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Molecular Crystals (molecular + crystal)
Selected AbstractsUV-vis-Induced Vitrification of a Molecular Crystal,ADVANCED FUNCTIONAL MATERIALS, Issue 10 2007T. Naito Abstract A charge-transfer complex of 2,5-dimethyl- N,N,-dicyanoquinonediimine (DM) with silver (crystalline Ag(DM)2, defined as ,) is irreversibly transformed by UV-vis illumination. Depending on the illumination conditions, three new types of solids (defined as ,, ,, and ,) with different structural and physical properties are obtained and examined by a variety of analytical techniques, including solid-state, high-resolution, cross-polarization magic angle spinning (CP-MAS) 13C,NMR, elemental analysis (EA), mass spectrometry (MS), X-ray absorption fine structure (XAFS), and powder X-ray diffraction (XRD). The CP-MAS, EA, MS, and XAFS results indicate that compound , is a glass state of Ag(DM)2. The transformation from crystalline (,) to amorphous (,) solid Ag(DM)2 is an irreversible exothermic glass transition (glass-transition temperature 155.2,°C; ,H,=,,126.8,kJ,mol,1), which implies that the glass form is thermodynamically more stable than the crystalline form. Compound , (Ag(DM)1.5) consists of silver nanoparticles (diameter (7,±,2),nm ) dispersed in a glassy matrix of neutral DM molecules. The N,CN,Ag coordination bonds of the , form are not maintained in the , form. Decomposition of , by intense illumination results in a white solid (,), identified as being composed of silver nanoparticles (diameter (60,±,10),nm). Physical and spectroscopic (XAFS) measurements, together with XRD analysis, indicate that the silver nanoparticles in both , and , are crystalline with lattice parameters similar to bulk silver; however, the magnetic susceptibilities differ from bulk silver. [source] Guest,Guest,Host Multicomponent Molecular Crystals: Entrapment of Guest,Guest in Honeycomb Networks Formed by Self-Assembly of 1,3,5-Tri(4-hydroxyaryl)benzenesCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2010Jarugu, Narasimha Moorthy Prof. Abstract Sterically-engineered rigid trigonal molecular modules based on 1,3,5-tri(4-hydroxyphenyl)benzenes H1 and H2 undergo O-H,,,O hydrogen-bonded self-assembly into eight-fold catenated hexagonal (6,3) and two-fold interpenetrated undulated square (4,4) networks, respectively. In the presence of [18]crown-6 as a guest, the triphenol H1 is found to self-assemble into a honeycomb network with hexagonal voids created between three triphenol building blocks. The guest [18]crown-6 molecules are found to be nicely nested in hexagonal enclosures. The empty spaces within the crowns can be further filled with neutral (MeOH/water, MeOH/MeNO2) or ionic guest species such as KI/KAcAc to furnish novel multicomponent assemblies, that is, guest,guest,host, that typify Russian dolls. In contrast, triphenol H2 is found to yield analogous multicomponent molecular crystals in which the guest crown,K+ acts as a spacers in the hydrogen-bonded self-assembly that leads to distorted chicken wire networks. [source] Dipole Moment Enhancement in Molecular Crystals from X-ray Diffraction DataCHEMPHYSCHEM, Issue 14 2007Mark A. Spackman Prof. Abstract Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50,% or more), or because the experimental determinations suggest enhancements of 100,% or more,much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated. [source] Epitaxial Growth of Highly Oriented Fibers of Semiconducting Polymers with a Shish-Kebab-Like SuperstructureADVANCED FUNCTIONAL MATERIALS, Issue 17 2009Martin Brinkmann Abstract Highly oriented fibers of regioregular poly(3-alkylthiophene)s (P3ATs) showing a "shish-kebab" morphology are prepared by oriented epitaxial crystallization in a mixture of 1,3,5-trichlorobenzene (TCB) and pyridine. The superstructure of the P3AT fibers consists of an oriented thread-like core several hundreds of micrometers long, the "shish", onto which lateral crystalline fibrils made of folded polymer chains, the "kebabs", are connected in a periodic way with a periodicity in the range 18,30,nm. The P3AT-chain axis is oriented parallel to the fiber axis whereas the ,-stacking direction is oriented perpendicular to it. The oriented character of the shish-kebab fibers results in polarized optical absorption and photoluminescence. The formation of oriented precursors by epitaxial orientation of polymer chains onto long needles of a molecular crystal,TCB in the present case,appears to be an original alternative to the crystallization usually performed under external flow conditions. [source] Raman spectroscopy with simultaneous measurement of two orthogonally polarized Raman spectraJOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2003G. A. Thomson Abstract A Raman microscope was modified to allow the independent acquisition of two orthogonally polarized components of a Raman spectrum in a single