Lattice Dynamics of Quinacridone Polymorphs: A Combined Raman and Computational Approach.

Polarized low-frequency Raman microscopy and a posteriori dispersion-corrected density functional simulations are combined to investigate the lattice vibrations of the α, β, and γ polymorphs of the model organic semiconductor quinacridone, which are known to display different optical and electronic properties. The comparison between experiments and calculations allows for unambiguous mode assignment and identification of the scattering crystal faces. Conversely, the agreement between simulations and experiments validates the adopted computational methods, which correctly describe the intermolecular interaction of the molecular material.

Visualizing a Single-Crystal-to-Single-Crystal [2+2] Photodimerization through its Lattice Dynamics: An Experimental and Theoretical Investigation.

In homogeneous solid-state reactions, the single-crystal nature of the starting material remains unchanged, and the system evolves seamlessly through a series of solid solutions of reactant and product. Among [2+2] photodimerizations of cinnamic acid derivatives in the solid state, those involving salts of the 4-aminocinnamic acid have been recognized to proceed homogeneously in a "single-crystal-to-single-crystal" fashion by X-ray diffraction techniques. Here the bromide salt of this compound class is taken as a model system in a Raman spectroscopy study at low wavelengths, to understand how such a mechanism defines the trend of the crystal lattice vibrations during the reaction.

Surface Induced Phenytoin Polymorph. 1. Full Structure Solution by Combining Grazing Incidence X-ray Diffraction and Crystal Structure Prediction.

Understanding the behavior and properties of molecules assembled in thin layers requires knowledge of their crystalline packing. The drug phenytoin (5,5-diphenylhydantoin) is one of the compounds that can be grown as a surface induced polymorph. By using grazing incidence X-ray diffraction, the monoclinic unit cell of the new can be determined, but, due to crystal size and the low amount of data, a full solution using conventional structure solving strategies fails.

Surface Induced Phenytoin Polymorph. 2. Structure Validation by Comparing Experimental and Density Functional Theory Raman Spectra.

A method for structure solution in thin films that combines grazing incidence X-ray diffraction data analysis and crystal structure prediction was presented in a recent work (Braun et al. Cryst. Growth Des.

Singlet exciton fission via an intermolecular charge transfer state in coevaporated pentacene-perfluoropentacene thin films.

Singlet exciton fission is a spin-allowed process in organic semiconductors by which one absorbed photon generates two triplet excitons. Theory predicts that singlet fission is mediated by intermolecular charge-transfer states in solid-state materials with appropriate singlet-triplet energy spacing, but direct evidence for the involvement of such states in the process has not been provided yet. Here, we report on the observation of subpicosecond singlet fission in mixed films of pentacene and perfluoropentacene.

Bulk and Surface-Stabilized Structures of Paracetamol Revisited by Raman Confocal Microscopy.

We revisit the polymorphism of paracetamol by means of a micro-Raman technique, which has proved to be a powerful tool for structure recognition. Distinct lattice phonon spectra clearly identified the pure phases. Confocality enabled us to detect phase mixing between form II and either I or III on a micrometric scale in the same crystallite.

Toward a Reliable Description of the Lattice Vibrations in Organic Molecular Crystals: The Impact of van der Waals Interactions.

This work assesses the reliability of different van der Waals (vdW) methods to describe lattice vibrations of molecular crystals in the framework of density functional theory (DFT). To accomplish this task, calculated and experimental lattice phonon Raman spectra of a pool of organic molecular crystals are compared. We show that the many-body dispersion (MBD@rsSCS) van der Waals method of Ambrosetti et al.

DFT-Assisted Polymorph Identification from Lattice Raman Fingerprinting.

A combined experimental and theoretical approach, consisting of lattice phonon Raman spectroscopy and density functional theory (DFT) calculations, is proposed as a tool for lattice dynamics characterization and polymorph phase identification. To illustrate the reliability of the method, the lattice phonon Raman spectra of two polymorphs of the molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]benzothiophene are investigated. We show that DFT calculations of the lattice vibrations based on the known crystal structures, including many-body dispersion van der Waals (MBD-vdW) corrections, predict experimental data within an accuracy of ≪5 cm (≪0.

Predicting the anchoring of liquid crystals at a solid surface: 5-cyanobiphenyl on cristobalite and glassy silica surfaces of increasing roughness.

We employ atomistic molecular dynamics simulations to predict the alignment and anchoring strength of a typical nematic liquid crystal, 4-n-pentyl-4'-cyano biphenyl (5CB), on different forms of silica. In particular, we study a thin (~20 nm) film of 5CB supported on surfaces of crystalline (cristobalite) and amorphous silica of different roughness. We find that the orientational order at the surface and the anchoring strength depend on the morphology of the silica surface and its roughness.

Epitaxial growth of π-stacked perfluoropentacene on graphene-coated quartz.

Chemical-vapor-deposited large-area graphene is employed as the coating of transparent substrates for the growth of the prototypical organic n-type semiconductor perfluoropentacene (PFP). The graphene coating is found to cause face-on growth of PFP in a yet unknown substrate-mediated polymorph, which is solved by combining grazing-incidence X-ray diffraction with theoretical structure modeling. In contrast to the otherwise common herringbone arrangement of PFP in single crystals and "standing" films, we report a π-stacked arrangement of coplanar molecules in "flat-lying" films, which exhibit an exceedingly low π-stacking distance of only 3.

