GDIS: a visualization program for molecular and periodic systems

Development of agomelatine nanocomposite formulations by wet media milling

Nanocrystal formulations of the BCS class II agomelatine, were developed by wet media milling. The most suitable stabilizer was identified and effects of process and formulation variables on the nanocrystal size and ζ-potential were evaluated employing a Box-Behnken experimental design. The optimized nanosuspensions were dried and subsequently evaluated for redispersibility and physicochemical properties. Computational simulation of solid state properties was applied to rationalize crystal fracture. It was found that low viscosity hydroxypropylcellulose with sodium dodecyl sulfate is the most suitable stabilizer. Stabilizer concentration exerts a statistically significant effect on particle size, which depends on the mill's rotation speed. The milling process induces a polymorphic transition to form II, which could affect size reduction kinetics. The solidified nanosuspensions' redispersibility is deteriorating progressively with storage time, with only minor differences between drying methods, retaining enhanced dissolution rate. Crystal lattice simulations suggest high mechanical anisotropy of form I crystals, which could be an additional reason for fast particle size reduction prior to the polymorphic transformation. Wet media milling, combined with a suitable drying method, can be an efficient technique for the production of stable nanocrystals of agomelatine. Particle informatics methods can enhance our understanding of the mechanisms responsible for agomelatine's nanocomminution.

Influence of Monovalent Salts on α-Glycine Crystal Growth from Aqueous Solution: Molecular Dynamics Simulations at Constant Supersaturation Conditions

The growth of α-glycine crystals from aqueous solution is investigated at constant supersaturations by utilizing the constant chemical potential molecular dynamics method. The study considers two faces (010) and (011) that predominantly determine the α-glycine crystal morphology. The general Amber force field (GAFF) with two different charge sets derived from semi-empirical calculations using the complete neglect of differential overlap method (CNDO) and from density functional calculations using the double-numerical plus d- and p-polarization basis set (DNP) is applied to describe α-glycine. The extended simple point charge model is used to simulate water. It is observed that the GAFF/DNP set leads to a much slower integration of glycine molecules into the crystal structure than the GAFF/CNDO set. The GAFF/CNDO set, however, causes the growth even at concentrations well below the experimental solubility. For the GAFF/DNP set, the influence of potassium chloride (KCl) and sodium chloride (NaCl) on the face growth rates is investigated. The parameters recently proposed by Yagasaki et al. [J. Chem. Theory Comput. 2020, 16, 2460-2473] are used to describe salt ions, as standard GAFF parameters lead to the unexpected formation of salt clusters at a concentration lower than the experimental solubility value. According to our simulation results, both salts suppress the growth of the (011) and (010) faces. The inhibiting effect of NaCl is much stronger than that of KCl for the (011) face, while both salts have a similar inhibiting effect on the (010) face. The results are in line with the experimental observations of the impact of salt ions on the α-glycine growth rates for the (011) face reported in literature.

New developments in the GDIS simulation package: Integration of VASP and USPEX

A popular first principles simulation code, the Vienna Ab initio Simulation Package (VASP), and a crystal structure prediction (CSP) package, the Universal Structure Predictor: Evolutionary Xtallography (USPEX) have been integrated into the GDIS visualization software. The aim of this integration is to provide users with a unique and simple interface through which most of the steps of a typical crystal optimization or prediction work. This involved, for the latter, not only setting up a CSP calculation with complete support for the latest version of USPEX, but also displaying the many structure results by linking each structure geometry and its energy via interactive graphics. For the optimization part, any structure displayed by GDIS can now be the starting point for VASP calculations, with support for its most commonly used parameters. Atomic and electronic structures can be displayed as well as dynamic properties such as total energy, force, volume, and pressure for each ionic step. It is not only possible to start calculations from the GDIS visualization software, using an in-place task manager, but a running calculation can also be followed, allowing a greater control of the simulation process. The GDIS software is available under the GNU public license in its second version.

