Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals

The self-consistent Madelung potential (SCMP) approach for calculating molecular wave functions for a subunit embedded in a symmetrical environment constituted by the copies of the subunit is implemented with semiempirical NDDO model Hamiltonians and supplemented with empirically parameterized dispersion–repulsion interaction potentials. This model yields sublimation enthalpies in good agreement with available experimental data for a series of molecular crystals, including imidazol, benzimidazole, urea, urethane, dicyaneamide, formamide, uracil, cytosine, maleic anhydride, succinic anhydride, and 1,3,5-triamino-2,4,6-trinitro-benzene. The SCMP-NDDO method, which avoids difficulties concerning the parametrization of charges in the molecular mechanics force fields, is proposed mainly for the treatment of molecular crystals with large unit cells. It might be particularly useful where important charge reorganization is expected under the effect of the crystal field. Charge distributions, obtained by the SCMP and the simple dielectric cavity self-consistent reaction field models, are compared and analyzed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 38–50, 1998     

Polarized Absorption,Spontaneous and Stimulated Blue Light Emission of J‐type Tetraphenylbutadiene Monocrystals

Blue amplified spontaneous emission at room temperature is demonstrated from the exposed face of the strongly emitting organic semiconductor 1,1,4,4‐tetraphenyl‐1,3‐butadiene in single crystal form. The symmetry of the crystal and calculation of lattice sums indicate the J‐type organization of the molecular transition moments. The minimum in the lowest exciton dispersion branch, from which emission takes place, is found at the edge of the Brillouin zone leading to a dominant vibronic emission since the zero‐phonon line is forbidden. The observed gain narrowed line is attributed to the vibronic replica which becomes amplified with increased pumping. The reported emission is along the normal to the exposed crystal face, important for the development of vertical cavity geometry lasers based on organic single crystals. The threshold excitation fluence of 400 μJ cm^?2 is comparable to other organic crystalline systems, even if the amplification path is much reduced as a consequence of the vertical geometry. Considering these relevant aspects, the optical characterization of this material is provided. The polarized absorption spectra are reported and the properties of the lowest‐energy excitonic state investigated. Calculation of the electronic transitions for the isolated molecule, lattice sums for the transition at lowest energy, and the symmetry of the crystal allow attributing the largest face of the samples and the observed optical bands in the spectra. Polarized time‐resolved spectra are also reported allowing to identify the intrinsic excitonic emission.     

Synthesis,structural analysis,spectral investigations,and DFT calculations of 1‐(3‐amino‐4‐thia‐1,2‐diazaspiro[4.11]hexadec‐2‐en‐1‐yl)ethan‐1‐one

1‐(3‐amino‐4‐thia‐1,2‐diazaspiro[4.11]hexadec‐2‐en‐1‐yl)ethan‐1‐one was synthesized and experimentally characterized by using FT‐IR, ¹H NMR, ¹³C NMR, and UV–Vis spectroscopy. The structure of the compound was confirmed by single‐crystal X‐ray diffraction. In the crystal structure, the molecules are linked by pairs of N‐H⋯N hydrogen bonds, forming centrosymmetric dimers with the graph‐set motif. The water molecule also plays an important role in the stabilization of the crystal structure, bridging the dimers to form a two‐dimensional supramolecular network. The molecular geometry, frontier molecular orbitals, vibrational frequencies, electronic properties, and molecular electrostatic potential were calculated using density functional theory (DFT) with the B3LYP/6‐311G(d,p) basis set. Geometric parameters, vibrational assignments, and electronic properties such as calculated energies, excitation energies, and oscillator strengths were compared with the experimental data, and it was seen that the theoretical results support the experimental parameters.     

Methyl 4‐O‐β‐l‐fucopyranosyl α‐­d‐­glucopyranoside hemihydrate

The crystal structure of methyl 4‐O‐β‐l ‐fuco­pyran­osyl α‐d ‐gluco­pyran­oside hemihydrate C₁₃H₂₄O₁₀·0.5H₂O is organized in sheets with antiparallel strands, where hydro­phobic interaction accounts for partial stabilization. Infinite hydrogen‐bonding networks are observed within each layer as well as between layers; some of these hydrogen bonds are mediated by water mol­ecules. The conformation of the disaccharide is described by the glycosidic torsion angles: ?_H = ?6.1° and ψ_H = 34.3°. The global energy minimum conformation as calculated by molecular mechanics in vacuo has ?_H = ?58° and ψ_H = ?20°. Thus, quite substantial changes are observed between the in vacuo structure and the crystal structure with its infinite hydrogen‐bonding networks.     

