Two-dimensional structure control by molecular width variation with metal coordination

The self-assembled monolayer of bipyridine derivative 1, which has two alkyl chains on each end, at the HOPG/1-phenyloctane interface was studied by in situ scanning tunneling microscopy (STM). The detailed mechanism of a spontaneous change in the monolayer packing pattern by Pd coordination was studied. Uncomplexed 1 existed in a bent form in the monolayer, and the alkyl chains were interdigitated, whereas Pd-complexed 1 was in a straight form and the alkyl chains were not interdigitated. An intermediate state of 1 was successfully observed during metal coordination. The structure was the bent form with noninterdigitated alkyl chains. Equilibrium intermolecular distances reported from ab initio calculations indicate that the molecular width of the central aromatic part of uncomplexed 1 (7.5 A) is substantially smaller than that of the peripheral alkyl chain part (9.2 A). The bent form was suitable for covering up the surface to maximize the packing density. However, the molecular width of the aromatic unit of Pd-complexed 1 (9.1 A) was almost identical to that of the alkyl chain unit (9.2 A). Therefore, Pd-complexed 1 took the straight form in the monolayer. The observation of surface coverage by STM suggests that the bent form increases the packing density by as much as 16% compared with that of the straight form. These results indicate that the control of molecular width can be used to design molecular templates for nanostructure formation.     

Crystal Engineering of Supramolecular 1,4-Benzene Bisamides by Side-Chain Modification – Towards Tuneable Anisotropic Morphologies and Surfaces

Benzene bisamides are promising building blocks for supramolecular nano-objects. Their functionality depends on morphology and surface properties. However, a direct link between surface properties and molecular structure itself is missing for this material class. Here, we investigate this interplay for two series of 1,4-benzene bisamides with symmetric and asymmetric peripheral substitution. We elucidated the crystal structures, determined the nano-object morphologies and derived the wetting behaviour of the preferentially exposed surfaces. The crystal structures were solved by combining single-crystal and powder X-ray diffraction, solid-state NMR spectroscopy and computational modelling. Bulky side groups, here t-butyl groups, serve as a structure-directing motif into a packing pattern, which favours the formation of thin platelets. The use of slim peripheral groups on both sides, in our case linear perfluorinated, alkyl chains, self-assemble the benzene bisamides into a second packing pattern which leads to ribbon-like nano-objects. For both packing types, the preferentially exposed surfaces consist of the ends of the peripheral groups. Asymmetric substitution with bulky and slim groups leads to an ordered alternating arrangement of the groups exposed to the surface. This allows the hydrophobicity of the surfaces to be gradually altered. We thus identified two leitmotifs for molecular packings of benzene bisamides providing the missing link between the molecular structure, the anisotropic morphologies and adjustable surface properties of the supramolecular nano-objects.     

Influence of branched chains on the mesomorphic properties of symmetrical and unsymmetrical triphenylene discotic liquid crystals

A series of novel symmetrical and unsymmetrical triphenylene‐based discotic liquid crystalline materials with one or six branched peripheral alkoxy chains have been prepared. These materials have been compared with analogous known symmetrical and unsymmetrical compounds to reveal a balance between steric and space‐filling effects of the peripheral branched chains, which significantly affects intermolecular forces of attraction and packing, and hence affects melting and isotropisation temperatures of the liquid crystalline materials. The desired result of reduction of melting points and enhancement of isotropisation temperatures has been accomplished by use of branched alkoxy chains in both symmetrical and unsymmetrical materials.     

The effect of fluorination: a crystallographic and computational study of mesogenic alkyl 4-[2-(perfluorooctyl)ethoxy]benzoates

The series of alkyl 4-[2-(perfluorooctyl)ethoxy]benzoates (F8-n) shows a systematic change of crystal structures depending on the length of the alkyl chain: separate packing of perfluorooctyl (Rf) and alkyl (Rh) chains from each other for shorter (n=2) and longer (n=11) members, alternate packing of Rf and Rh chains for middle (n=6,7) members, and an intermediate type of packing for n=4. Semiempirical MO calculations show slightly repulsive interactions between the Rf chains, and attractive ones between Rf and Rh chains and between Rh and the core of a molecular pair. It is concluded that fluorination determines the molecular shape of the crystal structures by making the chain rigid. It is confirmed that the interactions between Rf chains are small compared with those between other moieties and that they are forced to aggregate owing to the exclusion from other moieties. Thus, the effect is dependent on the geometries and intermolecular interactions of the other moieties.     