Development of a Nanocrystal Formulation of a Low Melting Point API Following a Quality by Design Approach

Preparation of nanocrystal formulations by wet media milling and spray-drying is a reliable technique to enhance dissolution and ameliorate absorption limitations of poorly soluble BCS II drugs. However, when thermosensitive compositions are dried at high temperatures, the risks of particle aggregation and thermal degradation must be considered. The present study investigates the effects of nanosuspension formulation variables when performing the spray drying process at equidistant temperatures above and below the melting point. Towards this purpose, Fenofibrate is exploited as a model drug of unfavorable pharmacokinetic profile and low melting point (79–82 °C), properties that render thermal processing a nontrivial task. Rationalizing the system’s behavior by combining molecular simulations with QbD methodology, the preparation of stable nanocrystals can be “steered” in order to avoid undesirable melting. The statistically resolved operational conditions showed that Fenofibrate Critical Quality Attribute–compliant nanosuspensions i.e., bearing hydrodynamic diameter and ζ-potential of 887 nm and −16.49 mV, respectively, were obtained by wet milling drug to Pharmacoat and mannitol weighted optimum ratios of 4.075% and 0.75%, after spray drying at the desired temperature of 77 °C. In conclusion, we present a quality assurance methodology of nano-comminution generally applicable for thermo-labile BCS II drugs.

The atomic structure and dynamics at the CaCO3 vaterite-water interface: A classical molecular dynamics study

Classical molecular and lattice dynamics were applied to explore the structure and dynamics of water on different surfaces of vaterite, the least abundant calcium carbonate polymorph. Surfaces were generated starting from the three possible structural models for vaterite (monoclinic, hexagonal/trigonal, and triclinic) and pre-screened using their surface energies in an implicit solvent. Surfaces with energies lower than 0.55 J/m² were then run in explicit water. The majority of these surfaces dissolve in less than 100 ns, highlighting the low stability of this phase in abiotic environments. Three stable surfaces were identified; they exhibited only minor structural changes when in contact with explicit water and did not show any tendency to dissolve during 1 µs molecular dynamics simulations. The computed water density profiles show that all these surfaces have two distinct hydration layers. The water residence time at the various calcium sites was computed to be within 0.7 and 20.5 ns, which suggests that specific Ca ions will be more readily available to bind with organic molecules present in solution. This analysis is a step forward in understanding the structure of this complex mineral and its role in biomineralization, as it provides a solid theoretical background to explore its surface chemistry. In particular, this study provides realistic surface models and predicts the effect of water exchange at the surface active sites on the adsorption of other molecules.

Overcoming the Solubility Barrier of Ibuprofen by the Rational Process Design of a Nanocrystal Formulation

Wet media milling, coupled with spay drying, is a commonly proposed formulation strategy for the production and solidification of nanosuspensions in order to overcome the solubility barrier of BCS Class II substances. However, the application of mechanically and thermally intensive processes is not straightforward in the cases of ductile and/or low melting point substances that may additionally be susceptible to eutectic formation. Using ibuprofen (IBU) as a model drug with non-favorable mechanical and melting properties, we attempt to rationalize nanocrystal formulation and manufacturing in an integrated approach by implementing Quality by Design (QbD) methodology, particle informatics techniques and computationally assisted process design. Wet media milling was performed in the presence of different stabilizers and co-milling agents, and the nanosuspensions were solidified by spray-drying. The effects of key process parameters (bead diameter, milling time and rotational speed) and formulation variables (stabilizer type and drug/stabilizer ratio) on the critical quality attributes (CQAs), i.e., Z-average size, polydispersity index (PDI), ζ-potential and redispersibility of spray-dried nanosuspensions were evaluated, while possible correlations between IBU free surface energy and stabilizer effectiveness were studied. The fracture mechanism and surface stabilization of IBU were investigated by computer simulation of the molecular interactions at the crystal lattice level. As a further step, process design accounting for mass-energy balances and predictive thermodynamic models were constructed to scale-up and optimize the design space. Contemplating several limitations, our multilevel approach offers insights on the mechanistic pathway applicable to the substances featuring thermosensitivity and eutectic tendency.

