Predicting Inclusion Behaviour and Framework Structures in Organic Crystals

We have used well‐established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well‐known inclusion behaviour. Using these methods, we are able to generate both close‐packed crystal structures and high‐energy open frameworks containing voids of molecular dimensions. Some of these high‐energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent‐accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules.     

Structure prediction, disorder and dynamics in a DMSO solvate of carbamazepine

We have applied crystal structure prediction methods to understand and predict the formation of a DMSO solvate of the anti-convulsant drug carbamazepine (CBZ), in which the DMSO molecules are disordered. Crystal structure prediction calculations on the 1:1 CBZ:DMSO solvate revealed the generation of two similar low energy structures which differ only in the orientation of the DMSO molecules. Analysis of crystal energy landscapes generated at 0 K suggests the possibility of solvent disorder. A combined computational and experimental study of the changes in the orientation of the DMSO within the crystal structure revealed that the nature of the disorder changes with temperature. At low temperature, the DMSO disorder is static whilst at high temperature the DMSO configurations can interconvert by a 180° rotation of the DMSO molecules within the lattice. This 180° rotation of the DMSO molecules drives a phase change from a high temperature dynamically disordered phase to a low temperature phase with static disorder. Crystallisation of a DMSO solvate of the related molecule epoxycarbamazepine resulted in a different degree of DMSO disorder in the crystal structure, despite the similarity of the carbamazepine and epoxycarbamazepine molecules. We believe consideration of disorder and its contribution to entropy and crystal free energies at temperature other than 0 K is fundamental for the accuracy of future energy rankings in crystal structure prediction calculations of similar solvated structures.     

Synthesis, ionisation potentials and electron affinities of hexaazatrinaphthylene derivatives

Several hexaazatrinaphthylene derivatives and a tris(thieno)hexaazatriphenylene derivative have been synthesised by reaction of the appropriate diamines with hexaketocyclohexane. The crystal structure of 2,3,8,9,14,15-hexachloro-5,6,11,12,17,18-hexaazatrinaphthylene has been determined by X-ray diffraction; this reveals a molecular structure in good agreement with that predicted by density functional theory (DFT) calculations and pi-stacking with an average spacing between adjacent molecular planes of 3.18 A. Solid-state ionisation potentials have been measured by using UV photoelectron spectroscopy and fall in the range of 5.99 to 7.76 eV, whereas solid-state electron affinities, measured using inverse photoelectron spectroscopy, vary in the range -2.65 to -4.59 eV. The most easily reduced example is a tris(thieno)hexaazatriphenylene substituted with bis(trifluoromethyl)phenyl groups; DFT calculations suggest that the highly exothermic electron affinity is due both to the replacement of the outermost phenylene rings of hexaazatrinaphthylene with thieno groups and to the presence of electron-withdrawing bis(trifluoromethyl)phenyl groups. The rather exothermic electron affinities, the potential for adopting pi-stacked structures and the low intramolecular reorganisation energies obtained by DFT calculations suggest that some of these molecules may be useful electron-transport materials.     

Protonierung des 1,1,3,3,5,5‐Hexakis(dimethylamino)λ5‐[1,3,5]triphosphinins. Cyclotrimethylentriphosphinsäure. NMR‐Daten,Kristallstrukturen und quantenchemische Rechnungen