The crystalline and liquid crystalline structures of benzyl-tri-octadecylammonium bromide complete the puzzle: how do Group VA halide salts with one-four long n-alkyl chains pack?

The first single crystal structure of a Group VA halide salt with three equivalent long n-alkyl chains, benzyltrioctadecylammonium bromide (BzN18Br), is reported. It consists of alternating interdigitated and non-interdigitated regions of alkyl chains separated by ionic planes. Two chains per molecule are paired and extend to one side in a non-interdigitated region. The third chain is on the opposite side of the ionic plane and pairs intermolecularly to form an adjacent, interdigitated region. The thickness of two nearly extended molecules defines the bilayer unit-two ionic planes flanked by a region with intramolecularly paired chains and separated by an interdigitated chain region. Powder X-ray diffraction and optical microscopy data of liquid crystalline BzN18Br are consistent with an enantiotropic smectic A₂ (SmA₂) phase: the three n-alkyl chains of each molecule are projected from one side of an ionic plane, and head groups of neighbouring molecules are oriented head-to-head, in a non-interdigitated bilayer assembly. The structure of BzN18Br fills an important gap in our knowledge about the crystal packing of ammonium and phosphonium salts with one-four equivalent long n-alkyl chains. A comparison of their packing arrangements is made and the transitional nature of the BzN18Br structures is demonstrated. Although salts with one, two, or three long n-alkyl chains form SmA₂ phases, each is distinctive in its molecular packing. A large molecular reorganization accompanies the crystal-to-liquid crystal transition of BzN18Br.     

Langmuir-Blodgett films as aligning layers for homeotropic alignment of liquid crystal molecules

The first single crystal structure of a Group VA halide salt with three equivalent long n-alkyl chains, benzyltrioctadecylammonium bromide (BzN18Br), is reported. It consists of alternating interdigitated and non-interdigitated regions of alkyl chains separated by ionic planes. Two chains per molecule are paired and extend to one side in a non-interdigitated region. The third chain is on the opposite side of the ionic plane and pairs intermolecularly to form an adjacent, interdigitated region. The thickness of two nearly extended molecules defines the bilayer unit-two ionic planes flanked by a region with intramolecularly paired chains and separated by an interdigitated chain region. Powder X-ray diffraction and optical microscopy data of liquid crystalline BzN18Br are consistent with an enantiotropic smectic A₂ (SmA₂) phase: the three n-alkyl chains of each molecule are projected from one side of an ionic plane, and head groups of neighbouring molecules are oriented head-to-head, in a non-interdigitated bilayer assembly. The structure of BzN18Br fills an important gap in our knowledge about the crystal packing of ammonium and phosphonium salts with one-four equivalent long n-alkyl chains. A comparison of their packing arrangements is made and the transitional nature of the BzN18Br structures is demonstrated. Although salts with one, two, or three long n-alkyl chains form SmA₂ phases, each is distinctive in its molecular packing. A large molecular reorganization accompanies the crystal-to-liquid crystal transition of BzN18Br.     

External field induced crystallization of poly(3-dodecylthiophene)

In order to investigate the effect of external field on the crystallization behavior of poly(3-dodecylthiophene) (P3DDT), the samples were recrystallized with different electrostatic field intensity, different pressure and different solidification direction in temperature gradient field. Measurements of differential scanning calorimetry and X-ray diffraction were operated to characterize these samples for analysis. The results suggest that after recrystallization, whether the external field is added or not, a more compact packing of molecular chains in P3DDT could be obtained without the change of the crystal structure model. Moreover, the addition of electrostatic field has greater effects on the crystallization of rigid main chains than on that of flexible side chains. Merely great pressure field can effect the rearrangements of molecular chains greatly. As for the temperature gradient field induced crystallization, different oriented solidification direction will lead to different effects on the compact degree and perfect degree of molecular chains packing.     

