Clay minerals and their gallery guests: an ab initio investigation into their interactions.

Clay minerals are ubiquitous and readily accessible in the natural environment and consequently have become an essential ingredient in the development of Western Society. Their structural properties are responsible for many of their uses, their layered-leaf composition enables the absorption of water and other solutes, for example. In this thesis, the focus of interest lies primarily in the chemical properties of the clay minerals, which is due to the large surface areas of varying atomistic environments comprising the mineral layers. Clay minerals offer a challenge to the electronic structure modeller as their atomistic composition is non-exact, consequently a number of constraints are automatically applied during the modelling process, the first being the choice of composition of the model. There are currently few examples of density functional theory studies using planewaves and the pseudopotential approximation, and the available experimental data is not necessarily directly applicable to theoretical data due in part, to the inexactness of the clay mineral composition. Consequently, in the studies presented in this thesis, as much time has been spent in considering the modelling methods as on the results obtained and the implication of these in the modelling environment chosen. This thesis records investigations into the decarboxylation of a fatty acid into an alkane and CO$_{2}$ with the modelling of a catalytic environment of an aluminium-bearing clay mineral; the identification of a transition state of this reaction pathway using lattice dynamics and finally, the mechanism of reduction within iron-bearing clay minerals

The integrated DL_POLY/DL_FIELD/DL_ANALYSER software platform for molecular dynamics simulations for exploration of the synthonic interactions in saturated benzoic acid/hexane solutions

Three separately developed software Molecular Dynamics packages at Daresbury Laboratory, namely DL_FIELD (DL_F), DL_POLY and DL_ANALYSER, have been integrated to form an efficient computational infrastructure to investigate the detailed solution chemistry of saturated benzoic acid in hexane solutions. These software capabilities are demonstrated, in combination with the Synthonic Engineering tools and density functional theory (DFT) calculations, to assess the extent that the solute-solute intermolecular synthonic interactions in solution mirrors the synthons in the crystal structure. The results show that the majority of the COOH groups are forming OH … O H-bonds, which are a combination of classic OH … O homo-dimers and three membered H-bonding clusters. The formation of pi-pi stacking interactions is observed, but in far fewer numbers than observed for the OH … O interactions. The DFT simulations of the IR spectra of the multiple benzoic acid aggregates extracted from the MD trajectories provides further in-depth analysis of previously published IR data, by matching simulated peaks to the experimental peaks, hence identifying the exact bonding modes that are responsible for such peaks. This study demonstrates the value of a multi-scale and multi-technique approach to exploring the molecular transition pathway from solution to crystal structure

A statistical analysis of achievement in self-study summer books

In this article we present all the results obtained from our research based on the use of self-study books. In a previous report we outlined the way pupils and parents used the holiday books, whereas in this article we will focus our attention on the evaluation of the activities done by the students during their summer holidays. We will, in particular, analyse the results obtained by pupils from state and private schools, by boys and girls and by second and third cycle pupils.En el presente artículo exponemos todos los resultados obtenidos en una investigación que tuvo como objetivo estudiar el uso de los cuadernos de verano de inglés en primaria. En un informe publicado anteriormente presentamos el uso dado a estos cuadernos de vacaciones por los alumnos y padres, pero ahora vamos a prestar especial atención a los resultados obtenidos al evaluar las actividades realizadas. En particular, comparamos estadísticamente los resultados obtenidos por el alumnado de colegios públicos y privados, por los chicos y las chicas, y por el alumnado del segundo y tercer ciclo de primaria

Double Linker Triphenylamine Dyes for Dye-Sensitized Solar Cells

Most organic dyes synthesized for dye-sensitized solar cells (DSC) use a single linker group to bind to the metal oxide photo-anode. Here we describe the synthesis and testing of two new triphenylamine dyes containing either two carboxylic acids 5-[2-(4-diphenylamino-phenyl)-vinyl]-isophthalic acid (10) or two cyanoacrylic acids (2Z, 2′Z)-3, 3′-(5-((E)-4-(diphenylamino) styryl)-1, 3-phenylene) bis (2-cyanoacrylic acid) (8) as linker groups. Full characterization data are reported for these dyes and their synthetic intermediates. DSC devices have been prepared from these new dyes either by passive or fast dyeing and the dyes have also been tested in co-sensitized DSC devices leading to a PCE (η = 5.4%) for the double cyanoacrylate linker dye (8) co-sensitized with D149. The dye:TiO2 surface interactions and dye excitations are interpreted using three modelling methods: density functional theory (at 0 K); molecular dynamics (at 298 K); time dependent density functional theory. The modelling results show the preferred orientation of both dyes on an anatase (1 0 1) TiO2 surface to be horizontal, and both the simulated and experimental absorption spectra of the dye molecules indicate a red shifted band for (8) compared to (10). This is in line with broader light harvesting and Jsc for (8) compared to (10)

