Morphology and packing behavior of model ethylene/propylene copolymers with precise methyl branch placement

The packing behavior of ethylene/propylene (E/P) copolymers with precise methyl group placement on every 15th and 21st chain carbon atom (denominated HP15 and HP21) was investigated. Lamellar morphology with lamella thicknesses by far exceeding the distance between side groups gives strong evidence that the crystals contain pendant methyl groups as defects. The packing of chains in the lattice requires that adjacent E/P copolymer molecules stagger thereby forming a triclinic lattice with a hexagonal subcell of methylene groups. Defects inside the crystalline region are concentrated in planes oblique to the chain stems. The relationship between subcell and unit cell seems to be a function of the thermal history of the copolymer involving transient states. The atactic structure leads to conformationally disordered crystals (Wunderlichs CONDIS crystals) and enforces deviations from an all-trans stem conformation. These deviations shorten the chains and are stronger for HP15 than for HP21, a fact that has been supported by Raman spectroscopy performed on recrystallized samples of both materials. In fact, a Raman signature band found at 1,084 cm^–1 for only HP15 indicates the presence of disordered chain conformations adjacent to singularities.Dedicated to Professor Erhard W. Fischer on the occasion of his 75th birthday.     

Conversion of the aggregation state of merocyanine dye, modification of the subcell packing of arachidic acid, and removal of the majority of n-octadecane by hydrothermal treatment in the liquid phase in a mixed Langmuir-Blodgett film of the ternary system

We have investigated the influence of heat treatment in an air atmosphere (HT) and hydrothermal treatment in the liquid phase (HTTL) on the H-aggregate in a mixed Langmuir-Blodgett (LB) film of merocyanine dye with an octadecyl group (MS(18))-arachidic acid (C(20))-n-octadecane (AL(18)) ternary system by means of polarized visible and IR absorption spectroscopy. HT causes the variation from the H-aggregate to the monomer, the increment in the number of gauche conformers in the MS(18) hydrocarbon chain, the slight orientation change in the C(20) hydrocarbon chain, and the complete evaporation of AL(18). The dissociation of MS(18) is probably ascribed to the complete evaporation of AL(18) from the mixed LB film and the increase in thermal mobility of the long axis of the MS(18) hydrocarbon chain during HT. However, HTTL can easily and rapidly induce the conversion of the MS(18) aggregation state from H- to J-aggregates, the modification of the C(20) subcell packing from hexagonal to orthorhombic, and the removal of most of the AL(18) molecules. The conversion of the MS(18) aggregation state can be interpreted to consist of two processes from the H-aggregate to the monomer and from the monomer to the J-aggregate. In the initial stage of HTTL, the MS(18) aggregation state changes from the H-aggregate to the monomer, which is caused by the removal of almost all of the AL(18) molecules from the mixed LB film to warm water via the thermal energy of warm water. Then, the large relative permittivity of warm water is expected to relate strongly to the subsequent variation from the monomer to the J-aggregate. This transformation results in the decrease in the total value of the electrostatic energy based on the MS(18) permanent dipole interaction. Moreover, the modification of the C(20) subcell packing is possibly due to the hydrophobic effect, where the C(20) hydrocarbon chains cohere again in the warm water during HTTL. Consequently, it has been found that HTTL is quite effective to reorganize the chromophore alignment of MS(18), to modify the subcell packing of C(20) and to erase the majority of AL(18) molecules in the mixed LB film of the MS(18)-C(20)-AL(18) ternary system in a short time.     

Conformational and packing energy calculations on ethylene copolymers

A conformational analysis was performed on the isolated chains of ethylene-propene and ethylene-1-butene copolymers. The lowest energy conformations in accordance with the chain repeating distance of polyethylene were used in packing energy calculations. The results of our calculations suggest that both methyl and ethyl groups are tolerated in the crystalline conformation of a single polyethylene chain, but only the methyl group is acceptable in the crystalline state if the packing energies and the lattice deformations are taken into account.     

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.     

