Modeling disordered morphologies in organic semiconductors

Organic thin film devices are investigated for many diverse applications, including light emitting diodes, organic photovoltaic and organic field effect transistors. Modeling of their properties on the basis of their detailed molecular structure requires generation of representative morphologies, many of which are amorphous. Because time‐scales for the formation of the molecular structure are slow, we have developed a linear‐scaling single molecule deposition protocol which generates morphologies by simulation of vapor deposition of molecular films. We have applied this protocol to systems comprising argon, buckminsterfullerene, N,N‐Di(naphthalene‐1‐yl)‐N,N'‐diphenyl‐benzidine, mer‐tris(8‐hydroxy‐quinoline)aluminum(III), and phenyl‐C₆₁‐butyric acid methyl ester, with and without postdeposition relaxation of the individually deposited molecules. The proposed single molecule deposition protocol leads to formation of highly ordered morphologies in argon and buckminsterfullerene systems when postdeposition relaxation is used to locally anneal the configuration in the vicinity of the newly deposited molecule. The other systems formed disordered amorphous morphologies and the postdeposition local relaxation step has only a small effect on the characteristics of the disordered morphology in comparison to the materials forming crystals. © 2013 Wiley Periodicals, Inc.     

Oxatriphyrins(2.1.1) Incorporating an ortho‐Phenylene Motif

An understanding of fundamental aspects of archetypal organic structural motifs remains a key issue faced by the experimental and theoretical chemists. Two possible bonding modes for a disubstituted benzene ring, that is a meta and para, determines the π delocalization for oligomeric structures. When the less abundant ortho‐substituted variant is introduced into a triphyrin(2.1.1) skeleton an aromatic molecule is obtained and the carbocyclic ring participates in the conjugation of the macrocycle. The two‐electron reduction and introduction of boron(III) changes the aromatic character and results in an anti‐aromatic structure which has been confirmed by single‐crystal analysis and supported by theoretical calculations.     

On Some Problems of Inorganic Supramolecular Chemistry

In this study, some features that distinguish inorganic supramolecular host–guest objects from traditional architectures are considered. Crystalline inorganic supramolecular structures are the basis for the development of new functional materials. Here, the possible changes in the mechanism of crystalline inorganic supramolecular structure self‐organization at high interaction potentials are discussed. The cases of changes in the host structures and corresponding changes in the charge states under guest intercalation, as well as their impact on phase stability and stoichiometry are considered. It was demonstrated that the deviation from the geometrical and topological complementarity conditions may be due to the additional energy gain from forming inorganic supramolecular structures. It has been assumed that molecular recognition principles can be employed for the development of physicochemical analysis and interpretation of metastable states in inorganic crystalline alloys.     

Extensively Reversible Thermal Transformations of a Bistable,Fluorescence‐Switchable Molecular Solid: Entry into Functional Molecular Phase‐Change Materials

Functional phase‐change materials (PCMs) are conspicuously absent among molecular materials in which the various attributes of inorganic solids have been realized. While organic PCMs are primarily limited to thermal storage systems, the amorphous–crystalline transformation of materials like Ge‐Sb‐Te find use in advanced applications such as information storage. Reversible amorphous–crystalline transformations in molecular solids require a subtle balance between robust supramolecular assembly and flexible structural elements. We report novel diaminodicyanoquinodimethanes that achieve this transformation by interlinked helical assemblies coupled with conformationally flexible alkoxyalkyl chains. They exhibit highly reversible thermal transformations between bistable (crystalline/amorphous) forms, along with a prominent switching of the fluorescence emission energy and intensity.     

Extensively Reversible Thermal Transformations of a Bistable,Fluorescence‐Switchable Molecular Solid: Entry into Functional Molecular Phase‐Change Materials

Functional phase‐change materials (PCMs) are conspicuously absent among molecular materials in which the various attributes of inorganic solids have been realized. While organic PCMs are primarily limited to thermal storage systems, the amorphous–crystalline transformation of materials like Ge‐Sb‐Te find use in advanced applications such as information storage. Reversible amorphous–crystalline transformations in molecular solids require a subtle balance between robust supramolecular assembly and flexible structural elements. We report novel diaminodicyanoquinodimethanes that achieve this transformation by interlinked helical assemblies coupled with conformationally flexible alkoxyalkyl chains. They exhibit highly reversible thermal transformations between bistable (crystalline/amorphous) forms, along with a prominent switching of the fluorescence emission energy and intensity.     

Enzyme Instructed Self‐assembly of Naphthalimide‐dipeptide: Spontaneous Transformation from Nanosphere to Nanotubular Structures that Induces Hydrogelation

Understanding the structure‐morphology relationships of self‐assembled nanostructures is crucial for developing materials with the desired chemical and biological functions. Here, phosphate‐based naphthalimide (NI) derivatives have been developed for the first time to study the enzyme‐instructed self‐assembly process. Self‐assembly of simple amino acid derivative NI‐Yp resulted in non‐specific amorphous aggregates in the presence of alkaline phosphatase enzyme. On the other hand, NI‐FYp dipeptide forms spherical nanoparticles under aqueous conditions which slowly transformed into partially unzipped nanotubular structures during the enzymatic catalytic process through multiple stages which subsequently resulted in hydrogelation. The self‐assembly is driven by the formation of β‐sheet type structures stabilized by offset aromatic stacking of NI core and hydrogen bonding interactions which is confirmed with PXRD, Congo‐red staining and molecular mechanical calculations. We propose a mechanism for the self‐assembly process based on TEM and spectroscopic data. The nanotubular structures of NI‐FYp precursor exhibited higher cytotoxicity to human breast cancer cells and human cervical cancer cells when compared to the nanofiber structures of the similar Fmoc‐derivative. Overall this study provides a new understanding of the supramolecular self‐assembly of small‐molecular‐weight hydrogelators.     