measurement. Preliminary performance was demonstrated by simultaneously measuring the intensity of both polarized components of the silicon Raman band at 520 cm,1 as a silicon wafer was rotated through 360° under a polarized laser Raman probe. Polarization-resolved Raman spectra of a complex molecular crystal are also presented, illustrating the increase in spectral information available with the modified system. Copyright © 2003 John Wiley & Sons, Ltd. [source] Odd electrons in molecular chemistry, surface science, and solid state magnetismINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2007E. F. Sheka Abstract A unified theoretical or computational odd-electrons approach is suggested to nanomaterials, making possible their consideration on the same conceptual basis as well as on the same computational footing. The current paper presents the approach application to the chemistry of fullerenes, carbon single-walled nanotubes, surface science of silicon crystal, as well as to the molecular magnetism of both molecular crystals composed of transitional metal complexes and solid polymerized fullerenes. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Electric field-derived point charges to mimic the electrostatics in molecular crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2006Andrew E. Whitten Abstract Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree,Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1063,1070, 2006 [source] Wave functions derived from experiment.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2003Abstract The constrained Hartree,Fock method using experimental X-ray diffraction data is extended and applied to the case of noncentrosymmetric molecular crystals. A new way to estimate the errors in derived properties as a derivative with respect to added Gaussian noise is also described. Three molecular crystals are examined: ammonia [NH3], urea [CO(NH2)2], and alloxan [(CO)4(NH)2]. The energetic and electrical properties of these molecules in the crystalline state are presented. In all cases, an enhancement of the dipole moment is observed upon application of the experimental constraint. It is found that the phases of the structure factors are robustly determined by the constrained Hartree,Fock model, even in the presence of simulated noise. Plots of the electron density, electrostatic potential, and the electron localization function for the molecules in the crystal are displayed. In general, relative to the Hartree,Fock model, there is a depletion of charge around hydrogen atoms and lone pair regions, and a build-up of charge within the molecular framework near nuclei, directed along the bonds. The electron localization function plots reveal an increase in the pair density between vicinal hydrogen atoms. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 470,483, 2003 [source] Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2001Donald E. Williams Abstract A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6-31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. XH bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154,1166, 2001 [source] Synthesis, pharmacology, crystal properties, and quantitative solvation studies from a drug transport perspective for three new 1,2,4-thiadiazolesJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 9 2010German L. Perlovich Abstract A novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments and comparative analysis of molecular conformational states, packing architecture, and hydrogen bonds networks were carried out. Thermodynamic aspects of sublimation processes of studied compounds were determined using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n -hexane and n -octanol were studied within the wide range of temperature intervals and thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. Distribution processes of compounds in buffer/n -octanol and buffer/n -hexane systems (describing different types of membranes) were investigated. Analysis of transfer processes of studied molecules from the buffer to n -octanol/n -hexane phases was carried out by the diagram method with evaluation of the enthalpic and entropic terms. This approach allows us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3754,3768, 2010 [source] Molecular crystal global phase diagrams.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010In the first part of this series [Keith et al. (2004). Cryst. Growth Des.4, 1009,1012; Mettes et al. (2004). Acta Cryst. A60, 621,636], a method was developed for constructing global phase diagrams (GPDs) for molecular crystals in which crystal structure is presented as a function of intermolecular potential parameters. In that work, a face-centered-cubic center-of-mass lattice was arbitrarily adopted as a reference state. In part two of the series, experimental crystal structures composed of tetrahedral point group molecules are classified to determine what fraction of structures are amenable to inclusion in the GPDs and the number of reference lattices necessary to span the observed structures. It is found that 60% of crystal structures composed of molecules with point-group symmetry are amenable and that eight reference lattices are sufficient to span the observed structures. Similar results are expected for other cubic point groups. [source] Molecular crystal global phase diagrams.