Conformational polymorphs of 3‐cyclopropyl‐5‐(3‐methyl‐[1,2,4]triazolo[4,3‐a]pyridin‐7‐yl)‐1,2,4‐oxadiazole

The dipharmacophore compound 3‐cyclopropyl‐5‐(3‐methyl‐[1,2,4]triazolo[4,3‐a]pyridin‐7‐yl)‐1,2,4‐oxadiazole, C₁₂H₁₁N₅O, was studied on the assumption of its potential biological activity. Two polymorphic forms differ in both their molecular and crystal structures. The monoclinic polymorphic form was crystallized from more volatile solvents and contains a conformer with a higher relative energy. The basic molecule forms an abundance of interactions with relatively close energies. The orthorhombic polymorph was crystallized very slowly from isoamyl alcohol and contains a conformer with a much lower energy. The basic molecule forms two strong interactions and a large number of weak interactions. Stacking interactions of the `head‐to‐head' type in the monoclinic structure and of the `head‐to‐tail' type in the orthorhombic structure proved to be the strongest and form stacked columns in the two polymorphs. The main structural motif of the monoclinic structure is a double column where two stacked columns interact through weak C—H…N hydrogen bonds and dispersive interactions. In the orthorhombic structure, a single stacked column is the main structural motif. Periodic calculations confirmed that the orthorhombic structure obtained by slow evaporation has a lower lattice energy (0.97 kcal mol^?1) compared to the monoclinic structure.     

Quantum mechanical studies on model α‐pleated sheets

Pauling and Corey proposed a pleated‐sheet configuration, now called α‐sheet, as one of the protein secondary structures in addition to α‐helix and β‐sheet. Recently, it has been suggested that α‐sheet is a common feature of amyloidogenic intermediates. We have investigated the stability of antiparallel β‐sheet and two conformations of α‐sheet in solution phase using the density functional theoretical method. The peptides are modeled as two‐strand acetyl‐(Ala)₂‐N‐methylamine. Using stages of geometry optimization and single point energy calculation at B3LYP/cc‐pVTZ//B3LYP/6‐31G* level and including zero‐point energies, thermal, and entropic contribution, we have found that β‐sheet is the most stable conformation, while the α‐sheet proposed by Pauling and Corey has 13.6 kcal/mol higher free energy than the β‐sheet. The α‐sheet that resembles the structure observed in molecular dynamics simulations of amyloidogenic proteins at low pH becomes distorted after stages of geometry optimization in solution. Whether the α‐sheets with longer chains would be increasingly favorable in water relative to the increase in internal energy of the chain needs further investigation. Different from the quantum mechanics results, AMBER parm94 force field gives small difference in solution phase energy between α‐sheet and β‐sheet. The predicted amide I IR spectra of α‐sheet shows the main band at higher frequency than β‐sheet. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Crystal structure of 5,6‐bis(9H‐carbazol‐9‐yl)benzo[c][1,2,5]thiadiazole: distortion from a hypothetical higher‐symmetry structure

Nucleophilic substitution of F atoms in 5,6‐difluorobenzo[c ][1,2,5]thiadiazole (DFBT) for carbazole could be potentially interesting as a novel way of synthesizing building blocks for new conjugated materials for applications in organic chemistry. The crystal structures of 5,6‐bis(9H‐carbazol‐9‐yl)benzo[c ][1,2,5]thiadiazole (DCBT), C₃₀H₁₈N₄S, and its hydrate, C₃₀H₁₈N₄S·0.125H₂O, were investigated using single‐crystal X‐ray analysis. The hydrate contains two symmetry‐independent DCBT molecules. The dihedral angles between the plane of the central benzothiadiazole fragment and that of the carbazole units vary between 50.8 and 69.9°, indicating conformational flexibility of the DCBT molecule in the crystals, which is consistent with quantum chemical calculations. The analysis of the crystal packing of DCBT revealed that the experimental triclinic structure could be described as a distortion from a hypothetical higher‐symmetry monoclinic structure. The quantum chemical calculations of two possible monoclinic structures, which are related to the experimental structure by a shifting of molecular layers, showed that the proposed structures are higher in energy by 5.4 and 10.1 kcal mol⁻¹. This energy increase is caused by less dense crystal packings of the symmetric structures, which results in a decrease of the number of intermolecular interactions.     