Double Molecular Encapsulation of Tetrahydrofuran by an Amphiphilic Calix-[4]-arene

The crystal structure of para-octanoylcalix-[4]-arene·2 tetrahydrofuran complex reveals double inclusion of the guest molecules, one deep in the aromatic cavity and the other held in a four-fingered molecular hand formed by the aliphatic chains, the inclusion changes the molecular packing from a bilayer system in the absence of guest, to a head-to-tail antiparallel chain packing.     

Double Molecular Encapsulation of Tetrahydrofuran by an Amphiphilic Calix-[4]-arene

The crystal structure of para-octanoylcalix-[4]-arene·2 tetrahydrofuran complex reveals double inclusion of the guest molecules, one deep in the aromatic cavity and the other held in a four-fingered molecular hand formed by the aliphatic chains, the inclusion changes the molecular packing from a bilayer system in the absence of guest, to a head-to-tail antiparallel chain packing.This revised version was published online in July 2005 with a corrected issue number.     

The interlayer swelling and molecular packing in organoclays

Understanding the interlayer swelling and molecular packing in organoclays is important to the formation and design of polymer nanocomposites. This paper presents recent experimental and molecular simulation studies on a variety of organoclays that show a linear relationship between the increase of d-spacing and the mass ratio between organic and clay. A denser molecular packing is observed in organoclays containing surfactants with hydroxyl-ethyl units. Moreover, our simulation results show that the head (nitrogen) groups are essentially tethered to the clay surface while the long hydrocarbon chains tend to adopt a layering structure with disordered conformation, which contrasts with the previous assumptions of either the chains lying parallel to the clay surface or being tilted at rather precise angles.     

Molecular fibers based on the honeycomb-like self-assembly of an alpha-helical polypeptide

We have succeeded in fabricating well-grown molecular fibers of a polypeptide on substrates by using a conventional solution spin-coating and drying process. These molecular fibers were found to consist of a honeycomb-like molecular assembly formed via the hexagonal close packing of the polypeptide chains in the alpha-helix conformation.     

Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study

The packing structures of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) thiolates on implicit gold surfaces were studied in explicit aqueous solutions of 1M NaCl using molecular dynamics simulations. The simulations were based on individual DNA chains placed in hexagonal simulation boxes of different sizes, representing various packing densities. The total potential energy per DNA chain was compared. The optimal packing structures were determined based on the minimal potential energy within the limits of the conditions that were evaluated in this study. The optimal packing density of ssDNA was found to be 0.19 DNA chains/nm(2), which is consistent with that determined experimentally. Furthermore, the optimal packing density of dsDNA was shown to be approximately 58% of the packing density for ssDNA, indicating that the packing of ssDNA should be approximately 58% of its optimal packing in order to achieve the best hybridization.     

Fabrication of positively charged catanionic vesicles from ion pair amphiphile with double-chained cationic surfactant