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010In previous parts of this series [Mettes et al. (2004). Acta Cryst. A60, 621,636; McClurg & Keith (2010). Acta Cryst. A66, 38,49] a method for constructing global phase diagrams (GPDs) for molecular crystals was developed and the method was applied to single-component ordered crystal structures of tetrahedral molecules. GPDs are useful for visualizing what types of crystal structures a given molecule may assume depending on molecular form/interaction. Their construction uses group-theoretical methods which enumerate all possible symmetry breakings during a statistical mechanical high-to-low temperature search. In this work these results are expanded upon by outlining a method to determine a sufficiently rich parameter space to represent the experimentally observed crystal structures in a data set derived from the Cambridge Structural Database. This is significant because previous work (Mettes et al., 2004) did not specify the number of parameters needed for GPDs. Although there are suggestions in the literature that thousands of parameters are required to adequately describe tetrahedral molecule intermolecular potentials, it is found that 15 parameters are sufficient to represent the structures of the test data. The origin of this difference and its implications for determining GPD parameter values from a more detailed intermolecular potential and for interpreting GPD parameter values are discussed. [source] Diffuse scattering from large-angle, thermally induced, orientational disorder in molecular crystalsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2007John Reid Large-angle rotational motion (libration) characteristic of molecular solids has not been properly included in many scattering calculations because of the need to develop scattering theory through small-angle approximations. A simple but effective approach to calculating the influence of large-angle librations on the thermal disorder scattering given by molecular solids is to treat the molecules as independent librators, each in a harmonic potential well, using the mathematics appropriate for large-angle rotations. The resulting probability distribution for angular misorientations is Gaussian and this distribution can be used to smear the molecular form factor, enabling the librational influence on the scattering to be calculated. It is shown how to apply this direct approach quite generally and by way of examples the technique is used with the molecular solids sulfur hexafluoride (SF6), adamantane (C10H16) and buckminsterfullerene (C60). For these materials, the molecular Fourier transform (i.e. the molecular form factor) have been calculated in selected planes in reciprocal space, followed by the separate effects of librational and translational smearing. It is found that the librational smearing produces a large effect on the form factor, particularly at larger scattering vectors, that is not sensitive to approximations in the argument. Additionally, the Debye,Waller effect of vibrational motion is included in the calculations, showing quantitatively the decreasing influence of vibrations on the scattering with increasing scattering vector. Both effects illustrate with pedagogic clarity how different processes modify the basic molecular scattering. [source] Molecular crystal global phase diagrams.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2004A method is described to produce global phase diagrams for single-component molecular crystals with separable internal and external modes. The phase diagrams present the equilibrium crystalline phase as a function of the coefficients of a general intermolecular potential based on rotational symmetry-adapted basis functions. It is assumed that phase transitions are driven by orientational ordering of molecules with a fixed time-averaged shape. The mean-field approximation is utilized and the process begins in a high-temperature disordered reference state, then spontaneous symmetry-breaking phase transitions and phase structure information at lower temperature are sought. The information is mapped onto phase diagrams using the intermolecular expansion coefficients as independent variables. This is illustrated by global phase diagrams for molecules having tetrahedral symmetry (e.g. carbon tetrachloride, adamantane and white phosphorus). Uses of global phase diagrams include crystal structure data mining, guidance for crystal design and