Computer simulations and analysis of structural and energetic features of some crystalline energetic materials

A database of 43 literature X-ray crystal structure determinations for compounds with known, or possible, energetic properties has been collected along with some sublimation enthalpies. A statistical study of these crystal structures, when compared to a sample of general organic crystals, reveals a population of anomalously short intermolecular oxygen-oxygen separations with an average crystal packing coefficient of 0.77 that differs significantly from 0.70 found for the general population. For the calculation of lattice energies, three atom-atom potential energy schemes and the semiempirical SCDS-PIXEL scheme are compared. The nature of the packing forces in these energetic materials is further analyzed by a study of the dispersive versus Coulombic contributions to overall lattice energies and to molecule-molecule energies in pairs of near neighbors in the crystals, a partitioning made possible by the unique features of the SCDS-PIXEL scheme. It is shown that dispersion forces are stronger than Coulombic forces, contrary to common belief. The low abundance of hydrogen atoms in these molecules, the close oxygen-oxygen contacts, and the high packing coefficients explain the observation that, for these energetic materials, crystal densities are anomalously high compared to those of most organic materials. However, an understanding, not to mention prediction or control, of the deeper mechanisms for the explosive power of these crystalline materials, such as the role of lattice defects, remains beyond present capabilities.     

Atomistic calculations on the high-temperature condis phase of poly(trans-1,4-butadiene) (PTBD)

The structure of the low-temperature phase of poly(trans-1,4-butadiene) was calculated by means of semiempirical atomistic potentials. Without using any symmetry assumptions there is good agreement with experimental data. In order to understand the high-temperature phase, packing energy calculations were performed with different chain conformations. There are a great number of possible packing modes. They show an approximately linear relation between defect volume and defect energy. The results of these calculations are taken as a basis for a thermodynamic treatment (cooperative pair theory) of the phase transition. The experimental transition enthalpy can only partially be explained by intermolecular interactions, and the defect energy of the various intramolecular equilibrium conformations is not sufficient to explain the difference. A refined treatment with a simultaneous inter-and intramolecular minimization of the energy reveals that the chains are not in their intramolecular equilibrium state. This results in an additional intramolecular defect energy which seems to lead to an understanding of the experimental transition data.     

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.     

Crystallization Force—A Density Functional Theory Concept for Revealing Intermolecular Interactions and Molecular Packing in Organic Crystals

Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short‐range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal‐growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self‐assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5‐methyl‐2‐[(2‐nitrophenyl)amino]‐3‐thiophenecarbonitrile, so‐called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.     

Intermolecular covalent pi-pi bonding interaction indicated by bond distances, energy bands, and magnetism in biphenalenyl biradicaloid molecular crystal

Density-functional theory (DFT) calculations were performed for energy band structure and geometry optimizations on the stepped pi-chain, the isolated molecule and (di)cations of the chain, and various related molecules of a neutral biphenalenyl biradicaloid (BPBR) organic semiconductor 2. The dependence of the geometries on crystal packing provides indirect evidence for the intermolecular covalent pi-pi bonding interaction through space between neighboring pi-stacked phenalenyl units along the chain. The two phenalenyl electrons on each molecule, occupying the singly occupied molecular orbitals (SOMOs), are participating in the intermolecular covalent pi-pi bonding making them partially localized on the phenalenyl units and less available for intramolecular delocalization. The band structure shows a relatively large bandwidth and small band gap indicative of good pi-pi overlap and delocalization between neighboring pi-stacked phenalenyl units. A new interpretation is presented for the magnetism of the stepped pi-chain of 2 using an alternating Heisenberg chain model, which is consistent with DFT total energy calculations for 2 and prevails against the previous interpretation using a Bleaney-Bowers dimer model. The obtained transfer integrals and the magnetic exchange parameters fit well into the framework of a Hubbard model. All presented analyses on molecular geometries, energy bands, and magnetism provide a coherent picture for 2 pointing toward an alternating chain with significant intermolecular through-space covalent pi-pi bonding interactions in the molecular crystal. Surprisingly, both the intermolecular transfer integrals and exchange parameters are larger than the intramolecular through-bond values indicating the effectiveness of the intermolecular overlap of the phenalenyl SOMO electrons.     

