of ferrocenyl versus phenyl groups

BACKGROUND

Highly ordered chiral secondary structures as well as multiple (tunable) recognition sites are the keys to success of polysaccharide carbamate-based chiral selectors in enantioseparation science. Hydrogen bonds (HBs), dipole-dipole, and π-π interactions are classically considered the most frequent noncovalent interactions underlying enantioselective recognition with these chiral selectors. Very recently, halogen, chalcogen and π-hole bonds were also identified as interactions working in polysaccharide carbamate-based selectors to promote enantiomer distinction. On the contrary, the function of dispersion interactions in this field was not explored so far.

RESULTS

The enantioseparation of chiral ferrocenes featuring chiral axis or chiral plane as stereogenic elements was performed by comparing five polysaccharide carbamate-based chiral columns, with the aim to identify enantioseparation outcomes that could be reasonably determined by dispersion forces, making available a reliable experimental data set for future theoretical studies to confirm the heuristic hypothesis. The effects of mobile phase polarity and temperature on the enantioseparation were considered, and potential recognition sites on analytes and selectors were evaluated by electrostatic potential (V) analysis and molecular dynamics (MD). In this first part, the enantioseparation of 3,3'-dibromo-5,5'-bis-ferrocenylethynyl-4,4'-bipyridine bearing two ferrocenylethynyl units linked to an axially chiral core was performed and compared to that of the analyte featuring the same structural motif with two phenyl groups in place of the ferrocenyl moieties. The results of this study showed the superiority of the ferrocenyl compared to the phenyl group, as a structural element favouring enantiodifferentiation.

SIGNIFICANCE AND NOVELTY

Even if dispersion (London) forces have been envisaged acting in liquid-phase enantioseparations, focused studies to explore possible contributions of dispersion forces with polysaccharide carbamate-based selectors are practically missing. This study allowed us to collect experimental information that support the involvement of dispersion forces as contributors to liquid-phase enantioseparation, paving the way to a new picture in this field.

Application of zinc oxide nano-tube as drug-delivery vehicles of anticancer drug

CONTEXT

Zinc oxide nano-tube (ZnONT) nano-structures, which possess chemical stability and non-toxicity in the human body, are considered promising for delivering different drugs. Within this work, we scrutinized the drug delivery capability of the ZnONT and its adsorptional properties as a drug delivery vehicle (DDV) for hydroxyurea (HU) as an anti-cancer drug through density functional theory along with the solvent impacts. Based on the optimized structures, it can be suggested that Zn atoms of ZnONT are the ideal sites on this nano-tube for the adsorption of HU. HU had a strong physical adsorption through the O atom of carbonyl groups onto the local pyramidal site of the ZnONT. At 1.96 Å and Ead of -39.28 kcal/mol, in the configuration which was favorable in terms of energy, there was an interaction between the O atoms of -C=O group of the drug and a Zn atom of the ZnONT. In order to scrutinize the excited state properties of the HU-ZnONT complex, we also examined the UV/Vis data of the HU/ZnONT interaction system. Following the adsorption of HU onto the surface of the ZnONT, there was a significant red-shift based on the maximum absorption wavelength, showing that the ZnONT is an ideal candidate for optic sensors in order to detect and monitor the drug molecule. HU could be released in the cancer tissues where pH was low based on the drug release mechanism. The current work thoroughly investigated the mechanism of interaction between the ZnONT and HU, showing that ZnONT can be used for the smart drug delivery of HU. Overall, the findings suggest that ZnONT could be used as an efficient drug-delivery system for the HU drug to treat various types of cancer.

METHODS

In this work we used B3LYP-gCP-D3 functional and the basis set LANL2DZ on the transition metal (Zn) and the basis set cc-pVDZ on the others. GAMESS software program was employed for performing the calculations. we performed analyses, including charge transport, molecular electrostatic potential surface (MEP), energetic, electronic, natural bond orbitals (NBOs), and structural optimizations.