Protonation of 1,1,3,3,5,5‐Hexakis(dimethylamino)‐λ⁵‐[1,3,5]triphosphinine. Cyclotrimethylenetriphosphinic Acid. NMR Data, Crystal Structures, and Quantum Chemical Calculations Preparation of 1,1,3,3,5,5‐hexakis(dimethylamino)‐1,2‐dihydro‐3λ⁵,5λ⁵‐[1,3,5]triphosphininium‐tetrafluoroborate ( 3 ) und 1,1,3,3,5,5‐hexakis(dimethylamino)‐λ⁵‐[1,3,5]triphosphinanetriium‐tris(tetrafluoroborate) ( 4 ) from 1,1,3,3,5,5‐hexakis(dimethylamino)‐1λ⁵,3λ⁵,5λ⁵‐triphosphinine 1 and HBF₄ · O(C₂H₅)₂ are described. The structures of 3 und 4 are elucidated by n. m. r. and X‐ray structural analyses. By hydrolysis of 4 with conc. hydrochloric acid 1,3,5‐trioxo‐1λ⁵,3λ⁵,5λ⁵‐[1,3,5]triphosphinane‐1,3,5‐triol (cyclotrimethylene‐triphosphinic acid) ( 8 ) is formed. Neutralisation with NaOH yields its sodium salt 9 . 8 and 9 are characterized by their n. m. r. spectra. Quantum chemical calculations have been investigated for the compounds 1 ′– 4 ′ and the trianion 9 . The systems 1 ′– 4 ′ are distinguished from 1 – 4 by the size of the ligands at phosphorus which is reduced from N(CH₃)₂ to NH₂, respectively. The aims of the calculations are to elucidate hybridisations and molecular structures, Lewis or resonance structures, electronic charge distributions and NMR chemical shifts.     

Reorganization and growth of metastable alpha-N2 critical nuclei into stable beta-N2 crystals

We report on results on the crystal nucleation and growth of nitrogen. Using molecular dynamics simulations, we show that while nucleation proceeds into the metastable alpha-phase (i.e., the crystalline phase associated with the lowest free energy barrier of formation), growth of the crystallite proceeds through a reorganization of the nucleus into the thermodynamically stable beta-phase.     

Influence of pore dimension and sorption configuration on the heat of sorption of hexane on monodimensional siliceous zeolites

Sorption of n-hexane on monodimensional pure silica SSZ-35, CIT-5, ZSM-12, and ZSM-22 zeolites with different pore dimension and on recently synthesized ITQ-29 was studied by IR spectroscopic and computational chemistry methods. Heats of sorption of n-hexane on these zeolites was determined experimentally from the temperature dependence of the intensity of IR bands of sorbed hexane as well as from theoretical calculations. Calculations have shown the different orientations of sorbed hexane molecules inside zeolite channels, which depend on the type of zeolite and loading. At high loadings, ordering of hexane inside the channels is observed due to optimization of sorbate-sorbate and sorbate-zeolite interaction energies. Such ordering is responsible for the increase of the sorption energy. A decrease of the sorption energy upon increasing the pore dimension of zeolite was observed, in agreement with results previously published in the literature. Effects of pore diameter of zeolites and ordering of molecules inside zeolite channels on the sorption energy of hexane are discussed.     

Electronic structure of crystalline copper phthalocyanine

The electronic structure of copper-phthalocyanine (CuPc) has been studied both experimentally and theoretically. Experiments have been performed on alpha and beta crystalline phases, using photoemission spectroscopy to probe core levels and valence band spectra. Different photon energies have been used, in order to probe different sample depths. Only minor differences have been observed in the experimental data on the two different phases, except for a small charge effect on the beta phase crystal. First-principles calculations have been performed using the density functional for molecular and three-dimensional periodic solids (Dmol(3)) code on both the single CuPc molecule and the beta phase, allowing the identification of the different atomic and angular contributions to the experimental density of states. In particular, the highest occupied molecular level is mainly due to Cu and N states. The comparison between theoretical data obtained for the CuPc in the beta phase and in the single molecule shows that the interchain interaction between the molecules is negligible, whereas slightly stronger intrachain interactions occur.     

Nonreactive molecular dynamics force field for crystalline hexahydro-1,3,5-trinitro-1,3,5 triazine

An empirical nonreactive force field has been developed for molecular dynamics (MD)/Monte Carlo simulation of the formation, diffusion, and agglomeration of point defects in the crystal lattice of the alpha modification of hexahydro-1,3,5-trinitro-1,3,5 triazine (RDX) using flexible molecules. Bond stretching and angle bending are represented by Morse and harmonic functions, and torsion by a truncated cosine series. Nonbonded interactions, both inter- and intramolecular, are described by Buckingham potentials separately parametrized. Intermolecular electrostatic interactions are treated via a Coulomb term coupled with a smooth 15.0 A cutoff radius. Parameters were taken in part from earlier published works and were determined partly by fitting to known molecular and crystal properties of RDX. In MD simulations at constant pressure and temperature, the model was able to stabilize and maintain the correct crystal structure, symmetry, and molecular conformation of alpha-RDX. Vibrational frequencies, lattice binding energy and dimensions, coefficients of thermal expansion, and several unusually short intermolecular distances are all reproduced in satisfactory agreement with experimental data.     

