Computational study of solvent effects on the molecular self-assembly of tetrolic acid in solution and implications for the polymorph formed from crystallization

The solution behavior of a model compound, tetrolic acid (TTA), is studied via molecular dynamics simulations in four organic solvents. The results suggest that strong interactions between TTA and solvent molecules (ethanol or dioxane) prevent the formation of carboxylic acid dimers in solution and thus promote the crystallization of TTA in a catemer-based form or a solvate form. Weak interactions, however, between TTA and solvent molecules (carbon tetrachloride or chloroform) facilitate the formation of carboxylic acid dimers in solution and thus promote the crystallization of a dimer-based crystal. Detailed solvent structure plays an important role in determining the relative stability of various growth synthons in solution and also the barriers along the pathway connecting them. This work illustrates the potential of molecular simulations to aid in the rational selection of solvents to obtain desired polymorphs during crystallization.     

Investigation of the relative stabilities of various allotropic phases of elemental tellurium under pressure and their interconversion paths by electronic structure calculations and crystal structure analyses

Elemental tellurium adopts a number of different structures under pressure. The relative stabilities of these allotropes and the interconversion between them were examined on the basis of first principles electronic band structure calculations with and without external pressure. The relative stabilities of the allotropes were also analyzed by estimating the overall strength of covalent bonding on the basis of the Te-Te overlap populations determined from tight-binding electronic structure calculations. The crystal structures of the allotropes were analyzed to determine how one form can transform into another form under pressure. Our study leads to the energy profile of tellurium as a function of pressure consistent with experiment, shows that the relative stabilities of the allotropic phases of Te are mainly governed by the overall strength of covalent bonding, and that all the allotropes are intimately related in structure, and one form can be readily converted to another form under pressure via a simple interconversion path.     

Acetic acid-water interaction in solid interfaces

The adsorption of acetic acid on a proton-ordered water ice surface is modeled using periodic plane-waves density-functional theory. The structures of acetic acid adsorbed as a monomer or oligomers, hydrated or not, are calculated through gradient optimization. The resulting quantum electronic density of states are compared to metastable impact electron spectroscopy (MIES) results and lead to selection of the most plausible structures of acetic acid on water ice. Hypotheses are formulated for the structure of the acid film growing on the ice surface including mainly cyclic dimers and hydrated forms. Adsorptions of single water molecules on acetic acid crystal surfaces are also studied after optimization of the acetic acid crystal bulk and surface structure. More comparisons with spectroscopic studies are proposed in the accompanying paper.     

Structure and stability of small boron and boron oxide clusters

To rationally design and explore a potential energy source based on the highly exothermic oxidation of boron, density functional theory (DFT) was used to characterize small boron clusters with 0-3 oxygen atoms and a total of up to ten atoms. The structures, vibrational frequencies, and stabilities were calculated for each of these clusters. A quantum molecular dynamics procedure was used to locate the global minimum for each species, which proved to be crucial given the unintuitive structure of many of the most stable isomers. Additionally, due to the plane-wave, periodic DFT code used in this study a straightforward comparison of these clusters to the bulk boron and B2O3 structures was possible despite the great structural and energetic differences between the two forms. Through evaluation of previous computational and experimental work, the relevant low-energy structures of all but one of the pure boron clusters can be assigned with great certainty. Nearly all of the boron oxide clusters are described here for the first time, but there are strong indications that the DFT procedure chosen is particularly well suited for the task. Insight into the trends in boron and boron oxide cluster stabilities, as well as the ultimate limits of growth for each, are also provided. The work reported herein provides crucial information towards understanding the oxidation of boron at a molecular level.     

Probing the Crystal Structure Landscape by Doping: 4‐Bromo, 4‐Chloro,and 4‐Methylcinnamic Acids

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4‐bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4‐methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4‐chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii, all but two of the multiple solid solutions obtained in the methyl‐doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of π⋅⋅⋅π interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen.     