Gliding on Ice in Search of Accurate and Cost-Effective Computational Methods for Astrochemistry on Grains: The Puzzling Case of the HCN Isomerization

The isomerization of hydrogen cyanide to hydrogen isocyanide on icy grain surfaces is investigated by an accurate composite method (jun-Cheap) rooted in the coupled cluster ansatz and by density functional approaches. After benchmarking density functional predictions of both geometries and reaction energies against jun-Cheap results for the relatively small model system HCN···(H2O)2, the best performing DFT methods are selected. A large cluster containing 20 water molecules is then employed within a QM/QM' approach to include a realistic environment mimicking the surface of icy grains. Our results indicate that four water molecules are directly involved in a proton relay mechanism, which strongly reduces the activation energy with respect to the direct hydrogen transfer occurring in the isolated molecule. Further extension of the size of the cluster up to 192 water molecules in the framework of a three-layer QM/QM'/MM model has a negligible effect on the energy barrier ruling the isomerization. Computation of reaction rates by the transition state theory indicates that on icy surfaces, the isomerization of HNC to HCN could occur quite easily even at low temperatures thanks to the reduced activation energy that can be effectively overcome by tunneling.

Understanding the Effect of Functionalization on Loading Capacity and Release of Drug from Mesoporous Silica Nanoparticles: A Computationally Driven Study

MCM-41, a type of mesoporous silica nanoparticle, has garnered widespread interests as a useful carrier for drug delivery wherein the drug gets adsorbed into the pores of the carrier. To understand the adsorption mechanism and release of the drug at the molecular level, in the current study, it was attempted to generate a computational model for the loading of 5-fluorouracil (5-FU), a chemotherapeutic agent into surface-modified MCM-41. The molecular surface models of the mesoporous silica (MCM-41) nanoparticle with different surface substitutions were created. In the first stage, molecular mechanics (MM) simulations were carried out to obtain the optimized surface structures. Subsequently, a 5-FU drug molecule in its different forms was docked on top of different MCM-41 surfaces to understand the adsorption orientation and energetics. To further validate the results, more accurate quantum mechanical (QM) calculations were also carried out, and the energetics between the QM and MM calculations are found to be similar. All the substitutions (-NH₂, -CN, -COOH) except the methyl substitution exhibited favorable interactions compared to the unsubstituted MCM-41 surface which was in accordance with the experimental observations. The release rate of 5-FU from MCM-41 and aminopropyl-substituted MCM-41 (MCM-NH₂) was studied using molecular dynamics simulations which revealed that the release rate of 5-FU from the MCM-NH₂ surface was slower compared to that of plain MCM-41. The detailed surface characteristics and the adsorption energies from the molecular simulations correlating the loading capacity and release are reported in here.

Can Mesoporous Silica Speed Up Degradation of Benzodiazepines? Hints from Quantum Mechanical Investigations

This work reports for the first time a quantum mechanical study of the interactions of a model benzodiazepine drug, i.e., nitrazepam, with various models of amorphous silica surfaces, differing in structural and interface properties. The interest in these systems is related to the use of mesoporous silica as carrier in drug delivery. The adopted computational procedure has been chosen to investigate whether silica–drug interactions favor the drug degradation mechanism or not, hindering the beneficial pharmaceutical effect. Computed structural, energetics, and vibrational properties represent a relevant comparison for future experiments. Our simulations demonstrate that adsorption of nitrazepam on amorphous silica is a strongly exothermic process in which a partial proton transfer from the surface to the drug is observed, highlighting a possible catalytic role of silica in the degradation reaction of benzodiazepines.

Adsorption Features of Various Inorganic Materials for the Drug Removal from Water and Synthetic Urine Medium: A Multi-Technique Time-Resolved In Situ Investigation

Pharmaceutical active compounds, including hundreds of different substances, are counted among the emerging contaminants in waterbodies, whose presence raises a growing concern for the ecosystem. Drugs are metabolized and excreted mainly through urine as an unchanged active ingredient or in the form of metabolites. These emerging contaminants are not effectively removed with the technologies currently in use, making them a relevant environmental problem. This study proposes the treatment of urine and water at the source that can allow an easier removal of dissolved drugs and metabolites. The treatment of synthetic urine, with dissolved ibuprofen as a model compound, by adsorption, using various classes of inorganic materials, such as clays, hierarchical zeolites and ordered mesoporous silica (MCM-41), is presented. A multi-technique approach involving X-ray powder diffraction, solid-state NMR, UV-Vis and Raman spectroscopies was employed to investigate the adsorption process in inorganic adsorbents. Moreover, the uptake, the ensuing competition, the efficiency and selectivity as well as the packing of the model compound in ordered mesoporous silica during the incipient wetness impregnation process were all thoroughly monitored by a novel approach, involving combined complementary time-resolved in situ ¹H and ¹³C MAS NMR spectroscopy as well as X-ray powder diffraction.

