Characterizing the nature of virtual amorphous silicon

Virtual samples of approximations to real amorphous silicon, a-Si, have been prepared using several different processing routes. These include a fast quench from the melt followed by a long slow annealing period using molecular dynamics, a Reverse Monte Carlo approach, and an ab initio minimization. The characterization of these virtual a-Si samples includes a consideration of structural data (the radial distribution function, angular order, etc.), electronic properties (through the density of states), and thermodynamic information (chiefly the nature of the phase transformation from a-Si to liquid). The properties of a-Si are compared to network models, via the continuous random network model, and to experiment. We investigated the stability of virtual a-Si and consider its implications for use in future simulation studies. We have demonstrated the necessity for the accuracy provided by ab initio-based models to describe the interatomic potentials. Throughout this study, we have monitored the role of order in determining physical properties, as characterized by traditional routes (such as angular correlations) and more novel ones (the signature cell method).     

Multiscale modeling of self-assembled monolayers of thiophenes on electronic material surfaces

Computer simulation programs, spanning different time and length scales, are used to describe the fundamentals of thin film growth morphology in organic self-assembled monolayers using thiophenes on gold as representative systems. Ab initio calculations created a catalog of the energetics between two N-[4-(thien-2ylethynyl)phenyl] hydroxyl ("1P" molecules) in vacuum and interactions in three orthogonal orientations (parallel, perpendicular, and gamma-phase) to a Au (111) surface. This energetic dataset was supplied as the input for kinetic Monte Carlo simulations of dimer and trimer representations of small organic molecules to describe both sub-monolayer and multilayer growth on a series of hypothetical model substrates. On strongly binding metallic-like substrates, sub-monolayers of the model organic molecules formed ordered phases in the x and y directions at high temperatures and a disordered polycrystalline structure at low temperatures with the molecules lying down. Only at high temperatures was a "phase inversion" observed from a completely flat to an upright structure, suggesting the upright phase to be kinetically limited. Results for multilayer deposition of 1P molecules on three substrates which differ in their binding energy to the molecule (from non-interacting to strongly binding substrates) provided a rich view of the polymorphism that can result from differing choices of temperature and flux conditions. Irrespective of the binding energy of the molecule to the substrate, on highly corrugated surfaces we always observed 3D-island growth of multiple layers of the thiophenes, in contrast to Stranski-Krastanov or Frank-van der Merwe growth on more uniform substrates. The qualitative picture we obtained agrees with the growth habits of other small organic molecule systems like the acene series. Finally, molecular dynamics studies were used to understand the packing structures of stable polymorphs of thiophene SAMs. Different deposition conditions and substrate-molecule binding captured different regimes of growth morphology, some of which have already been observed experimentally.     

[1]Benzothienopyrimidines. I. Etude de la 3H-benzothieno[3,2-d]pyrimidone-4

3H-benzothieno[3,2-d]pyrimidin-4-one (3) was synthesized by bimolecular cyclising the 3-amino-2-carbethoxybenzothiophene (1) with formamide. The electrophilic substituion of 3 afforded N-methylated lactam derivavtives, the structure of which was assigned by 'H nmr and unequivocal synthesis. The sysnthesis of benzothieno[3,2-d]pyrimidine (7) was achieved by desulphurization of the 3H-benzothieno[3,2-d]-[3,2-d]pyrimisine-4-thione (6) or by oxydation of the 4-hydrazinobenzothieno[3,2-d]primidine (5).     

Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.     

Structure–activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study

A cannabinoid pseudoreceptor model for the CB1-receptor has been constructed for 31 cannabinoids using the molecular modelling software YAK. Additionally, two CoMFA studies were performed on these ligands, the first of which was conducted prior to the building of the pseudoreceptor. Its pharmacophore is identical with the initial superposition of ligands used for pseudoreceptor construction. In contrast, the ligand alignment for the second CoMFA study was taken directly from the final cannabinoid pseudoreceptor model. This altered alignment gives markedly improved cross-validated r² values as compared to those obtained from the original alignment with values of 0.79 and 0.63, respectively, for five components. However, the pharmacophore alignment has the better predictive ability. Both the CoMFA and pseudoreceptor methods predict the free energy of binding of test ligands well.     

Computationally derived rules for persistence of C60 nanowires on recumbent pentacene bilayers

The tendency for C(60) nanowires to persist on two monolayers of recumbent pentacene is studied using molecular dynamics (MD) simulations. A review of existing experimental literature for the tilt angle adopted by pentacene on noble metal surfaces shows that studies cover a limited range from 55° to 90°, motivating simulation studies of essentially the entire range of tilt angles (10°-90°) to predict the optimum surface tilt angle for C(60) nanowire formation. The persistence of a 1D nanowire depends sensitively on this tilt angle, the amount of initial tensile strain, and the presence of surface step edges. At room temperature, C(60) nanowires oriented along the pentacene short axes persist for several nanoseconds and are more likely to occur if they reside between, or within, pentacene rows for ? ≤ ～60°. The likelihood of this persistence increases the smaller the tilt angle. Nanowires oriented along the long axes of pentacene molecules are unlikely to form. The limit of stability of nanowires was tested by raising the temperature to 400 K. Nanowires located between pentacene rows survived this temperature rise, but those located initially within pentacene rows are only stable in the range ?(1) = 30°-50°. Flatter pentacene surfaces, that is, tilt angles above about 60°, are subject to disorder caused by C(60) molecules "burrowing" into the pentacene surface. An initial strain of 5% applied to the C(60) nanowires significantly decreases the likelihood of nanowire persistence. In contrast, any appreciable surface roughness, even by half a monolayer in height of a third pentacene monolayer, strongly enhances the likelihood of nanowire formation due to the strong binding energy of C(60) molecules to step edges.