In this study, a pseudodouble-chained ion pair amphiphile, hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS), was prepared from a mixture of cationic surfactant, hexadecyltrimethylammonium bromide, and anionic surfactant, sodium dodecylsulfate. Positively charged catanionic vesicles were then successfully fabricated from HTMA-DS with the addition of cationic surfactants, dialkyldimethylammonium bromide (DXDAB), including ditetradecyldimethylammonium bromide (DTDAB), dihexadecyldimethylammonium bromide, and dioctadecyldimethylammonium bromide (DODAB), with a mechanical disruption approach. The control of charge characteristic and physical stability of the catanionic vesicles through the variations of DXDAB molar fraction and alkyl chain length was then explored by size, zeta potential, and Fourier transform infrared analyses. It was found that the molecular packing and/or molecular interaction of HTMA-DS with DXDAB rather than the electrostatic repulsion between the charged vesicles dominated the physical stability of the mixed HTMA-DS/DXDAB vesicles. The presence of DTDAB, which possesses short alkyl chains, could adjust the packing of the unmatched chains of HTMA⁺ and DS^? and promote the vesicle formation. However, the weak molecular interaction due to the short chains of DTDA⁺ could not maintain the vesicle structures in long-term storage. With increasing the alkyl chain length of DXDAB, it was possible to improve the vesicle physical stability through the enhanced molecular interaction in the vesicular bilayer. However, the long alkyl chains of DODAB unmatched with those of HTMA-DS, resulting in the vesicle disintegration in long-term storage. For the formation of stable charged catanionic vesicles of HTMA-DS/DXDAB, a good match in hydrophobic chains and strong molecular interaction were preferred for the vesicle-forming molecules.     

Helical Self-Assembly of Optically Active Phthalocyanine Derivatives: Effect of Zn?O Coordination Bond on Morphology and Handedness of Nanostructures

Two optically active phthalocyanine derivatives with eight peripheral chiral (S)-4′-(2-methylbutoxy)biphenyl moieties on the β-position of the phthalocyanine ring are synthesized. The circular dichroism (CD) spectra show signals in the Q absorption region for both compounds 1 and 2 in chloroform solution, indicating the effective chiral-information transfer from the peripheral chiral (S)-4′-(2-methylbutoxy)biphenyl side chains to the phthalocyanine chromophore at the molecular level. Their self-assembling properties are further investigated by using electronic absorption and Fourier transform infrared spectroscopy, transmission electronic microscopy, scanning electronic microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. Experimental results reveal the effect of the metal-coordination bond on molecular packing models in these nanostructures, which in turn results in the self-assembled nanostructures with different morphologies, from nanosheets for 1 to helical nanofibers for 2 . In addition, good semiconducting properties of the nanostructures fabricated from phthalocyanine derivatives 1 and 2 are revealed by current–voltage measurements.     

Computational tool to model the packing of polycyclic chains: structural analysis of amorphous polythiophene

A very efficient computational procedure, which was previously developed to generate and relax atomistic models of linear and comb-like amorphous polymers, has been adapted to model the amorphous phase of polycyclic systems. The strategy, which is a based in a generation algorithm that eliminates the torsion strain and a simple Monte Carlo Metropolis method to relax the generated structures, has been used to predict the density of amorphous polythiophene by combining NVT and NPT simulations. The theoretical value is in the excellent agreement with the experimental one, the former being overestimated by only 3-5%. Next, the molecular conformation and the packing of the rings were studied in detail. Interestingly, the amorphous phase of polythiophene can be described as a packing of elongated molecular chains more or less aligned in the same direction, in which the thiophene rings close in the space but belonging to different chains tend to adopt approximate parallel or antiparallel displaced pi-stacked arrangements.     