Probing the Crystal Structure Landscape by Doping: 4‐Bromo, 4‐Chloro,and 4‐Methylcinnamic Acids

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4‐bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4‐methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4‐chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii, all but two of the multiple solid solutions obtained in the methyl‐doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of π???π interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen.     

Insights into the Crystallisation Process from Anhydrous,Hydrated and Solvated Crystal Forms of Diatrizoic Acid

Diatrizoic acid (DTA), a clinically used X‐ray contrast agent, crystallises in two hydrated, three anhydrous and nine solvated solid forms, all of which have been characterised by X‐ray crystallography. Single‐crystal neutron structures of DTA dihydrate and monosodium DTA tetrahydrate have been determined. All of the solid‐state structures have been analysed using partial atomic charges and hardness algorithm (PACHA) calculations. Even though in general all DTA crystal forms reveal similar intermolecular interactions, the overall crystal packing differs considerably from form to form. The water of the dihydrate is encapsulated between a pair of host molecules, which calculations reveal to be an extraordinarily stable motif. DTA presents functionalities that enable hydrogen and halogen bonding, and whilst an extended hydrogen‐bonding network is realised in all crystal forms, halogen bonding is not present in the hydrated crystal forms. This is due to the formation of a hydrogen‐bonding network based on individual enclosed water squares, which is not amenable to the concomitant formation of halogen bonds. The main interaction in the solvates involves the carboxylic acid, which corroborates the hypothesis that this strong interaction is the last one to be broken during the crystal desolvation and nucleation process.     

Spontaneous formation of super water-repellent fractal surfaces in mixed wax systems

Alkylketene dimers (AKDs) and triglyceride waxes form fractal surfaces spontaneously and show super water-repellent property. Spontaneous formation of fractal structures on their surfaces takes place when the meta-stable crystalline phase of the waxes transforms to the thermodynamically stable form of crystal. The triglyceride waxes form the meta-stable alpha-phase in whole specimen when solidified from their melt. In the case of AKD, on the other hand, only a small portion of the specimen solidifies in the meta-stable form of crystal. The surface of the AKD, however, becomes fractal in the whole part. We have, thus, examined the fractal structure formation in the mixed wax systems in which one wax forms fractal surfaces and the other one does not. In the stearic acid/tristearin mixed system as a typical one, the super water-repellent fractal surfaces form in the higher composition region of tristearin than that of the eutectic point in their mixture.     

Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs

The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in (GGiCGAiGCCA)2. The structures contrast with the formation of tandem imino and sheared GA pairs flanked by GC pairs in the RNA self-complementary duplexes (GCGGACGC)2 and (GGCGAGCC)2, respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC substitutions result in less favorable loop stability. The results provide benchmarks for testing computations of molecular interactions that shape RNA three-dimensional structure.     

Evidence for conformational differences in aqueous and crystalline structures of α-bungarotoxin and cobratoxin

Laser Raman spectroscopy has been employed to investigate the structures of α-bungarotoxin (Bungarus multicinctus) and cobratoxin (Naja naja siamensis) in H₂O and D₂O solutions. Structures of the aqueous neurotoxins are compared with one another and with the X-ray crystal structures. The results indicate that the solution and crystal molecular structures of cobratoxin are in substantial agreement with one another, but those of α-bungarotoxin are not. Raman data provide no evidence for strained disulfides in aqueous α-bungarotoxin, although strained CSSC dihedral angles are indicated for the X-ray crystal structure. The data are interpreted as evidence for a strained molecular conformation of α-bungarotoxin in the crystal, which converts to a relaxed, more energetically favorable conformation in aqueous solution. Raman spectra also suggest more β-strand secondary structure in aqueous α-bungarotoxin (47 ± 5%) than in the crystalline form ( < 10%). The high β-strand content measured by Raman spectroscopy could be due to either a secondary structure in solution that is appreciably different than that of the crystal, or to the imprecision of the Raman method in distinguishing peptide configurations that are vibrationally equivalent but conformationally inequivalent. Aqueous α-bungarotoxin and cobratoxin also differ from one another in amino acid side chain orientations and interactions, though not in main chain conformations. Different geometries are indicated for cystine CCSS dihedral angles, and different hydrogen bonding states are indicated for internal tyrosines. Tyrosine-24 of α-bungarotoxin is shown to donate a strong hydrogen bond to a negative acceptor, deduced to be glutamate-41, whereas the equivalently positioned residue of cobratoxin is apparently hydrogen bonded to solvent molecules.     