Cost-effective composite methods for large-scale solid-state calculations

Following the development in recent years of progressively more accurate approximations to the exchange-correlation functional, the use of density functional theory (DFT) methods to examine increasingly large and complex systems has grown, in particular for solids and other condensed matter systems. However the cost of these calculations is high, often requiring the use of specialist HPC facilities. As such, for the purpose of large-scale high-throughput screening of material properties, a hierarchy of simplified DFT methods has been proposed that allows rapid electronic structure calculation of large systems, and we have recently extended this scheme to the solid state (sol-3c). Here, we analyze the applicability and scaling of the new sol-3c DFT methods to molecules and crystals composed of light-elements, such as small proteins and model DNA-helices. Furthermore, the calculation of the electronic structure of large to very large porous systems, such as metal-organic frameworks and inorganic nanoparticles, is discussed. The new composite methods have been implemented in the CRYSTAL17 code, which efficiently implements hybrid functionals and enables routine application of the new methods to large-scale calculations of such materials with excellent performance, even with small-scale computing resources.

Development of Silica-Based Biodegradable Submicrometric Carriers and Investigating Their Characteristics as in Vitro Delivery Vehicles

Nanostructured silica (SiO2)-based materials are attractive carriers for the delivery of bioactive compounds into cells. In this study, we developed hollow submicrometric particles composed of SiO2 capsules that were separately loaded with various bioactive molecules such as dextran, proteins, and nucleic acids. The structural characterization of the reported carriers was conducted using transmission and scanning electron microscopies (TEM/SEM), confocal laser scanning microscopy (CLSM), and dynamic light scattering (DLS). Moreover, the interaction of the developed carriers with cell lines was studied using standard viability, proliferation, and uptake assays. The submicrometric SiO2-based capsules loaded with DNA plasmid encoding green fluorescence proteins (GFP) were used to transfect cell lines. The obtained results were compared with studies made with similar capsules composed of polymers and show that SiO2-based capsules provide better transfection rates on the costs of higher toxicity.

Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences

In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.

Modeling amino-acid side chain infrared spectra: the case of carboxylic residues

Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.

Formamide Adsorption at the Amorphous Silica Surface: A Combined Experimental and Computational Approach

Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways. While the mineral–products relationship has been deeply studied for a large pool of materials, the fundamental description of formamide reactivity over mineral surfaces at a microscopic level is missing in the literature. In particular, a key step of formamide chemistry at surfaces is adsorption on available interaction sites. This report aims to investigate the adsorption of formamide over a well-defined amorphous silica, chosen as a model mineral surface. An experimental IR investigation of formamide adsorption was carried out and its outcomes were interpreted on the basis of first principles simulation of the process, adopting a realistic model of amorphous silica.

Ligand-functionalized Pt nanoparticles as asymmetric heterogeneous catalysts: molecular reaction control by ligand–reactant interactions

Stereoselective control on amino acid functionalized supported Pt nanoparticles by means of dispersion interactions.

On the competition between weak O-H···F and C-H···F hydrogen bonds, in cooperation with C-H···O contacts, in the difluoromethane - tert-butyl alcohol cluster

The 1:1 complex of tert-butyl alcohol with difluoromethane has been characterized by means of a joint experimental-computational investigation. Its rotational spectrum has been recorded by using a pulsed-jet Fourier-Transform microwave spectrometer. The experimental work has been guided and supported by accurate quantum-chemical calculations. In particular, the computed potential energy landscape pointed out the formation of three stable isomers. However, the very low interconversion barriers explain why only one isomer, showing one O-H···F and two C-H···O weak hydrogen bonds, has been experimentally characterized. The effect of the H → tert-butyl- group substitution has been analyzed from the comparison to the difluoromethane-water adduct.