Role of Molecular, Crystal, and Surface Chemistry in Directing the Crystallization of Entacapone Polymorphs on the Au(111) Template Surface

The pharmaceutical compound entacapone ((E)-2-cyano-3-(3,4-dihydroxy-5-nitrophenyl)-N,N-diethylprop-2-enamide) is important in the treatment of Parkinson’s disease, exhibiting interesting polymorphic behavior upon crystallization from solution. It consistently produces its stable form A with a uniform crystal size distribution on the surface of an Au(111) template while concomitantly forming its metastable form D within the same bulk solution. Molecular modeling using empirical atomistic force-fields reveals more complex molecular and intermolecular structures for form D compared to form A, with the crystal chemistry of both polymorphs being dominated by van der Waals and π–π stacking interactions with lower contributions (ca. 20%) from hydrogen bonding and electrostatic interactions. Comparative lattice energies and convergence for the polymorphs are consistent with the observed concomitant polymorphic behavior. Synthon characterization reveals an elongated needle-like morphology for form D crystals in contrast to the more equant form A crystals with the surface chemistry of the latter exposing the molecules’ cyano groups on its {010} and {011} habit faces. Density functional theory modeling of surface adsorption reveals preferential interactions between Au and the synthon GA interactions of form A on the Au surface. Molecular dynamics modeling of the entacapone/gold interface reveals the entacapone molecular structure within the first adsorbed layer to show nearly identical interaction distances, for both the molecules within form A or D with respect to the Au surface, while in the second and third layers when entacapone molecule–molecule interactions overtake the interactions between those of molecule–Au, the intermolecular structures are found to be closer to the form A structure than form D. In these layers, synthon GA (form A) could be reproduced with just two small azimuthal rotations (5° and 15°) whereas the closest alignment to a form D synthon requires larger azimuthal rotations (15° and 40°). The cyano functional group interactions with the Au template dominate interfacial interactions with these groups being aligned parallel to the Au surface and with nearest neighbor distances to Au atoms more closely matching those in form A than form D. The overall polymorph direction pathway thus encompasses consideration of molecular, crystal, and surface chemistry factors

Off-the-shelf DFT-DISPersion methods : Are they now “on-trend” for organic molecular crystals?

Organic molecular crystals contain long-range dispersion interactions that can be challenging for solid-state methods such as density functional theory (DFT) to capture, and in some industrial sectors are overlooked in favor of classical methods to calculate atomistic properties. Hence, this publication addresses the critical question of whether dispersion corrected DFT calculations for organic crystals can reproduce the structural and energetic trends seen from experiment, i.e., whether the calculations can now be said to be truly “on-trend.” In this work, we assess the performance of three of the latest dispersion-corrected DFT methods, in calculating the long-range, dispersion energy: the pairwise methods of D3(0) and D3(BJ) and the many-body dispersion method, MBD@rsSCS. We calculate the energetics and optimized structures of two homologous series of organic molecular crystals, namely, carboxylic acids and amino acids. We also use a classical force field method (using COMPASS II) and compare all results to experimental data where possible. The mean absolute error in lattice energies is 9.59 and 343.85 kJ/mol (COMPASS II), 10.17 and 16.23 kJ/mol (MBD@rsSCS), 10.57 and 18.76 kJ/mol [D3(0)], and 8.52 and 14.66 kJ/mol [D3(BJ)] for the carboxylic acids and amino acids, respectively. MBD@rsSCS produces structural and energetic trends that most closely match experimental trends, performing the most consistently across the two series and competing favorably with COMPASS II

Novel benzothiazole half-squaraines: model chromophores to study dye–TiO2 interactions in dye-sensitized solar cells

We report the synthesis of 9 new half squaraine (HfSQ) dyes; 5 containing a benzothiazole moiety and 4 containing an indolenine moiety. X-ray single crystal structural and characterisation data have been correlated with device data to understand the widely reported but poorly understood influence of S heteroatoms on DSC device performance. The S heteroatom in these new dyes has also been used as an atomic probe of the dye–TiO2 interface to dye binding and orientation. Thus, for the first time, using the S heteroatom probe, angle-resolved X-ray photoelectron (AR-XPS) data have shown these dyes sit horizontally at the dye–TiO2 interface confirmed by DFT computer modelling of novel and analogous HfSQ dyes with a benzoindole backbone

