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Well-formed crystals are polyhedral with flat facets and sharp edges. Nevertheless, a remarkable number of molecular crystals can bend and twist during growth. Many others can be distorted by applying external forces or creating heterogeneities by temperature gradient or photochemical reaction. As part of an effort to identify the forces that so commonly deform molecular crystals and to characterize their consequences, a force field is evaluated for its ability to predict mechanical distortions in nanocrystals. Macroscopic materials provide estimates of the expected responses that were tested here in silico for "molecular bimetallic strips" created from rods of iodoform and bromoform in smooth contact and nanocrystalline rods of iodoform with left and right screw dislocations. It was demonstrated that an optimized force field based largely on AMBER parameters matches expectations for elastic and plastic distortions, despite the fact that these mechanical responses are far removed from the force field parametrization set.

The azo dye, sunset yellow, is a prototypical, chromonic liquid crystal in which assembly in aqueous solution at high volume fraction leads to lyotropic mesophases with a “package of properties distinct in almost every aspect” (Lydon, J. Curr. Opin. Colloid Interface Sci. 2004, 8, 480). In particular, the isotropic to nematic transition in such phases, the consequence of stacking of dye molecules in chains, is difficult to bring into correspondence with athermal theories for rigid rods as well as modifications that consider chain interactions with one another. Chromonic mesogens, small molecules that stack to form lyotropic liquid crystals, prompt structural questions that have yet to be answered; a full understanding of structure should inform colligative properties. Herein, the single crystal structure of a guanidinium salt of the sunset yellow dianion, a known chromonic mesogen, is reported. The compound crystallizes as a dihydrate, tetrahydrofuran solvate in the orthorhombic space group Pnna, with a = 6.8426(5) Å, b = 20.048(1) Å, c = 21.466(2) Å. The sunset yellow molecules, point group approximately Cs, are disordered about a crystallographic diad axis.The structure is informative because pairwise interactions in the disordered crystal structure show a remarkable correspondence with the stereochemistry of sunset yellow molecules in solution and in the liquid crystal phase. The solution structure is here simulated by the combination of molecular dynamics,metadynamics, and quantum chemical computations. The comparable disorder in the fluid and solid states suggests the possibility that stacked aggregates adhere to growing crystals intact. Computations were used to evaluate proposals that stacking faults and branching points lower the X-ray correlation lengths while preserving extended structures. Evidence is found forstacking faults but not branches. The solution stereochemistry and stereodynamics has implications for the geometry of long rods, for which underst

The development of new functionals and methods to accurately describe van der Waals forces in density functional theory (DFT) has become popular in recent years, with the vast majority of studies assessing the accuracy of the energetics of collections of molecules, and to a lesser extent molecular crystalline systems. As the energies are a function of the atom positions, we assess the accuracy of DFT calculations from both a geometric and energetics point of view for the C21 reference data set of Otero-de-la-Roza and Johnson for molecular crystals, and a set of monosaccharide molecular crystals. In particular, we examine the performance of exchange-correlation functionals designed to handle van der Waals forces, including the vdW-DF, vdW-DF2, and XDM methods. We also assess the effect of using small and large basis sets, the choice of basis functions (local atomic orbitals using the SIESTA code versus planewaves using the Quantum ESPRESSO code), and the effect of corrections for basis set superposition errors. Finally, we examine the geometries and energies of the S22 reference set of molecular complexes. Overall, the most accurate geometries for both choices of basis functions are obtained with the vdW-DF2 functional, while the most accurate lattice energies are obtained using vdW-DF2 with local atomic orbitals and XDM with planewaves with mean absolute errors of less than 4 kJ/mol.

Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that 14C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these 14C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication.

The enantioselectivity of the autocatalytic alkylation of 2-tert-butylpyrimidyl-5-carbaldehyde, initiated by chiral crystals of N-(2-thienylcarbonyl)glycine, is predicted computationally. The results are in accord with the correlation of the stereochemical outcome of the reaction and the absolute structure of the crystals determined by the anomalous dispersion of X-rays and circular dichroism spectroscopy.

We investigate the performance of the vdW-DF functional of Dion et al. implemented in the SIESTA code. In particular, the S22 data set and several calixarene-based host–guest structures are examined to assess the performance of the functional. The binding energy error statistics for the S22 data set reveal that the vdW-DF functional performs very well when compared to a range of other methods of treating dispersion in density functional theory, and to vdW-DF implementations in other codes. For the calixarene host–guest structures, the structural properties and binding energies are compared to previous experimental and computational studies, and in most cases we find that vdW-DF provides superior results to other computational studies.

Density functional theory calculations have been performed on a range of magnesium and magnesium hydride nanoclusters to examine the 1 bar desorption temperatures. The vibrational entropies and enthalpies are calculated for each cluster, within the harmonic approximation, which permits calculation of the desorption Gibbs free energy of reaction. For the bulk system, good agreement is found with experiment for the desorption temperature and a range of structural and electronic properties. For the nanoparticulate systems, we report binding energies, along with desorption reaction entropies and enthalpies. The finite-temperature effects on the vibrational energies of all system sizes are examined, and the findings suggest that the harmonic approximation is too restricted to account for the experimentally observed reductions in the nanoparticulate reaction enthalpies.

Potassium sulfate crystals orient and overgrow 2-aminobenzenesulfonate (OSA), and many other sulfonated aromatic compounds, on particular facets during growth from solution. The energetics associated with adsorption of OSA and benzenesulfonate (BS) were calculated using both molecular mechanical and density functional methods, in order to assess the surface binding effectiveness of these compounds on various faces of potassium sulfate. It was found that both theoretical techniques predicted that OSA and BS bind to potassium sulfate to a similar extent. The surface binding capacities were also assessed experimentally by studying the growth rates of individual faces of K2SO4, with results showing similar findings to those from the computational studies.

We have used density functional calculations to examine the (101) surfaces of KDP, under vacuum, nitrogen, and aqueous conditions, and these simulations are found to agree well with nanoscale experimental studies demonstrating that the density functional calculations are providing a good description of the surfaces of this complex inorganic salt.