Interaction of SO2 with the Platinum (001), (011), and (111) Surfaces: A DFT Study

Given the importance of SO2 as a pollutant species in the environment and its role in the hybrid sulphur (HyS) cycle for hydrogen production, we carried out a density functional theory study of its interaction with the Pt (001), (011), and (111) surfaces. First, we investigated the adsorption of a single SO2 molecule on the three Pt surfaces. On both the (001) and (111) surfaces, the SO2 had a S,O-bonded geometry, while on the (011) surface, it had a co-pyramidal and bridge geometry. The largest adsorption energy was obtained on the (001) surface (Eads = −2.47 eV), followed by the (011) surface (Eads = −2.39 and −2.28 eV for co-pyramidal and bridge geometries, respectively) and the (111) surface (Eads = −1.85 eV). When the surface coverage was increased up to a monolayer, we noted an increase of Eads/SO2 for all the surfaces, but the (001) surface remained the most favourable overall for SO2 adsorption. On the (111) surface, we found that when the surface coverage was θ > 0.78, two neighbouring SO2 molecules reacted to form SO and SO3. Considering the experimental conditions, we observed that the highest coverage in terms of the number of SO2 molecules per metal surface area was (111) > (001) > (011). As expected, when the temperature increased, the surface coverage decreased on all the surfaces, and gradual desorption of SO2 would occur above 500 K. Total desorption occurred at temperatures higher than 700 K for the (011) and (111) surfaces. It was seen that at 0 and 800 K, only the (001) and (111) surfaces were expressed in the morphology, but at 298 and 400 K, the (011) surface was present as well. Taking into account these data and those from a previous paper on water adsorption on Pt, it was evident that at temperatures between 400 and 450 K, where the HyS cycle operates, most of the water would desorb from the surface, thereby increasing the SO2 concentration, which in turn may lead to sulphur poisoning of the catalyst.

First-Principles Insights into the Interface Chemistry between 4-Aminothiophenol and Zinc Phosphide (Zn3P2) Nanoparticles

Accurate prediction of the structures, stabilities, and electronic structures of hybrid inorganic/organic systems is an essential prerequisite for tuning their electronic properties and functions. Herein, the interface chemistry between the 4-aminothiophenol (4ATP) molecule and the (001), (101), and (110) surfaces of zinc phosphide (Zn₃P₂) has been investigated by means of first-principles density functional theory calculation with a correction for van der Waals interactions. In particular, the atomic-level insights into the fundamental aspects of the 4ATP adsorption, including the lowest-energy adsorption configurations, binding energetics, structural parameters, and electronic properties are presented and discussed. The 4ATP molecule is demonstrated to bind most strongly onto the least stable Zn₃P₂(001) surface (E _ads = -1.91 eV) and least strongly onto the most stable Zn₃P₂(101) surface (E _ads = -1.21 eV). Partial density of states analysis shows that the adsorption of 4ATP on the Zn₃P₂ surfaces is characterized by strong hybridization between the molecule's sulfur and nitrogen p-orbitals and the d-orbitals of the interacting surface Zn ions, which gave rise to electron density accumulation around the centers of the newly formed Zn-S and Zn-N chemical bonds. The thermodynamic crystal morphology of the nonfunctionalized and 4ATP-functionalized Zn₃P₂ nanoparticles was obtained using Wulff construction based on the calculated surface energies. The stronger binding of the 4ATP molecule onto the less stable (001) and (110) surfaces in preference to the most stable (101) facet resulted in the modulation of the Zn₃P₂ nanocrystal shape, with the reactive (001) and (110) surfaces becoming more pronounced in the equilibrium morphology.