A perspective on using experiment and theory to identify design principles in dye-sensitized solar cells

Dye-sensitized solar cells (DSCs) have been the subject of wide-ranging studies for many years because of their potential for large-scale manufacturing using roll-to-roll processing allied to their use of earth abundant raw materials. Two main challenges exist for DSC devices to achieve this goal; uplifting device efficiency from the 12 to 14% currently achieved for laboratory-scale ‘hero’ cells and replacement of the widely-used liquid electrolytes which can limit device lifetimes. To increase device efficiency requires optimized dye injection and regeneration, most likely from multiple dyes while replacement of liquid electrolytes requires solid charge transporters (most likely hole transport materials – HTMs). While theoretical and experimental work have both been widely applied to different aspects of DSC research, these approaches are most effective when working in tandem. In this context, this perspective paper considers the key parameters which influence electron transfer processes in DSC devices using one or more dye molecules and how modelling and experimental approaches can work together to optimize electron injection and dye regeneration. This paper provides a perspective that theory and experiment are best used in tandem to study DSC device

Evaluation of Force-Field Calculations of Lattice Energies on a Large Public Dataset, Assessment of Pharmaceutical Relevance, and Comparison to Density Functional Theory

Crystal lattice energy is a key property affecting the ease of processing pharmaceutical materials during manufacturing, as well as product performance. We present an extensive comparison of 324 force-field protocols for calculating the lattice energies of single component, organic molecular crystals (further restricted to Z′ less than or equal to one), corresponding to a wide variety of force-fields (DREIDING, Universal, CVFF, PCFF, COMPASS, COMPASSII), optimization routines, and other variations, which could be implemented as part of an automated workflow using the industry standard Materials Studio software. All calculations were validated using a large new dataset (SUB-BIG), which we make publicly available. This dataset comprises public domain sublimation data, from which estimated experimental lattice energies were derived, linked to 235 molecular crystals. Analysis of pharmaceutical relevance was performed according to two distinct methods based upon (A) public and (B) proprietary data. These identified overlapping subsets of SUB-BIG comprising (A) 172 and (B) 63 crystals, of putative pharmaceutical relevance, respectively. We recommend a protocol based on the COMPASSII force field for lattice energy calculations of general organic or pharmaceutically relevant molecular crystals. This protocol was the most highly ranked prior to subsetting and was either the top ranking or amongst the top 15 protocols (top 5%) following subsetting of the dataset according to putative pharmaceutical relevance. Further analysis identified scenarios where the lattice energies calculated using the recommended force-field protocol should either be disregarded (values greater than or equal to zero and/or the messages generated by the automated workflow indicate extraneous atoms were added to the unit cell) or treated cautiously (values less than or equal to −249 kJ/mol), as they are likely to be inaccurate. Application of the recommended force-field protocol, coupled with these heuristic filtering criteria, achieved an root mean-squared error (RMSE) around 17 kJ/mol (mean absolute deviation (MAD) around 11 kJ/mol, Spearman’s rank correlation coefficient of 0.88) across all 226 SUB-BIG structures retained after removing calculation failures and applying the filtering criteria. Across these 226 structures, the estimated experimental lattice energies ranged from −60 to −269 kJ/mol, with a standard deviation around 29 kJ/mol. The performance of the recommended protocol on pharmaceutically relevant crystals could be somewhat reduced, with an RMSE around 20 kJ/mol (MAD around 13 kJ/mol, Spearman’s rank correlation coefficient of 0.76) obtained on 62 structures retained following filtering according to pharmaceutical relevance method B, for which the distribution of experimental values was similar. For a diverse set of 17 SUB-BIG entries, deemed pharmaceutically relevant according to method B, this recommended force-field protocol was compared to dispersion corrected density functional theory (DFT) calculations (PBE + TS). These calculations suggest that the recommended force-field protocol (RMSE around 15 kJ/mol) outperforms PBE + TS (RMSE around 37 kJ/mol), although it may not outperform more sophisticated DFT protocols and future studies should investigate this. Finally, further work is required to compare our recommended protocol to other lattice energy calculation protocols reported in the literature, as comparisons based upon previously reported smaller datasets indicated this protocol was outperformed by a number of other methods. The SUB-BIG dataset provides a basis for these future studies and could support protocol refinement