MOLECULAR PACKING IN TRIACYL-sn-GLYCEROLS: INFLUENCES OF ACYL CHAIN LENGTH AND UNSATURATION

The molecular packing in triacylglycerols having different acyl chains has been examined by differential scanning calorimetry, powder X-ray diffraction and vibrational spectroscopy (infrared and Raman) techniques. In the triacylglycerols examined, the acyl chain length, unsaturation or the position of substitution on the glycerol were changed systematically to observe their influence on the molecular packing in different polymorphic forms. Variation in the 3-acyl chain length of 1,2-dipalmitoyl-3-acyl-sn-glycerols (PPX) influenced the molecular packing along the long axis in the stable polymorphic forms. Three different modes of packing were observed. If X ≤ 4, the compounds packed in a bilayer structure similar to diacylglycerols, or if X ≥ 10 and ≤ 16 the compounds packed in a bilayer structure but similar to mono acid triacylglycerols. However for intermediate 3-acyl chain lengths, as in PP6 and PP8 the stable packing can occured only through chain segregation resulting in a trilayer structure. In the triacylglycerols containing unsaturated acyl chains, 1,2-dioleoyl-3-acyl-sn-glycerols (00X) and 1,3-dioleoyl-Z-acyl-sn-glycerols (0X0) the stable polymorphic forms packed in a trilayer structure where the odd acyl chains segregated and formed a middle layer. In a metastable hexagonal packing (α-phase) the long range ordering is minimal. Because of this lack of specific chain-chain interaction the 3-short acyl chain compounds of PPX packed in a unimolecular length structure (except PP2) whereas the 3-long acyl chain compounds packed in a bilayer structure. In orthorhombic perpendicular and triclinic parallel packing where the specific chain-chain interaction is increased, the end plane methyl packing and the glycerol conformation played important roles in the formation of bi-, tri- and hexalayer structures. The driving force in the formation of these different structures is to minimize the crystal defects created by the odd acyl chains and to enhance the specific chain-chain interactions. The presence of an odd acyl chain influenced the lateral chain packing as well, e.g., the stability of the orthorhombic perpendicular packing is enhanced by the presence of an odd acyl chain and even in some cases it is favored over the triclinic parallel packing. The odd acyl chain at the 1- or 3position of -sn-glycerol stabilized the orthorhombic perpendicular packing. This indicates the glycerol conformation is probably perpendicular to the layer plane and thus is different from the monoacid triacylglycerols.     

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.     

Self-assembly of patterned monolayers with nanometer features: molecular selection based on dipole interactions and chain length

Patterned cocrystal monolayers self-assemble on HOPG in contact with solutions containing complementary pairs of 1,5-chain-substituted anthracene derivatives. Monolayer unit cells containing three or four molecules and spanning 9-11 nm are generated. The monolayers consist of alternating aromatic and aliphatic columns. The designs and dimensions of the cocrystal patterns (unit cells) are determined by (i) the preferred packing alignment of identical length side chains, (ii) the selectivity of each side chain for neighboring chains, (iii) the identities of the two side chains on each anthracene, and (iv) the 2D-chirality of 1,5-substituted anthracenes. The aliphatic columns form by interdigitation of identical length side chains arrayed in an antiparallel alignment, with the nth heavy atom of one side chain in registration with the (omega+2-n)th heavy atom of two adjacent chains ((omega <--> 2) packing). Adjacent side chains are attached, alternately, to anthracenes in one of the two flanking aromatic columns. The preference for (omega <--> 2) packing optimizes side-chain van der Waals interactions. The composition and fidelity of patterning in the cocrystal monolayers requires an additional source of "molecular recognition" in addition to side-chain length. Dipolar interactions, both attractive and repulsive, between ether groups in neighboring, (omega <--> 2) packed side chains, constitute a second recognition element needed for cocrystal self-assembly.     

Study of the conformational disorder in polyesters giving liquid-crystalline phases

Conformational and packing energy analyses have been performed by molecular mechanics calculations on the polyester derived from the condensation of 2-(4-hydroxyphenyl)-6-hydroxybenzoxazole with terephthalic acid, which presents a high degree of crystallinity in spite of the head-to-tail constitutional disorder. The line repetition groups in accordance with the experimental value of the c axis have been taken into account. Possible conformations of chains having constitutional and conformational disorder in the crystalline phase have been proposed. Packing energy calculations performed on pairs of chains give the close packing distances and indicate the best symmetry elements. The results are in agreement with the unit cell obtained by X-ray data, the thermodynamical properties of the polymer and the existence of liquid-crystal phases.     

Models of Adjacent Re‐Entry Folds in the β Form of Syndiotactic Polystyrene. Conformational and Packing Analysis by Molecular Mechanics

The adjacent re‐entry folds of chains of syndiotactic polystyrene crystallized in the β form have been investigated by molecular mechanics. Various models of fold of chains along bilayers have been found. The results are in agreement with the literature experimental data indicating that the fold surface is irregular. Both the conformational and the packing energy of folded chains have been minimized by various techniques using several set of potential functions. A theoretical prediction of the work of fold is given.