Interaction of H2O with the Platinum Pt (001), (011), and (111) Surfaces: A Density Functional Theory Study with Long-Range Dispersion Corrections

Platinum is a noble metal that is widely used for the electrocatalytic production of hydrogen, but the surface reactivity of platinum toward water is not yet fully understood, even though the effect of water adsorption on the surface free energy of Pt is important in the interpretation of the morphology and catalytic properties of this metal. In this study, we have carried out density functional theory calculations with long-range dispersion corrections [DFT-D3-(BJ)] to investigate the interaction of H₂O with the Pt (001), (011), and (111) surfaces. During the adsorption of a single H₂O molecule on various Pt surfaces, it was found that the lowest adsorption energy (E _ads) was obtained for the dissociative adsorption of H₂O on the (001) surface, followed by the (011) and (111) surfaces. When the surface coverage was increased up to a monolayer, we noted an increase in E _ads/H₂O with increasing coverage for the (001) surface, while for the (011) and (111) surfaces, E _ads/H₂O decreased. Considering experimental conditions, we observed that the highest coverage was obtained on the (011) surface, followed by the (111) and (001) surfaces. However, with an increase in temperature, the surface coverage decreased on all the surfaces. Total desorption occurred at temperatures higher than 400 K for the (011) and (111) surfaces, but above 850 K for the (001) surface. From the morphology analysis of the Pt nanoparticle, we noted that, when the temperature increased, only the electrocatalytically active (111) surface remained.

Free Energy of Ligand Removal in the Metal-Organic Framework UiO-66

We report an investigation of the "missing-linker phenomenon" in the Zr-based metal-organic framework UiO-66 using atomistic force field and quantum chemical methods. For a vacant benzene dicarboxylate ligand, the lowest energy charge-capping mechanism involves acetic acid or Cl^-/H₂O. The calculated defect free energy of formation is remarkably low, consistent with the high defect concentrations reported experimentally. A dynamic structural instability is identified for certain higher defect concentrations. In addition to the changes in material properties upon defect formation, we assess the formation of molecular aggregates, which provide an additional driving force for ligand loss. These results are expected to be of relevance to a wide range of metal-organic frameworks.

Supramolecular complexes involving non-symmetric viologen cations and hexacyanoferrate(ii) anions. A spectroscopic, crystallographic and computational study

We have investigated spectrally, crystallographically as well as computationally charge transfer complexes involving synthesized N-aryl-N′-methyl non-symmetric viologen cations and hexacyanoferrate(ii) anions.

Adsorption Properties of Triethylene Glycol on a Hydrated {101̅4} Calcite Surface and Its Effect on Adsorbed Water

Molecular dynamics (MD) and Born-Oppenheimer MD (BOMD) simulations were employed to investigate adsorption of aqueous triethylene glycol (TEG) on a hydrated {101̅4} calcite surface at 298 K. We analyzed the orientation of TEG adsorbed on calcite, as well as the impact of TEG on the water density and adsorption free energy. The adsorption energies of TEG, free energy profiles for TEG, details of hydrogen bonding between water and adsorbed TEG, and dihedral angle distribution of adsorbed TEG were estimated. We found that while the first layer of water was mostly unaffected by the presence of adsorbed TEG, the density of the second water layer was decreased by 71% at 75% surface coverage of TEG. TEG primarily attached to the calcite surface via two adjacent adsorption sites. Hydrogen bonds between water and adsorbed TEG in the second layer almost exclusively involved the hydroxyl oxygen of TEG. The adsorption energy of TEG on calcite in a vacuum environment calculated by classical MD amounted to 217 kJ/mol, which agreed very well with estimates found by using BOMD. Adsorption on hydrated calcite yielded a drastically lower value of 33 kJ/mol, with the corresponding adsorption free energy of 55.3 kJ/mol, giving an entropy increase of 22.3 kJ/mol due to adsorption. We found that the presence of TEG resulted in a decreased magnitude of the adsorption free energy of water, thus decreasing the calcite wettability. This effect can have a profound effect on oil and gas reservoir properties and must be carefully considered when evaluating the risk of hydrate nucleation.

Do solid-to-solid polymorphic transitions in DL-norleucine proceed through nucleation?

DL-Norleucine is a molecular crystal exhibiting two enantiotropic phase transitions. The high temperature α ↔ γ transition has been shown to proceed through nucleation and growth [Mnyukh et al., J. Phys. Chem. Solids, 1975, 36, 127]. We focus on the low temperature β ↔ α transition in a combined computational and experimental study. The temperature dependence of the structural and energetic properties of both polymorphic forms is nearly identical. Molecular dynamics simulations and nudged elastic band calculations of the transition process itself, suggest that the transition is governed by cooperative movements of bilayers over relatively large energy barriers.