Preparation of oriented β‐form poly(L‐lactic acid) by solid‐state extrusion

Melt‐crystallized, low molecular weight poly(L ‐lactic acid) (PLLA) consisting of α crystals was uniaxially drawn by solid‐state extrusion at an extrusion temperature (T_ext) of 130–170 °C. A series of extrusion‐drawn samples were prepared at an optimum T_ext value of 170 °C, slightly below the melting temperature (T_m) of α crystals (～180 °C). The drawn products were characterized by deformation flow profiles, differential scanning calorimetry (DSC) melting thermograms, wide‐angle X‐ray scattering (WAXD), and small‐angle X‐ray scattering as a function of the extrusion draw ratio (EDR). The deformation mode in the solid‐state extrusion of semicrystalline PLLA was more variable and complex than that in the extensional deformation expected in tensile drawing, which generally gave a mixture of α and β crystals. The deformation profile was extensional at a low EDR and transformed to a parabolic shear pattern at a higher EDR. At a given EDR, the central portion of an extrudate showed extensional deformation and the shear component became progressively more significant, moving from the center to the surface region. The WAXD intensities of the (0010)_α and (003)_β reflections on the meridian as well as the DSC melting thermograms showed that the crystal transformation from the initial α form to the oriented β form proceeded rapidly with increasing EDR at an EDR greater than 4. Furthermore, WAXD showed that the crystal transformation proceeded slightly more rapidly at the sheath region than at the core region. This fact, combined with the deformation profiles (shear at the sheath and extensional at the core), indicated that the crystal transformation was promoted by shear deformation under a high pressure rather than by extensional deformation. Thus, a highly oriented rod consisting of only β crystals was obtained by solid‐state extrusion of melt‐crystallized, low molecular weight PLLA slightly below T_m. The structure and properties of the α‐ and β‐form crystals were also studied. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 95–104, 2002     

Photoinduced Ratchet‐Like Rotational Motion of Branched Molecular Crystals

Photomechanical molecular crystals can undergo a variety of light‐induced motions, including expansion, bending, twisting, and jumping. The use of more complex crystal shapes may provide ways to turn these motions into useful work. To generate such shapes, pH‐driven reprecipitation has been used to grow branched microcrystals of the anthracene derivative 4‐fluoroanthracenecarboxylic acid. When these microcrystals are illuminated with light of λ=405 nm, an intermolecular [4+4] photodimerization reaction drives twisting and bending of the individual branches. These deformations drive a rotation of the overall crystal that can be repeated over multiple exposures to light. The magnitude and direction of this rotation vary because of differences in the crystal shape, but a typical branched crystal undergoes a 50° net rotation after 25 consecutive irradiations for 1 s. The ability of these crystals to undergo ratchet‐like rotation is attributed to their chiral shape.     

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane): single‐crystal X‐ray and theoretical study

Single crystals of (2S,5R)‐2‐isopropyl‐5‐methyl‐7‐(5‐methylisoxazol‐3‐yl)cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane), C₁₆H₂₆N₂O₅, have been studied via X‐ray diffraction. The tetraoxazocane ring adopts a boat–chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6‐31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,?1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O—C—O and N—C—O fragments. There is a two‐cross hyperconjugation in the N—C—O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C—O bond (σ*_C—O) and vice versa between lpO and σ*_C—N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,?1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C—H…N and C—H…O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,?1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C—H…N interactions being electrostatic in origin. The molecules are further stacked due to C—H…O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.     

Ab initio crystal structure predictions for flexible hydrogen‐bonded molecules. Part II. Accurate energy minimization

A method is described to perform ab initio energy minimization for crystals of flexible molecules. The intramolecular energies and forces are obtained directly from ab initio calculations, whereas the intermolecular contributions follow from a potential that had been parameterized earlier on highly accurate quantum‐chemical calculations. Glycol and glycerol were studied exhaustively as prototypes. Lists of hypothetical crystal structures were generated using an empirical force field, after which ab initio energy minimizations were performed for a few hundreds of these. The experimental crystal structures were found among the structures with lowest energy, provided that sufficiently large basis sets were used. Moreover, their crystal geometries were well reproduced. This approach enables a systematic comparison between the merits of force fields at various levels of sophistication. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 805–815, 2001     