Nucleation, growth, and form in crystals of peptide helices

A model for the nucleation of crystallization in peptide helices is presented. The crystal structures of four polymorphic forms of a hydrophobic helical decapeptide Boc-Leu-Aib-Phe-Phe-Leu-Aib-Ala-Ala-Leu-Aib-OMe (I) exemplify alternative packing modes in cylindrical molecules. Three crystal forms of peptide I are monoclinic P2(1), while one is orthorhombic P22121. The five different helical molecules characterized have very similar backbone conformations over much of the peptide length. A survey of 117 helical peptide structures with a length >/=8 residues reveals a preponderance of the triclinic (P1), monoclinic (P2(1)), and orthorhombic (P2(1)2(1)2(1)) crystal forms. Models for the formation of critical nuclei are based on helix association driven by solvophobic forces, resulting in the formation of raftlike structures. Raft association can be further driven by the imperative of minimizing solvent accessible surface area with the formation of blocks, which can be subsequently fitted in Lego set fashion by multiple hydrogen bond interactions in the head-to-tail region. This model provides a rationalization for observed crystal formation based on a postulated structure for an embryonic nucleus, which is determined by aggregation patterns and unconstrained by the dictates of symmetry.     

Mercury telluride crystals encapsulated within single walled carbon nanotubes: A density functional study

The structure and binding energies of mercury telluride crystals encapsulated within single walled carbon nanotubes (SWNTs) have been studied using density functional theory. The energies of three different pseudo one‐dimensional crystals of HgTe with 4:4, 3:3, and 2:2 coordination are compared. The initial structure for the 4:4 crystal was a 2 × 2 cubic motif derived from rock salt bulk structure, the 3:3 crystal corresponds to a novel structure found when HgTe was intercalated within SWNTs, and the 2:2 crystal is a chain motif derived from cinnabar (HgS) bulk structure. The isolated 3:3 crystal was found to be the most thermodynamically stable of the three structures. Calculations were performed on the 3:3 crystal inserted into three different SWNTs, (15, 0), (9, 9), and (17, 0), in order to investigate the perturbations on the molecular and electronic structure of the crystal and the SWNT, and the energy of formation of the HgTe@SWNT composites. The calculated structures are in good agreement with the experimental high resolution transmission electron microscopy images of the HgTe@SWNT composite. The calculated binding energies and density of states show that the interaction between nanotubes and the HgTe crystals is noncovalent. Since the energy difference of the “free” 4:4 and 3:3 structures is small and of the order of magnitude of the binding energies with the nanotubes, we carried out calculations on 4:4 HgTe structure inserted in to two different SWNTs, (15, 0) and (17, 0). The calculated binding energies show that, when the 4:4 structure is inserted into the smallest tube, the resultant composite has an energy comparable to the 3:3 structure, suggesting that this polymporph may also be found experimentally. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Ultraviolet stability of liquid crystals containing cyano and isothiocyanato terminal groups

The ultraviolet (UV) stabilities of liquid crystal compounds containing cyano (CN) and isothiocyanato (NCS) terminal groups are compared. UV exposure is found to degrade the clearing temperature, birefringence, dielectric constants and visco-elastic coefficient of the liquid crystal compounds. The measured data show that the NCS molecular structure exhibits a better UV stability than do the corresponding CN structures. Lewis resonance structures are used to explain this phenomenon.     