Crystal-to-crystal photoinduced reaction of dinitroanthracene to anthraquinone.

The photochemical reaction of 9,10-dinitroanthracene (DNO(2)A) to anthraquinone (AQ) + 2NO has been studied by means of lattice phonon Raman spectroscopy in the spectral region 10-150 cm(-1). In fact, crystal-to-crystal transformations are best revealed by following changes in the lattice modes, as even small modifications in the crystal structure lead to dramatic changes in symmetry and selection rules of vibrational modes. While analysis of the lattice modes allowed for the study of the physical changes, the chemical transformation was monitored by measuring the intramolecular Raman-active modes of both reactant and product.

Phonon dynamics and electron-phonon coupling in pristine picene.

The paper reports a complete analysis of the phonon structure of crystalline picene, a recently announced organic semiconductor. Both lattice and intramolecular vibrations are investigated. An exhaustive assignment of lattice phonons is obtained through polarized Raman spectra assisted by lattice dynamics calculations based on a well tested atom-atom potential model.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph.

Interaction of charge carriers with lattice and molecular phonons in crystalline pentacene.

The computational protocol we have developed for the calculation of local (Holstein) and non-local (Peierls) carrier-phonon coupling in molecular organic semiconductors is applied to both the low temperature and high temperature bulk crystalline phases of pentacene. The electronic structure is calculated by the semimpirical INDO/S (Intermediate Neglect of Differential Overlap with Spectroscopic parametrization) method. In the phonon description, the rigid molecule approximation is removed, allowing mixing of low-frequency intra-molecular modes with inter-molecular (lattice) phonons.

The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode.

The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials.

Influence of intermolecular vibrations on the electronic coupling in organic semiconductors: the case of anthracene and perfluoropentacene.

We have performed classical molecular dynamics simulations and quantum-chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room-temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian-like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry.

Molecular dynamics simulations for a pentacene monolayer on amorphous silica.

Molecular dynamics simulations are presented for "bulklike" and "filmlike" monolayers of pentacene deposited on a slab of amorphous silica. The two simulated systems, which mainly differ in the tilt angle between the pentacene molecules and the silica surface, exhibit structural and energetic properties that match the available measurements. The bulklike monolayer, the structure of which corresponds to that of the low-temperature polymorph of crystalline pentacene, is stable.

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee.

Car-Parrinello MD simulations for the Na+ -phenylalanine complex in aqueous solution.

Car-Parrinello molecular dynamics (CPMD) calculations are presented for a Na (+)(Phe) complex in aqueous solution and for various stable Na (+)(Phe) complexes and Na (+)(H 2O) n clusters in the gas phase (with up to six water molecules). The CPMD results are compared to available experimental and ab initio reference data, to DFT results obtained with various combinations of density functionals and basis sets, and to previous classical mechanics MD simulations. The agreement with the reference data in the gas phase validates the CPMD method, showing that it is a valid approach for studying these systems and that it describes correctly the competing Na (+)-Phe and Na (+)-H 2O interactions.

Are crystal polymorphs predictable? The case of sexithiophene.

Using sexithiophene as a benchmark compound, we present a very effective strategy for searching the potential energy minima of a crystalline material, described in terms of rigid molecules with Coulombic and atom-atom interactions. The strategy involves uniform sampling of the many-body energy hypersurface, mechanical identification of all constraints deriving from the crystallographic symmetry, and a "sight-resight" method, originally introduced in wildlife ecology, for assessing the completeness of the search. Thousands of distinct potential energy minima, with a surprising variety of structural arrangements, are identified for sexithiophene.

Do computed crystal structures of nonpolar molecules depend on the electrostatic interactions? The case of tetracene.

We present a strategy for comparing the global properties of competing potential models. By systematically sampling the potential energy surface of crystalline tetracene, we assess how the number, energy and structure of its minima are modified by switching on (or off) the Coulombic interactions. The increased complexity of the Coulombic potential leads to a more "rugged" potential energy surface with a larger number of minima, but the effect is not large.

Inherent structures of crystalline tetracene.

We have systematically sampled the potential energy surface of crystalline tetracene to identify its local minima. These minima represent all possible stable configurations and constitute the "inherent structures" of the system. The crystal is described in terms of rigid molecules with Coulombic and atom-atom interactions.

MD simulation of the Na+-phenylalanine complex in water: competition between cation-pi interaction and aqueous solvation.

The competition between cation-pi interaction and aqueous solvation for the Na+ ion has been investigated by molecular dynamics simulations, using the phenylalanine amino acid as the test pi system. Starting from one of the best standard force fields, we have developed new parameters that significantly improve the agreement with experimental and high quality quantum mechanical results for the complexes of Na+ with phenylalanine, benzene, and water. The modified force field performs very well in forecasting energy and geometry of cation coordination for the complexes.

High-pressure dissociation of crystalline para-diiodobenzene: optical experiments and Car-Parrinello calculations.

We have investigated the high-pressure properties of the molecular crystal para-diiodobenzene, by combining optical absorption, reflectance, and Raman experiments with Car-Parrinello simulations. The optical absorption edge exhibits a large red shift from 4 eV at ambient conditions to about 2 eV near 30 GPa. Reflectance measurements up to 80 GPa indicate a redistribution of oscillator strength toward the near-infrared.