Structure of 1,1,5,5-tetranitro-[4]peristylane. Structure solution from molecular packing analysis

Theoretical investigations of the substituent effect on the opto-electronic properties of the linearly fused napthadithiophene-based molecules

The optoelectronic and charge transport properties of eight linearly fused Napthadithiophene (NDT) molecules with different electron-withdrawing (EWG) and electron-donating (EDG) substituents are studied using the density functional theory (DFT) methods. The effect of the substitution of EWG and EDG on the molecular structure, frontier molecular orbitals, ionization energy, electron affinity, reorganization energy, crystal packing, and charge carrier mobility are studied. The crystal structure simulation method is used to optimize the possible crystal packing arrangements for the studied molecules. The energy and distribution of electron density on the frontier molecular orbitals are strongly influenced by the substitution of EWG and EDG, thereby changes in the absorption spectrum and charge transport properties. The unsubstituted NDT molecule possesses a maximum hole mobility of 2.8 cm2 V-1 s-1, which is due to the strong intermolecular interactions. Therefore, the NDT molecule can be used as a p-type semiconducting material. Among the studied molecules, the CCH-substituted NDT molecule, NDT-CCH, possesses a higher electron mobility of 1.13 cm2 V-1 s-1. The C2H5-substituted NDT molecule, NDT-C2H5, possesses ambipolar behavior with mobility of 4.77 × 10-2 cm2 V-1 s-1 and 1.70 × 10-2 cm2 V-1 s-1 for hole and electron, respectively.

A non-empirical intermolecular force-field for trinitrobenzene and its application in crystal structure prediction

An anisotropic atom-atom distributed intermolecular force-field (DIFF) for rigid trinitrobenzene (TNB) is developed using distributed multipole moments, dipolar polarizabilities, and dispersion coefficients derived from the charge density of the isolated molecule. The short-range parameters of the force-field are fitted to first- and second-order symmetry-adapted perturbation theory dimer interaction energy calculations using the distributed density-overlap model to guide the parameterization of the short-range anisotropy. The second-order calculations are used for fitting the damping coefficients of the long-range dispersion and polarization and also for relaxing the isotropic short-range coefficients in the final model, DIFF-srL2(rel). We assess the accuracy of the unrelaxed model, DIFF-srL2(norel), and its equivalent without short-range anisotropy, DIFF-srL0(norel), as these models are easier to derive. The model potentials are contrasted with empirical models for the repulsion-dispersion fitted to organic crystal structures with multipoles of iterated stockholder atoms (ISAs), FIT(ISA,L4), and with Gaussian Distributed Analysis (GDMA) multipoles, FIT(GDMA,L4), commonly used in modeling organic crystals. The potentials are tested for their ability to model the solid state of TNB. The non-empirical models provide more reasonable relative lattice energies of the three polymorphs of TNB and propose more sensible hypothetical structures than the empirical force-field (FIT). The DIFF-srL2(rel) model successfully has the most stable structure as one of the many structures that match the coordination sphere of form III. The neglect of the conformational flexibility of the nitro-groups is a significant approximation. This methodology provides a step toward force-fields capable of representing all phases of a molecule in molecular dynamics simulations.

Atomistic liquid crystalline structures of discotic bent-core-like mesogens formed by hydrogen bonding and interchain interactions

Integrated atomistic and molecular dynamic simulations are used to characterize the role hydrogen bonding and interchain interactions on structures and phase transitions of novel bent-core-like mesogenic materials that exhibit new self-assembly features, attractive to the development of functional materials. Multi-step simulations were carried out to model phase transitions and various spectra of two complex mesogenic materials formed from acid functionalized azo compounds, 4-[2,3,4-tri(octyloxy)phenylazo] benzoic acid and 4-[2,3,4- tri(heptyloxy)phenylazo] benzoic acid. The simulations contain three consecutive steps, involving molecular quantum chemistry, molecular crystal packing, and super cell molecular dynamics calculations. These two mesogens are supposed to form phasmidic molecular conformers. However, simulations point to the formation of complex discotic bent-core-like liquid crystals with tetramer mesogenic assemblies, in very good agreement with experimental observations. The wide range agreements between simulations and experimental results include transitions of crystal structures to columnar and uniaxial nematic phases, x-ray diffraction patterns of columnar phases, the structure of the two-dimensional complex bent-core-like tetramers, molecular Raman spectra, Raman depolarization spectra, and order parameters of nematic phases. The multi-step simulation methodology and its results shed light on this unique behaviour of plasmids with flexible side chains for simulation design of novel bent-core-like mesogenic materials.

Engineered Thermoplasma acidophilum factor F3 mimics human aminopeptidase N (APN) as a target for anticancer drug development

Human aminopeptidase N (hAPN) is an appealing objective for the development of anti-cancer agents. The absence of mammalian APN experimental structure negatively impinges upon the progression of structure-based drug design. Tricorn interacting factor F3 (factor F3) from Thermoplasma acidophilum shares 33% sequence identity with hAPN. Engineered factor F3 with two point directed mutations resulted in a protein with an active site identical to hAPN. In the present work, the engineered factor F3 has been co-crystallized with compound D24, a potent APN inhibitor introduced by our lab. Such a holo-form experimental structure helpfully insinuates a more bulky pocket than Bestatin-bound Escherichia coli APN. This evidence discloses that compound D24 targetting the structure of E. coli APN cannot bind to the activity cleft of factor F3 with high affinity. Thus, there is a potential risk of inefficiency to design hAPN targeting drug while using E. coli APN as the target model. We do propose here now that engineered factor F3 can be employed as a reasonable alternative of hAPN for drug design and development.

Crystal structure prediction from first principles

The prediction of structure at the atomic level is one of the most fundamental challenges in condensed matter science. Here we survey the current status of the field and consider recent developments in methodology, paying particular attention to approaches for surveying energy landscapes. We illustrate the current state of the art in this field with topical applications to inorganic, especially microporous solids, and to molecular crystals; we also look at applications to nanoparticulate structures. Finally, we consider future directions and challenges in the field.