Vibrational spectroscopic and density functional theory studies of chloranil-imidazole interaction

The present work reports vibrational spectra and density functional theory calculations for chloranil, imidazole and their complexes. The experimentally observed infrared and Raman bands have been assigned with the help of calculated vibrational frequencies and potential energy distribution analysis. Some bands of chloranil and imidazole have been found to shift on the complex formation due to partial electronic charge transfer from imidazole to chloranil. The charge transfer between these molecules is also corroborated by the electronic absorption spectroscopy and calculations. The theoretical values of the interaction energy of various possible chloranil-imidazole interactions suggest that the two molecules interact preferably via N and H atoms of imidazole and CO group of chloranil with their molecular planes almost perpendicular to each other.     

Ab initio and molecular mechanics study of n-phenyl phthalimide and its crystal structure

Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G^** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.     

Water adsorption on ZnO(1010): from single molecules to partially dissociated monolayers

Static and dynamic density functional calculations have been used to study the structure and energetics of water adsorbed on the main cleavage plane of ZnO. In the single molecule limit we find that molecular adsorption is strongly preferred. The water binding energy increases for higher coverages due to an almost isotropic attractive water-water interaction which leads to clustering and formation of monolayer islands in the low water coverage regime. A thermodynamic analysis further shows that the full water monolayer is clearly the most stable phase until water starts to desorb. The water monolayer is even more stabilized by a partial dissociation of the water molecules, yielding as most stable configuration a (2x1) superstructure where every second water molecule is cleaved. The dissociation barrier for this process is very small which allows for an auto-dissociation of the water molecules even at low temperatures as observed experimentally. Finally we find that the energy cost involved to form [1210]-oriented domain boundaries between (2x1) patches with different orientation is almost negligible which explains the abundance of such domain boundaries in STM images.     

Quantum chemical study of three polymorphs of the mononuclear spin-transition complex [Fe(DPPA)(NCS)2

The calculations of the high spin (HS) and low spin (LS) states of the [Fe(II)(DPPA)(NCS)(2)] complex have been performed at three experimentally observed geometries corresponding to three synthesized polymorphs with different spin-transition behavior. The structure optimization leads to a single molecular structure, suggesting that the existence of three geometries is not an intrinsic phenomenon but is induced by the crystal lattice. The structural difference between three forms can be reproduced by introducing the Madelung field of the crystal lattice. However, the calculations show that the differences in magnetic behavior of the three polymorphs cannot be attributed only to variations of the energy gap between two spin states.     

二乙炔及其衍生物的聚合和光学性能的量子化学研究

主要报道利用半经验分子轨道方法PM3研究的五个二乙炔衍生物的结构, 并预计了其分子晶体的光学和聚合性能。这些化合物的几何构型参数以及由此形成的晶体的堆积参量均用能量梯度方法优化。同时, 从实验上研究了其中三个化合物的晶体在热和光环境下的聚合状况。理论预计和实验结果基本吻合。计算表明, 可聚合晶体应具有适当的堆积距d(～0.55nm)和倾斜角θ(～50°)。     

Ab initioMODPOT/VRDDO/MERGE calculations on energetic compounds. III. Nitroexplosives: Polyaminopolynitrobenzenes (including DATB,TATB, and tetryl)