enumeration of likely or missing polymorphic structures. [source] Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2000The temperature evolution of atomic anisotropic displacement parameters (ADP's) of perdeuterobenzene and of urea in the temperature range between 12 and 123,K is investigated in terms of the model presented in paper I. For the benzene molecule, the temperature-dependent contributions to the ADP's are well described by three molecular librations and three molecular translations. For the urea molecule, the analysis revealed a low-frequency high-amplitude normal mode (~64,cm,1), which combines out-of-plane deformations of the NH2 groups with molecular libration. The pyramidalization motion allows the hydrogen-bonding pattern to be retained quite well, whereas this pattern is heavily distorted in the higher-frequency molecular librations. The results presented for urea go a step beyond those obtainable in a conventional rigid-body or segmented-rigid-body analysis because they show how correlations of atomic displacements in molecular crystals can be determined from the temperature evolution of ADP's. For both molecules, the analysis reveals temperature-independent contributions to the ADP's accounting for the high-frequency internal vibrations. It is the first time that such contributions have been extracted directly from single-crystal diffraction data for light atoms like hydrogen and deuterium as well as for heavier atoms like carbon, nitrogen and oxygen. These contributions agree well with those calculated from independent spectroscopic information. [source] Single-crystal diffuse scattering studies on polymorphs of molecular crystals.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009The drug benzocaine (ethyl 4-aminobenzoate), commonly used as a local anaesthetic, is a bimorphic solid at room temperature. Form (I) is monoclinic P21/c, while the metastable form (II) is orthorhombic P212121. Three-dimensional diffuse X-ray scattering data have been collected for the two forms on the 11-ID-B beamline at the Advanced Photon Source (APS). Both forms show strong and highly structured diffuse scattering. The data have been interpreted and analysed using Monte Carlo (MC) modelling on the basis that the scattering is purely thermal in origin and indicates the presence of highly correlated molecular motions. In both forms (I) and (II) broad diffuse streaks are observed in the 0kl section which indicate strong longitudinal displacement correlations between molecules in the ,031, directions, extending over distances of up to 50,Å. Streaks extending between Bragg peaks in the hk0 section normal to [100] correspond to correlated motions of chains of molecules extending along a that are linked by N,H...O=C hydrogen bonds and which occur together as coplanar ribbon pairs. The main difference between the two forms is in the dynamical behaviour of the ribbon pairs and in particular how they are able to slide relative to each other. While for form (I) a model involving harmonic springs is able to describe the motion satisfactorily, as simple excursions away from the average structure, there is evidence in form (II) of anharmonic effects that are precursors of a phase transition to a new low-temperature phase, form (III), that was subsequently found. [source] Guest,Guest,Host Multicomponent Molecular Crystals: Entrapment of Guest,Guest in Honeycomb Networks Formed by Self-Assembly of 1,3,5-Tri(4-hydroxyaryl)benzenesCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2010Jarugu, Narasimha Moorthy Prof. Abstract Sterically-engineered rigid trigonal molecular modules based on 1,3,5-tri(4-hydroxyphenyl)benzenes H1 and H2 undergo O-H,,,O hydrogen-bonded self-assembly into eight-fold catenated hexagonal (6,3) and two-fold interpenetrated undulated square (4,4) networks, respectively. In the presence of [18]crown-6 as a guest, the triphenol H1 is found to self-assemble into a honeycomb network with hexagonal voids created between three triphenol building blocks. The guest [18]crown-6 molecules are found to be nicely nested in hexagonal enclosures. The empty spaces within the crowns can be further filled with neutral (MeOH/water, MeOH/MeNO2) or ionic guest species such as KI/KAcAc to furnish novel multicomponent assemblies, that is, guest,guest,host, that typify Russian dolls. In contrast, triphenol H2 is found to yield analogous multicomponent molecular crystals in which the guest crown,K+ acts as a spacers in the hydrogen-bonded self-assembly that leads to distorted chicken wire networks. [source] Dipole Moment Enhancement in Molecular Crystals from X-ray Diffraction DataCHEMPHYSCHEM, Issue 14 2007Mark A. Spackman Prof. Abstract Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50,% or more), or because the experimental determinations suggest enhancements of 100,% or more,much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated. [source] | ||||||||||