Simulating preferential sorption of tartrate on prismatic calcite surfaces

Calculated binding energies of favorable adsorption configurations emphasize the importance of surface charge/energetics, structural match and water layers in mineral–organic interactions.

New insight into the stability of CaCO3 surfaces and nanoparticles via molecular simulation

Using updated and improved atomistic models for the polymorphs of calcium carbonate and their constituent ions in solution, we revisit the question of surface energetics and nanoparticle stability. Using a simple lattice-based Monte Carlo scheme, we generate nanoparticle configurations in vacuum for all three biologically relevant polymorphs of calcium carbonate and establish that the bulk energetic ordering of polymorphs persists to the nanoscale. In aqueous environments, results based on surface enthalpy alone indicate that formation of mineral-water interfaces is marginally favorable in many cases. Including an estimate of lost entropy due to formation of structured water layers is sufficient to reverse this observation, implying a delicate balance of enthalpy and entropy at crystalline CaCO3. In contradiction to some previous studies, we find that small calcite nanoparticles with diameters in the range of 1.8-4.1 nm do not retain an ordered structure on nanosecond time scales. The consequences of these results for simulation studies of biomineralization are discussed.

Vibrational Analysis of Brucite Surfaces and the Development of an Improved Force Field for Molecular Simulation of Interfaces

We introduce a nonbonded three-body harmonic potential energy term for Mg-O-H interactions for improved edge surface stability in molecular simulations. The new potential term is compatible with the Clayff force field and is applied here to brucite, a layered magnesium hydroxide mineral. Comparisons of normal mode frequencies from classical and density functional theory calculations are used to verify a suitable spring constant (k parameter) for the Mg-O-H bending motion. Vibrational analysis of hydroxyl librations at two brucite surfaces indicates that surface Mg-O-H modes are shifted to frequencies lower than the corresponding bulk modes. A comparison of DFT and classical normal modes validates this new potential term. The methodology for parameter development can be applied to other clay mineral components (e.g., Al, Si) to improve the modeling of edge surface stability, resulting in expanded applicability to clay mineral applications.

Solution-processed zinc phosphide (α-Zn3P2) colloidal semiconducting nanocrystals for thin film photovoltaic applications

Zinc phosphide (Zn3P2) is a promising earth-abundant material for thin film photovoltaic applications, due to strong optical absorption and near ideal band gap. In this work, crystalline zinc phosphide nanoparticles are synthesized using dimethylzinc and tri-n-octylphosphine as precursors. Transmission electron microscopy and X-ray diffraction data show that these nanoparticles have an average diameter of ∼8 nm and adopt the crystalline structure of tetragonal α-Zn3P2. The optical band gap is found to increase by 0.5 eV relative to bulk Zn3P2, while there is an asymmetric shift in the conduction and valence band levels. Utilizing layer-by-layer deposition of Zn3P2 nanoparticle films, heterojunction devices consisting of ITO/ZnO/Zn3P2/MoO3/Ag are fabricated and tested for photovoltaic performance. The devices are found to exhibit excellent rectification behavior (rectification ratio of 600) and strong photosensitivity (on/off ratio of ∼10(2)). X-ray photoelectron spectroscopy and ultraviolet photoemission spectroscopy analyses reveal the presence of a thin 1.5 nm phosphorus shell passivating the surface of the Zn3P2 nanoparticles. This shell is believed to form during the nanoparticle synthesis.