Ultraviolet stability of liquid crystals containing cyano and isothiocyanato terminal groups

The ultraviolet (UV) stabilities of liquid crystal compounds containing cyano (CN) and isothiocyanato (NCS) terminal groups are compared. UV exposure is found to degrade the clearing temperature, birefringence, dielectric constants and visco-elastic coefficient of the liquid crystal compounds. The measured data show that the NCS molecular structure exhibits a better UV stability than do the corresponding CN structures. Lewis resonance structures are used to explain this phenomenon.     

Solubilization of hydrophobic guest molecules in the monoolein discontinuous QL cubic mesophase and its soft nanoparticles

Hydrophobic bioactive guest molecules were solubilized in the discontinuous cubic mesophase (QL) of monoolein. Their effects on the mesophase structure and thermal behavior, and on the formation of soft nanoparticles upon dispersion of the bulk mesophase were studied. Four additives were analyzed. They were classified into two types based on their presumed location within the lipid bilayer and their influence on the phase behavior and structure. Differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS), polarized light microscopy, cryogenic-transmission electron microscopy (cryo-TEM), and dynamic light scattering (DLS) were used for the analysis. We found that carbamazepine and cholesterol (type I molecules) likely localize in the hydrophobic domains, but close to the hydrophobic-hydrophilic region. They induce strong perturbation to the mesophase packing by influencing both the order of the lipid acyl chains and interactions between lipid headgroups. This results in significant reduction of the phase transition enthalpy, and phase separation into lamellar and cubic mesophases above the maximum loading capacity. The inclusion of type I molecules in the mesophase also prevents the formation of soft nanoparticles with long-range internal order upon dispersion. In their presence, only vesicles or sponge-like nanoparticles form. Phytosterols and coenzyme Q10 (type II molecules) present only moderate effects. These molecules reside in the hydrophobic domains, where they cannot alter the lipid curvature or transform the QL mesophase into another phase. Therefore, above maximum loading, excess solubilizate precipitates in crystal forms. Moreover, when type II-loaded QL is dispersed, nanoparticles with long-range order and cubic symmetry (i.e., cubosomes) do form. A model for the growth of the ordered nanoparticles was developed from a series of intermediate structures identified by cryo-TEM. It proposes the development of the internal structure by fusion events between bilayer segments.     

Free-standing smectic films at high temperature

Optical reflectivity studies on free-standing liquid crystal films above the bulk smectic temperature range have revealed different melting phenomena. Our measurements are performed on tilted smectic phases (smectic C*, smectic C) using optical microscopy in polarized light in order to visualize the changes of the film structure. We observe the formation of twodimensional defect structures from string-like lines in very thick (about 1000 layers) as well as in thin (about 20 layers) films. In thick films these structures nucleate around the temperature of the bulk smectic-cholesteric phase transition, while in thin films the formation of the defects occurs well above this temperature and just before the thinning transitions. In thick and intermediate thickness films, cholesteric or nematic droplets and a 'quasi-smectic' structure are observed. The films exhibiting the 'quasi-smectic' structure definitely exist at higher temperatures than the smectic films with the same thickness.     

Free-standing smectic films at high temperature

Optical reflectivity studies on free-standing liquid crystal films above the bulk smectic temperature range have revealed different melting phenomena. Our measurements are performed on tilted smectic phases (smectic C*, smectic C) using optical microscopy in polarized light in order to visualize the changes of the film structure. We observe the formation of twodimensional defect structures from string-like lines in very thick (about 1000 layers) as well as in thin (about 20 layers) films. In thick films these structures nucleate around the temperature of the bulk smectic-cholesteric phase transition, while in thin films the formation of the defects occurs well above this temperature and just before the thinning transitions. In thick and intermediate thickness films, cholesteric or nematic droplets and a ‘quasi-smectic’ structure are observed. The films exhibiting the ‘quasi-smectic’ structure definitely exist at higher temperatures than the smectic films with the same thickness.     