Relationship Between Molecular Structure,Single crystal Packing and Self-Assembly Behavior: A Case Based on Pyrene Imide Derivatives

Development of new n-type one-dimensional (1D) self-assembly nanostructure and a clear understanding of the relationship between molecular structure and self-assembly behavior are important prerequisites for further designing and optimizing organic optoelectronic nanodevice. In this article, a series of n-type organic semiconductor materials based on pyrene imide were successfully synthesized through [4+2] cycloaddition reactions and their preliminary optical and electrochemical properties were studied. The simulated HOMO-LUMO bandgaps via DFT tallied with the experimental data well. The self-assembly of these materials showed needle or fiber-like morphologies, indicating that different conjugation degree or alkyl group had significant influence on their self-assembly behaviors. Furthermore, the single-crystal packing for these molecules were analyzed and it was found out that the changes of conjugated backbone and functional group would affect certain crystal lattice parameter significantly, such as the intermolecular packing distance and crystal size etc, which would further result in different self-assembly morphology.     

配合物型非线性光学材料的晶体工程

以分子基材料为目标的功能配合物的设计合成是近年来材料化学研究的重要领域，传统的分子设计尽管在分子水平上获得了很大的成功，但在由分子到晶体，由微观性质到宏观功能的晶体工程研究中遇到了极大的困难。因为宏观功能不仅要求分子本身具有良好的性能，同时还要求分子按照一定的方式堆积和排列犤１～３犦。例如二阶非线性光学材料不但要求分子具备较大的非线性超极化率和非对称中心，而且还要求分子在堆积过程中形成无心空间群的晶体。而自然界中大约超过７０％的手性分子在结晶时都形成有心的空间群，因此，如何实现分子的无心堆积是非…     

Molecular flexibility effects upon liquid dynamics

Simulation results for the diffusive behavior of polymer chain/penetrant systems are analyzed. The attractive range and flexibility of simple chain molecules were varied in order to gauge the effect on dynamics. In all cases, the dimensionless diffusion coefficient, D*, is found to be a smooth, single-valued function of the packing fraction, eta. The functions D*(eta) are found to be power laws with exponents that are sensitive to both chain stiffness and particle type. For a specific system type, the D*'s for both penetrant and chain-center-of-mass extrapolate to zero at the same packing fraction, eta0. This limiting packing fraction is interpreted to be the location of the glass transition, and (eta0-eta), the distance to the glass transition.     

Reactions in the solid state : III. Structural aspects of photochemical reactions in crystalline inclusion compounds

Stereoselective photochemical dimerization to products adopting the syn head-to-tail configuration is obtained by irradiation of crystalline inclusion compounds. The structural aspects of these reactions regarding the relations between the arrangement of the host molecules in the crystalline lattice forming the matrix and the packing of the potentially reactive molecules included in the matrix are discussed.The possibilities of using non-symetrical host molecules as a probe for stereoselective and enantioselective intramolecular reactions are also discussed.     

Adsorption of Chain Molecules

We analyze the influence of chain length on the adsorption isotherm using the framework of lattice theory. Each molecule is represented as a chain of segments occupying separate sites in the lattice. Adsorption equilibria (particularly adsorption isotherms) are analyzed for one-component and two-component mixtures of chain molecules. Copyright 1999 Academic Press.     

Ab initio dynamics study of poly-para-phenylene vinylene

We present an ab initio dynamics investigation within a density-functional perturbation theory framework of the properties of the conjugated polymer poly-para-phenylene vinylene (PPV) in both the isolated chain and crystalline states. The calculated results show that for an isolated chain, most of the vibrational modes correspond to experimentally observed modes in crystalline PPV. However, additional hitherto unidentified modes have been observed in experiment and our calculations on crystalline material have allowed us to assign these. We also present the results of calculations of the polarizability and permittivity tensors of the material, which are in reasonable agreement with the typical values for conjugated polymers. Dynamical Born effective charges [S. Baroni, S. de Gironcoli, A. Dal Corso, and P. Giannozzi, Rev. Mod. Phys. 73, 515 (2001)] are calculated and compared with atomic charges obtained from Mulliken population analysis [M. D. Segall, C. J. Pickard, R. Shah, and M. C. Payne, Mol. Phys. 89, 571 (1996)] and we conclude that effective charges are more appropriate for use in the study of the dynamics of the system. Notable differences are found in the infrared-absorption spectra obtained for the isolated chain and crystalline states, which can be attributed to the differences in the crystalline packing effects, which clearly play a key role in influencing the lattice dynamics of PPV.     