Density functional study of the conformers of Co4‐based single‐molecule magnet

We present a detailed density functional theory‐based investigation on the geometry and electronic structure of the [Co₄(hmp)₄(MeOH)₄Cl₄] molecule. It is experimentally found to behave as a molecular magnet. The all‐electron electronic structure calculations and geometry optimization of the 88‐atom molecule were carried out within the generalized gradient approximation to the exchange correlation energy. We also study the electronic structures and geometries of a few low‐lying conformers of this molecule. It is found that the magnetic anisotropy energy is highly sensitive to the geometric structure of the molecule. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 324–331, 2003     

Free‐energy model of asymmetry in side‐chain liquid‐crystalline diblock copolymers

Side‐chain liquid‐crystalline‐b‐amorphous copolymers combine the thermotropic ordering of liquid crystals (LCs) with the physics of block copolymer phase segregation. In our earlier experiments, we observed that block copolymer order–order and order–disorder transitions could be induced by LC transitions. Here we report the development of a free‐energy model to understand the interplay between LC ordering and block copolymer morphology in an incompressible melt. The model considers the interaction between LC moieties, the stretching of amorphous chains from curved interfaces, interfacial surface contributions, and elastic deformation of the nematic phase. The LC block is modeled with Wang and Warner's theory, in which nematogens interact through mean‐field potentials, and the LC backbone is modeled as a wormlike chain. Free energy is estimated for various morphologies: homogeneous, lamellar, cylinder micelle, and spherical micelle. Phase diagrams were constructed by iteration over temperature and composition ranges. The resulting composition diagrams are highly asymmetric, and a variety of first‐order transitions are predicted to occur at the LC clearing temperature. Qualitatively, nematic deformation energies destabilize curved morphologies, especially when the LC block is in the center of the block copolymer micelle. The thermodynamics of diblocks with laterally attached, side‐on mesogens are also explored. Discussion focuses on how well the model captures experimental phenomena and how the predicted phase boundaries are affected by changes in polymer architecture. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2671–2691, 2001     

Structural characterization,gelation ability,and energy‐framework analysis of two bis(long‐chain ester)‐substituted 4,4′‐biphenyl compounds

There are few examples of single‐crystal structure determinations of gelators, as gel formation requires that the dissolved gelator self‐assemble into a three‐dimensional network structure incorporating solvent via noncovalent interactions rather than self‐assembly followed by crystallization. In the solid‐state structures of the isostructural compounds 4,4′‐bis[5‐(methoxycarbonyl)pentyloxy]biphenyl (BBO6‐Me), C₂₆H₃₄O₆, and 4,4′‐bis[5‐(ethoxycarbonyl)pentyloxy]biphenyl (BBO6‐Et), C₂₈H₃₈O₆, the molecules sit on a crystallographically imposed center of symmetry, resulting in strictly coplanar phenyl rings. BBO6‐Me behaves as an organogelator in various alcohol solvents, whereas BBO6‐Et does not. The extended structure reveals bundles of molecules that form a columnar superstructure. Framework‐energy calculations reveal much stronger interaction energies within the columns (−52 to −78 kJ mol⁻¹) than between columns (−2 to −16 kJ mol⁻¹). The intracolumnar interactions are dominated by a dispersion component, whereas the intercolumnar interactions have a substantial electrostatic component.     

DFT and neutron diffraction study of 1,6-anhydro-β-D-glucopyranose (levoglucosan)

Geometries of 27 generated conformers of levoglucosan were optimized in vacuo at DFT level of theory combining several functionals with high quality basis sets. For the sake of comparison a reference molecular and crystal geometry obtained from 30 K single crystal neutron diffraction data was used. Analysis of the conformers’ geometries revealed that in all stable conformers intramolecular two-or three centre hydrogen bonds were formed. Relative energy of the conformer, which approximated the molecule in the crystal structure the most, was only ∼3 kcal/mol higher, than the energy of the most stable conformer in vacuo. The largest discrepancies between the geometries calculated in vacuo and experimental geometry concentrated in the vicinity of anomeric C1. These differences were reduced by involving O1 to intermolecular hydrogen bond using a simple model of the respective hydrogen bond in the crystal.      