Quantum chemical ab initio MODPOT /VRDDO calculations have been carried out on the following aminonitrobenzenes for which crystal structures had been determined experimentally: 4-nitroaniline; N,N-dimethyl-p-nitroaniline; 2,4,6-trinitroaniline; 1,3-diamino-2,4,6-trinitrobenzene (DATB—Form I); 1,3,5-triamino-2,4,6-trinitrobenzene (TATB); 2,3,4,6-tetranitroaniline; N-methyl-N,2,4,6-tetranitroaniline (Tetryl); and N-(β,β,β-trifluoroethyl)-N,2,4,6-tetranitroaniline. These quantum chemical calculations were performed on the molecules in their conformations as found in their crystal structures. The calculations were carried out with our own ab initio programs which also incorporate as options several desirable features for calculations on large molecules: ab initio effective core model potentials (MODPOT) which enable calculations of valence electrons only explicitly, yet accurately, and a charge conserving integral prescreening evaluation (which we named VRDDO-variable retention of diatomic differential overlap) especially effective for spatially extended molecules. Aminonitrobenzenes are especially interesting since there are inherent intramolecular ring distortions and deviations from planarity and intramolecular hydrogen bonds as well as intermolecular hydrogen bonds causing further deviations from planarity. The theoretical indices resulting from the quantum chemical calculations are relevant to a number of properties and behavioral characteristics of these molecules, both intramolecular and intermolecular. The charges on the atoms [from the gross atomic populations (GAP 's)] are needed for calculation of the atomic multipole–atomic multipole electrostatic contributions (a dominant factor) to the intermolecular interaction energies. These electrostatic interaction energies are part of the input necessary for calculations on the crystal packing and densities of these molecules. These GAP 's are also of value in interpreting the experimental photoelectron and ESCA spectra of these molecules. The total overlap populations (TOP 's) between atoms are related to the inherent bond strengths and can serve as a quantitative replacement for the old empirical bond length-bond order-bond energy relationship still used by explosives chemists to identify the “target bonds” (the weakest bonds). The TOP 's are of considerable value in predicting and tracing initiation and subsequent steps of explosive phenomena. The molecular orbital energies of the lowest unoccupied orbitals are of interest since nitroexplosives have been implicated in testicular toxicity and the initial metabolic activation appears to proceed through a one-electron reduction of the nitroexplosive.     

Comparison of bulk and thin film structures of the liquid crystal 28OBC: measurements and simulations

Freely-suspended liquid crystalline films of ethyl 4'-n-octyloxybiphenyl-4-carboxylate (28OBC) were prepared and transferred onto different substrates which enable detailed structural characterization. The structures of these thin film assemblies, which are only accessible in this way, were determined and compared with the crystal and molecular structure of 28OBC as formed by crystallization from toluene solution. The compound crystallizes in the monoclinic space group P21/c, a = 11.168(1) A, b = 7.595(2) A, c = 49.106(1) A, beta = 94.01(1) degree, Z = 8. The two symmetrically independent molecules of the asymmetric unit have been used as starting geometries for semi-empirical MO calculations. The difference between the experimentally observed and the optimized molecular structures is interpreted as the influence of the crystal field. The structures of the crystalline and E film phases have been investigated by SAXR and TED and the former has been found to be different from the bulk structure. The structural relationships between the different phases are discussed and a suggestion for the crystalline film structure is given as deduced from simulations of electron diffraction patterns.     

Molecular recognition and crystal energy landscapes: an X-ray and computational study of caffeine and other methylxanthines

We introduce a new approach to crystal-packing analysis, based on the study of mutual recognition modes of entire molecules or of molecular moieties, rather than a search for selected atom-atom contacts, and on the study of crystal energy landscapes over many computer-generated polymorphs, rather than a quest for the one most stable crystal structure. The computational tools for this task are a polymorph generator and the PIXEL density sums method for the calculation of intermolecular energies. From this perspective, the molecular recognition, crystal packing, and solid-state phase behavior of caffeine and several methylxanthines (purine-2,6-diones) have been analyzed. Many possible crystal structures for anhydrous caffeine have been generated by computer simulation, and the most stable among them is a thermodynamic, ordered equivalent of the disordered phase, revealed by powder X-ray crystallography. Molecular recognition energies between two caffeine molecules or between caffeine and water have been calculated, and the results reveal the largely predominant mode to be the stacking of parallel caffeine molecules, an intermediately favorable caffeine-water interaction, and many other equivalent energy minima for lateral interactions of much less stabilization power. This last indetermination helps to explain why caffeine does not crystallize easily into an ordered anhydrous structure. In contrast, the mono- and dimethylxanthines (theophylline, theobromine, and the 1,7-isomer, for which we present a single-crystal X-ray study and a lattice energy landscape) do crystallize in anhydrous form thanks to the formation of lateral hydrogen bonds.     