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 simulation studies of the structure of phosphorylcholine self-assembled monolayers

We report a study of the structure of phosphorylcholine self-assembled monolayers (PC-SAMs) on Au(111) surfaces using both molecular mechanics (MM) and molecular dynamics (MD) simulation techniques. The lattice structure (i.e., packing densities and patterns) of the PC chains was determined first, by examining the packing energies of different structures by MM simulations in an implicit solvent. The chain orientation (i.e., antiparallel and parallel arrangements of the PC head groups) was then evaluated. The initial azimuthal angles of the PC chains were also adjusted to ensure that the optimal lattice structure was found. Finally, the two most probable lattice structures were solvated with explicit water molecules and their energies were compared after 1.5 ns of MD simulations to verify the optimal structures obtained from MM. We found that the optimal lattice structure of the PC-SAM corresponds to a radical7 x radical7 R19degree lattice structure (i.e., surface coverage of 50.4 A(2)molecule) with a parallel arrangement of the head groups. The corresponding thickness of the optimal PC-SAM is 13.4 A which is in agreement with that from experiments. The head groups of the PC chains are aligned on the surface in such a way that their dipole components are minimized. The P-->N vector of the head groups forms an angle of 82 degrees with respect to the surface normal. The tilt direction of molecular chains was observed to be towards their next nearest neighbor.     

Molecular Shape and Crystal Packing: a Study of C12H12 Isomers,Real and Imaginary

Isomeric C₁₂H₁₂ hydrocarbon molecules with widely different constitution and shape are analysed for their packing ability. Some correspond to known compounds with known crystal structures, but some are invented hypothetical molecules designed to have low packing efficiency. For each isomer, a large number of close‐packed, low‐energy crystal structures was generated by computer, with lattice energies within a range of a few kJ mol⁻¹. Molecules with linear chains, triple bonds and Me groups tend to have larger molecular volume, lower lattice energy and lower crystal density than cyclic or cage isomers. The calculated crystal structures for each isomer show an inverse relationship between packing energy and cell volume. Although the slope dE/dV varies from molecule to molecule, the product of slope and free space stays roughly constant; less efficient crystal packings thus appear to be less sensitive to an increase in cell volume. Lattice‐vibrational frequencies and the corresponding contributions to thermal vibrational entropy were estimated for real and virtual crystal structures. For a given isomer, as expected, a higher entropy goes with a larger cell volume, but different isomers show different entropy/volume relationships. At 300 K, TΔS differences among computational polymorphs may compete with ΔH differences, thus making the lattice‐vibrational entropy estimation a relevant factor in crystal‐structure prediction.     

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.     

Ab Initio prediction of possible crystal structures for general organic molecules

The performance of a new crystal packing procedure for the ab initio prediction of possible molecular crystal structures is presented. The method is based upon only molecular information, i.e., no unit cell parameters are assumed to be known. The search for the global crystal energy minimum and all local minima inside an energy window is derived from Monte Carlo simulated annealing methods and has been applied to various organic molecules containing heteroatoms and polar groups. A systematic evaluation of the search method and of the quality of the potential energy function has been established. It is demonstrated that the packing of general organic molecules is possible even with standard force fields like CHARMM provided that the charges defining the electrostatic interactions are based upon physical models rather than transferable empirical parameters. Concepts of crystal packing that were based till now upon assumptions and speculations could be proved or disproved by solving directly the extended global optimization problem related to crystal packing. Crystal structures of molecules as complex as those treated in this article have not been, till now, predicted by a computational approach. In one case, a disagreement between the predicted and experimental structure was evident and, based upon the computations, we suspect that the published structure is the wrong one. © 1992 by John Wiley & Sons, Inc.