Temperature- and pressure-dependent densities, self-diffusion coefficients, and phase behavior of monoacid saturated triacylglycerides: toward molecular-level insights into processing

Using molecular-dynamics (MD) simulations the densities and self-diffusion coefficients of a range of liquid monoacid triacylglycerides (TAGs) have been studied as a function of temperature and, for the first time, pressure. While offset by their ambient properties, the response of the TAGs to temperature and pressure is qualitatively similar. Application of pressure was found to significantly increase densities and reduce diffusion of the TAG molecules, suggesting that it may have as much a role in processing and crystallizing TAGs as supercooling does. A solution of glycerol tripalmitate and glycerol trihexanoate was also studied, showing that application of pressure should lead to a significant decrease in the saturation point of the solution, which is an important consideration for processing TAGs. Different solid/liquid interfaces of glycerol tripalmitate have also been investigated. Although crystal growth could not be observed, dissolution of one interface was seen in the MD simulations. The results suggest that over moderate distances the melting of TAGs may be cooperative in nature, rather than involving dissolution of individual TAG molecules.

First principles study of hydrated/hydroxylated TiO2 nanolayers: from isolated sheets to stacks and tubes

Periodic density functional calculations are carried out to investigate the structure and the stability of hydrated/hydroxylated TiO(2) layered compounds, nanosheets, and nanotubes. Due to a very efficient interlayer hydrogen bonding, the ABA-stacked "step 3" H(2)Ti(3)O(7) compound is found to be the most stable bulk phase, in agreement with the experiment. For single sheets in a water-rich environment other forms are instead favored, all close in energy, namely, "step 2" titanates, hydroxylized-anatase-like layers, and lepidocrocite-TiO(2). Finally, it is shown that a lepidocrocite-TiO(2) sheet, when hydroxylated only on one side, spontaneously forms a scroll-like nanotube. The nanotube diameter estimated from our models perfectly matches the approximately 3 nm value observed for the internal diameters of Na-free titania nanotubes.

Molecular modeling of phosphonate molecules onto barium sulfate terraced surfaces

The adsorption of phosphonate molecules onto mineral surfaces is of interest due to their use as scale inhibitors. Molecular modeling is an important tool that can aid the fundamental understanding of how these inhibitors operate. This paper presents an empirical molecular mechanics study of the adsorption of a series of straight chain phosphonate molecules onto barium sulfate. It has been found that inhibition can be predicted for this straight chain series of molecules, which differ by the number of phosphonate groups present as well as by the chain length. Even more importantly, the modeling results can predict which faces will be preferred, and this has been verified by scanning and transmission electron microscopy on the resultant barite particles. It has been found that, in general, lattice matching results in the lowest replacement energy for all of the organic molecules investigated. The agreement between the experiment and the model confirms that the dominant mechanism of interaction for the additives on barium sulfate is via the deprotonated phosphonate groups with the barium ions on the surface.

Robert Boyle's chiral crystal chemistry: Computational re-evaluation of enantioselective adsorption on quartz

While searching for early examples of interactions of organic chromophores with minerals in the context of a systematic study of the process of dyeing crystals, we came across Robert Boyle's description of an experiment that may have been evidence of the enantioselective adsorption of a natural product, carminic acid (7-beta-D-glucopyranosyl-9,10-dihydro-3,5,6,8-tetrahydroxy-1-methyl-9,10-dioxo-2-anthracenecarboxylic acid), to the chiral surfaces of alpha-quartz, three centuries before such interactions became the subject of active chemical investigations. In order to determine whether Boyle did indeed observe enantioselective adsorption--albeit unbeknownst to him--we attempted to dye quartz with carminic acid according to his recipe. Quartz adsorbs carminic acid only because on heating it develops a network of microfissures that adsorb dye. This process depends on capillarity, not on specific non-covalent interactions; there is no evidence of enantioselectivity adsorption to heated crystals or enantioselective epitaxy to unheated crystals. These failures changed the focus of our inquiry: Why have almost all attempts to demonstrate the enantioselective adsorption of additives to quartz crystal surfaces been generally confounding and equivocal? In order to answer this question, we complement our experimental historical re-investigation with contemporary computational techniques for modeling crystal surface structure and the adsorption of additives. Minimizations of the energies associated with the adsorption of carminic acid to relaxed, hydrated d- and l-quartz {10(-)0} surfaces are analyzed in light of quartz's abysmal record as an enantioselective stationary phase.