1,1,3,3,5,5-Hexakis(dimethylamino)-λ5-[1,3,5]triphosphinin – Darstellung,Kristallstruktur und NMR-Daten

1,1,3,3,5,5-Hexakis(dimethylamino)-λ⁵-[1,3,5]triphosphinine – Synthesis, Crystal Structure, and NMR Data Preparation of 1,1,3,3,5,5-hexakis(dimethylamino)-λ⁵-[1,3,5]triphosphinine ( 4 ) and the path of its formation from methyl-bis(dimethylamino)difluorophosphorane ( 1 ) and n-butyllithium are described. The chemical behaviour of compounds of type [R₂P=CH–]_n is compared with that of the isoelectronic dichlorophosphazenes [Cl₂P=N–]_n. The structure of 4 is eludicated by n.m.r. spectra and X-ray structural analysis.     

Crystal engineering on industrial diaryl pigments using lattice energy minimizations and X-ray powder diffraction

Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was found experimentally as a metastable gamma phase of PY12. Calculations on mixed crystals (solid solutions) showed that mixed crystals of PY12 and PY13 should adopt the PY13 structure with planar molecules, resulting in high color strengths; this was proven experimentally (Pigment Yellow 188). Similarly, the high color strength of mixed crystals consisting of PY13 and PY14 (Pigment Yellow 174), and PY13/PY83 (Pigment Yellow 176) is explained by the crystal structures.     

Molecular Recognition and Crystal Energy Landscapes: An X‐ray and Computational Study of Caffeine and Other Methylxanthines

We introduce a new approach to crystal‐packing analysis, based on the study of mutual recognition modes of entire molecules or of molecular moieties, rather than a search for selected atom–atom contacts, and on the study of crystal energy landscapes over many computer‐generated polymorphs, rather than a quest for the one most stable crystal structure. The computational tools for this task are a polymorph generator and the PIXEL density sums method for the calculation of intermolecular energies. From this perspective, the molecular recognition, crystal packing, and solid‐state phase behavior of caffeine and several methylxanthines (purine‐2,6‐diones) have been analyzed. Many possible crystal structures for anhydrous caffeine have been generated by computer simulation, and the most stable among them is a thermodynamic, ordered equivalent of the disordered phase, revealed by powder X‐ray crystallography. Molecular recognition energies between two caffeine molecules or between caffeine and water have been calculated, and the results reveal the largely predominant mode to be the stacking of parallel caffeine molecules, an intermediately favorable caffeine–water interaction, and many other equivalent energy minima for lateral interactions of much less stabilization power. This last indetermination helps to explain why caffeine does not crystallize easily into an ordered anhydrous structure. In contrast, the mono‐ and dimethylxanthines (theophylline, theobromine, and the 1,7‐isomer, for which we present a single‐crystal X‐ray study and a lattice energy landscape) do crystallize in anhydrous form thanks to the formation of lateral hydrogen bonds.     

Solid-state modeling of the terahertz spectrum of the high explosive HMX

The experimental solid-state terahertz (THz) spectrum (3-120 cm(-1)) of the beta-crystal form of the high explosive octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been analyzed using solid-state density functional theory calculations. Various density functionals (both generalized gradient approximation and local density approximation) are compared in terms of their abilities to reproduce the experimentally observed solid-state structure and low-frequency vibrational motions. Good-to-excellent agreement between solid-state theory and experiment can be achieved in the THz region where isolated-molecule calculations fail to reproduce the observed spectral features, demonstrating a clear limitation of using isolated-molecule calculations for the assignment of THz frequency motions in molecular solids. The deficiency of isolated-molecule calculations is traced to modification of the molecular structure in the solid state through crystal packing effects and the formation of weak C-H...O hydrogen bonds.