Time‐dependent deformation of structurally chiral polymer networks in stabilized cholesteric liquid crystals

Polymerization of crosslinkable liquid crystal monomers in chiral liquid crystalline media stabilizes the phase and enables distinct electro‐optic properties relative to small‐molecule analogs. Particularly interesting are cases where the polymerization forms a crosslinked polymer network that maintains a “structural” chirality. Recent reports have employed this methodology to realize a diverse set of electro‐optic responses in polymer stabilized cholesteric liquid crystals (PSCLCs) including reflection bandwidth broadening, reflection wavelength tuning, and dynamic scattering modes. It has been proposed that the mechanism at the root of these electro‐optic responses is an ion‐mediated, electromechanical deformation of the stabilizing and structurally chiral polymer network. In an effort to better understand the nature of these deformations, here we have characterized the electro‐optic response of PSCLCs with different polymer concentrations and crosslink densities. The dynamic response of PSCLCs to electric fields exhibits a time‐dependent behavior reminiscent of the creep of polymeric materials to mechanical deformations. The electro‐optic response can be described as the superposition of two contributions: the fast deformation of a relatively soft component of the polymer network (1–2 s) and the slower (10–20 s) deformation of a harder component. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 1087–1093     

Crystalline Behavior and Structure of a Liquid Crystal Compound, 5‐{[4′‐(((Pentyl)oxy)‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne

Single crystals of two liquid crystal compounds, 5‐{[4′‐(((pentyl)oxy)‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO5) and 5‐{[(4′‐nonyloxy‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO9), have been prepared by solution growth technique. The morphologies and structures of A3EO5 and A3EO9 crystals were investigated by wide angle X‐ray diffraction (WXRD), atom force microscope (AFM) and transmission electron microscope (TEM). In contrast to the same series of compounds which have a longer alkyl tail, 5‐{[(4′‐heptoxy‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO7), 5‐{[(4′‐heptoxy‐4‐biphenylyl)oxy]carbonyl}‐1‐pentyne (A3E′O7) and A3EO9, A3EO5 shows strikingly different crystalline behavior. The former three compounds have only one crystal form, whereas A3EO5 exhibits polymorphism. Specifically, A3EO5 crystals grown from toluene solution show two crystal forms. The first one is crystal I which adopts a monoclinic P112/m space group with unit cell parameters of a?5.79 Å, b?8.34 Å, c?43.92 Å, γ?96°, and the other one is crystal II which adopts a monoclinic P112 space group with unit cell parameters of a?5.55 Å, b?7.38 Å, c?31.75 Å, γ?94°. When using dioxane as the solvent to grow A3EO5 crystal, we can selectively obtain crystal I. A3EO5 melt‐grown crystals also have two crystal forms which derive from crystal I and crystal II, respectively. The different crystalline behavior of the compounds should correlate with their different electron dipole moment resulting from the different length of alkyl tail.     

Thermodynamic Phase Transition Through Crystal‐to‐Crystal Process of Photochromic 1,2‐Bis(5‐phenyl‐2‐propyl‐3‐thienyl)perfluorocyclopentene

A photochromic diarylethene, 1,2‐bis(5‐phenyl‐2‐propyl‐3‐thienyl)perfluorocyclopentene ( 1a ), was found to have two polymorphic crystal forms, α‐ and β‐crystals. From X‐ray crystallographic analysis, the space groups of α‐ and β‐crystals were determined to be P2₁/c and C2/c, respectively. The difference between two crystal forms is ascribed to the orientation of two of four molecules in the unit cell. The thermodynamic phase transition from α‐ to β‐forms occurred via a crystal‐to‐crystal process, as confirmed by differential scanning calorimetry measurements, optical microscopic observations in the reflection mode and under crossed Nicols, and powder X‐ray diffraction measurements. The movement of the molecules in the crystal was evaluated by analyzing the change of face indices before and after the phase transition.     

Complexes of C60 fullerene with simple donor molecules: Theoretical study

The complex formation between fullerene C60 and simple donor molecules such as dimethyl ether, dimethylamine, dimethylsulfide, furan, pyrrole, and thiophene has been studied applying the hybrid MP2/6‐31G(d′):PM3 ONIOM approach for geometry optimization. Local implementation of Møller–Plesset perturbation theory in combination with 6‐31G(d) and 6‐311G(d,p) basis sets was used for binding energies estimation of fullerene complexes. Two factors were found to contribute most to the complex stability: the polarizability and molecular volume of donor molecule. As follows from positive stabilization energies at the Hartree–Fock level, the stabilization of fullerene complexes is entirely due to dispersion interactions in accordance with available experimental data. The calculations show that for donors of similar molecular volume the binding energy of molecular complex increases with polarizability of donor molecules. Similarly, for such complexes the partial charges on molecules increase with decreasing of ionization potentials of donor molecules. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002