Models for biomedical interfaces: a computational study of quinone-functionalized amorphous silica surface features

The structural and IR features of amorphous silica surfaces, functionalized by ortho-benzoquinone groups, were computed to obtain a deeper knowledge of multifunctional coatings with antimicrobial properties.

β-Cristobalite (001) surface as 4-formaminoantipyrine adsorbent: First principle study of the effect on adsorption of surface modification

Silica based materials find applications as excipients and particularly as drug delivery agents for pharmaceutical drugs. Their performance can be crucially affected by surface treatments, as it can modify the adsorption (and release) of these formulations. The role of surface modification on the features of 4-formaminoantipyrine (FAA) adsorbed on β-cristobalite (001) surface is studied by means of simulations based on the Density Functional Theory (DFT). Starting from the results of FAA in interaction with a dehydroxylated surface; a fully hydroxylated surface and a functionalized surface with benzalkonium chloride (BC) surfactant have been added to study the configurational landscape. Calculations suggest that the trend for FAA preferential adsorption on silica surfaces is: dehydroxylated>hydroxylated>BC-functionalized. The potential for hydrogen bonding causes the main contribution to the bonding while dispersion forces present an additional contribution independently of whether the drug is hydrogen-bonded or BC-bonded to the surface. Adsorption takes mainly place through nitrogen atoms in the heterocyclic ring, the carbonyl and amine functional groups. Associated mode's shifts and concurrent changes in bond length are also observed showing accordance between electronic and geometrical structure results. BC surfactant reduces the number of formed H-bonds and lowers the attractive molecule-surface interaction being it useful to prevent particle agglomeration and could favor drug release in therapies that requires faster but controlled delivery.

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Elucidating the fundamental forces in protein crystal formation: the case of crambin

This study demonstrates the feasibility of periodic all-electron hybrid density functional theory calculations in the description of protein crystals, using crambin as a test case.

Molecular simulations of proteins have been usually accomplished through empirical or semi-empirical potentials, due to the large size and inherent complexity of these biological systems. On the other hand, a theoretical description of proteins based on quantum-mechanical methods would however provide an unbiased characterization of their electronic properties, possibly offering a link between these and the ultimate biological activity. Yet, such approaches have been historically hindered by the large amount of requested computational power. Here we demonstrate the feasibility of periodic all-electron density functional theory calculations in the description of the crystal of the protein crambin (46 aminoacids), which is determined with exceptional structural accuracy. We have employed the hybrid B3LYP functional, coupled to an empirical description of London interactions (D*) to simulate the crambin crystal with an increasing amount of lattice water molecules in the cell (up to 172H₂O per cell). The agreement with the experiment is good for both protein geometry and protein–water interactions. The energetics was computed to predict crystal formation energies, protein–water and protein–protein interaction energies. We studied the role of dispersion interactions which are crucial for holding the crambin crystal in place. B3LYP-D* electrostatic potential and dipole moment of crambin as well as the electronic charge flow from crambin to the solvating water molecules (0.0015e per H₂O) have also been predicted. These results proved that quantum-mechanical simulations of small proteins, both free and in their crystalline state, are now feasible in a reasonable amount of time, by programs capable of exploiting high performance computing architectures, allowing the study of protein properties not easily amenable through classical force fields.

On combining temperature and pressure effects on structural properties of crystals with standard ab initio techniques

A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values.

Unanticipated favoured adsorption affinity of Th(iv) ions towards bidentate carboxylate functionalized carbon nanotubes (CNT–COOH) over tridentate diglycolamic acid functionalized CNT: density functional theoretical investigation

CNT–COOH has higher adsorption affinity for Th⁴⁺ in aqueous solution compared to CNT–DGA, whereas pristine CNT has nil.

Tailoring the dissolution rate enhancement of aminoglutethimide by functionalization of MCM-41 silica: a hydrogen bonding propensity approach

Chlorine ions can mediate the adsorption and enhance the dissolution release of aminoglutethimide from pristine and functionalized MCM-41 mesoporous silica.

A DFT study on the interaction between glycine molecules/radicals and the (8, 0) SiCNT

The geometrical structures, energetics and electronic properties of glycine molecules as well as dehydrogenated radical interaction with silicon carbide nanotubes (SiCNTs) are investigated based on density functional theory (DFT) for the first time.