Challenges of crystal structure prediction of diastereomeric salt pairs

A methodology for the computational prediction of the crystal structures and resolution efficiency for diastereomeric salt pairs is developed by considering the polymorphic system of the diastereomeric salt pair (R)-1-phenylethylammonium (R/S)-2-phenylpropanoate. To alleviate the mathematical complexity of the search for minima in the lattice energy due to the presence of two flexible entities in the asymmetric unit, the range of rigid-body lattice energy global optimizations was guided by a statistical analysis of the Cambridge Structural Database for common ion-pair geometries and ion conformations. A distributed multipole model for the dominant electrostatic interactions and high-level ab initio calculations for the intramolecular energy penalty for conformational distortions are used to quantify the relative stabilities of the p- and n-salt forms. While the ab initio prediction of the known structure of the p-salt as the most stable structure was insensitive to minor changes in the rigid-ion conformations considered, the relative stabilities of the known polymorphs and hypothetical structures of the n-salt were very sensitive. Although this paper provides a significant advance over traditional search algorithms and empirical force fields in determining the structures and relative stabilities of diastereomeric salt pairs, the sensitivity of the computed lattice energies to the fine details of the ion conformations overtaxes current computational models and renders the design of diastereomeric resolution processes by computational chemistry a challenging problem.     

1D nano- and microbelts self-assembled from the organic-inorganic hybrid molecules: oxadiazole-containing cyclotriphosphazene

A new oxadiazole-containing cyclotriphosphazene, namely, hexakis-(4-(5-phenyl-1,3,4-oxazodiazol-2-yl)-phenoxy)-cyclotriphosphazene (HPCP) was synthesized. Single-crystal nano- and microbelts of HPCP were self-assembly via two simple solution methods. The shapes of the as-prepared nano- and microstructures can be readily controlled by varying the solvent and aging time in the self-assembly process. A growth mechanism was proposed for the formation of the 1D morphological structures. Crystal structure analysis demonstrated that the overlap between the aryl units attached to the cyclotriphosphazene backbone forms effective intermolecular π-π linking for crystal growth. Electronic and optical properties of the as-prepared nano- and microstructures are investigated.     

Bond energies and structures of ammonia-sulfuric acid positive cluster ions

New particle formation in the atmosphere is initiated by nucleation of gas-phase species. The small molecular clusters that act as seeds for new particles are stabilized by the incorporation of an ion. Ion-induced nucleation of molecular cluster ions containing sulfuric acid generates new particles in the background troposphere. The addition of a proton-accepting species to sulfuric acid cluster ions can further stabilize them and may promote nucleation under a wider range of conditions. To understand and accurately predict atmospheric nucleation, the stabilities of each molecular cluster within a chemical family must be known. We present the first comprehensive measurements of the ammonia-sulfuric acid positive ion cluster system NH(4)(+)(NH(3))(n)(H(2)SO(4))(s). Enthalpies and entropies of individual growth steps within this system were measured using either an ion flow reactor-mass spectrometer system under equilibrium conditions or by thermal decomposition of clusters in an ion trap mass spectrometer. Low level ab initio structural calculations provided inputs to a master equation model to determine bond energies from thermal decomposition measurements. Optimized ab initio structures for clusters up through n = 3, s = 3 are reported. Upon addition of ammonia and sulfuric acid pairs, internal proton transfer generates multiple NH(4)(+) and HSO(4)(-) ions within the clusters. These multiple-ion structures are up to 50 kcal mol(-1) more stable than corresponding isomers that retain neutral NH(3) and H(2)SO(4) species. The lowest energy n = s clusters are composed entirely of ions. The addition of acid-base pairs to the core NH(4)(+) ion generates nanocrystals that begin to resemble the ammonium bisulfate bulk crystal starting with the smallest n = s cluster, NH(4)(+)(NH(3))(1)(H(2)SO(4))(1). In the absence of water, this cluster ion system nucleates spontaneously for conditions that encompass most of the free troposphere.