Controlling Single Molecule Conductance by a Locally Induced Chemical Reaction on Individual Thiophene Units

Among the prerequisites for the progress of single‐molecule‐based electronic devices are a better understanding of the electronic properties at the individual molecular level and the development of methods to tune the charge transport through molecular junctions. Scanning tunneling microscopy (STM) is an ideal tool not only for the characterization, but also for the manipulation of single atoms and molecules on surfaces. The conductance through a single molecule can be measured by contacting the molecule with atomic precision and forming a molecular bridge between the metallic STM tip electrode and the metallic surface electrode. The parameters affecting the conductance are mainly related to their electronic structure and to the coupling to the metallic electrodes. Here, the experimental and theoretical analyses are focused on single tetracenothiophene molecules and demonstrate that an in situ‐induced direct desulfurization reaction of the thiophene moiety strongly improves the molecular anchoring by forming covalent bonds between molecular carbon and copper surface atoms. This bond formation leads to an increase of the conductance by about 50 % compared to the initial state.     

Density Functional Theory Investigations on Vibrational Spectra,Molecular Structure,and Properties of the L‐Serine,L‐Cysteine,and L‐Aspartic Acid Molecules

In this paper, we present a thorough investigation of the conformational space to characterize all possible gas‐phase structures of the neutral L‐serine, L‐cysteine, and L‐aspartic acid molecules. A total of 120 trial structures were generated for L‐aspartic acid and 96 trial structures for L‐serine and L‐cysteine by combining all internal single‐bond rotamers. Various combinations of the Hartree–Fock and density functional theory/B3LYP methods with different bases were used to optimize all possible trial structures. The theoretical studies on the structure, harmonic vibrational spectra, and molecular properties of these amino acids are presented. The assignments of the calculated wave numbers resulting from potential energy distributions were performed using the VEDA 4 program to allow a good interpretation of the theoretical vibrational spectra of the title compounds. The fundamental harmonic frequencies were found to be in good agreement with data in the literature. A natural bond orbital analysis was performed to investigate the charge delocalization throughout the molecules for the three test compounds. Moreover, an extensive discussion of the highest occupied molecular orbital–lowest unoccupied molecular orbital energy gap as well as other related molecular properties are reported.     

MICROPOROUS INORGANIC MEMBRANES

Recent development in microporous inorganic membranes represents a significant advance in materials for separation and chemical reaction applications. This paper provides an in-depth review of synthesis and properties of two groups (amorphous and crystalline) of microporous inorganic membranes. Amorphous microporous silica membranes can be prepared by the sol-gel and phase separation methods. Flat sheet, tubular and hollow fiber amorphous carbon membranes have been fabricated by various pyrolysis methods from polymer precursors. A large number of synthesis methods have been developed to prepare good quality polycrystalline zeolite membranes. Several techniques, including vapor and liquid approaches, are reviewed for pore structure modification to prepare microporous inorganic membranes from mesoporous inorganic membranes. Chemical, microstructural and permeation properties of these microporous membranes are summarized and compared among the several microporous membranes discussed in this paper. Theory for gas permeation through microporous membranes is also reviewed, with emphasis on comparison of theoretical with the experimental data. These inorganic microporous membranes offer excellent separation properties by the mechanisms of preferential adsorption, selective configurational diffusion or molecular sieving.     

Single Lipid Bilayers Constructed on Polymer Cushion Studied by Sum Frequency Generation Vibrational Spectroscopy

Planar solid supported single lipid bilayers on mica, glass, or other inorganic surfaces have been widely used as models for cell membranes. To more closely mimic the cell membrane environment, soft hydrophilic polymer cushions were introduced between the hard inorganic substrate and the lipid bilayer to completely avoid the possible substrate-lipid interactions. In this article, sum frequency generation (SFG) vibrational spectroscopy was used to examine and compare single lipid bilayers assembled on the CaF(2) prism surface and on poly (L-lactic acid) (PLLA) cushion. By using asymmetric lipid bilayers composed of a hydrogenated 1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol (DPPG) leaflet and a deuterated 1,2-dipalmitoyl-(d62)-sn-glycerol-3-phosphoglycerol (d-DPPG) leaflet, it was shown that the DPPG lipid bilayers deposited on the CaF(2) and PLLA surfaces have similar structures. SFG has also been applied to investigate molecular interactions between an antimicrobial peptide Cecropin P(1) (CP1) and the lipid bilayers on the above two different surfaces. Similar results were again obtained. This research demonstrated that the hydrophilic PLLA cushion can serve as an excellent substrate to support single lipid bilayers. We believe that it can be an important cell membrane model for future studies on transmembrane proteins, for which the possible inorganic substrate-bilayer interactions may affect the protein structure or function.     

Effect of the Side‐Chain‐Distribution Density on the Single‐Conjugated‐Polymer‐Chain Conformation

The spatial arrangement of the side chains of conjugated polymer backbones has critical effects on the morphology and electronic and photophysical properties of the corresponding bulk films. The effect of the side‐chain‐distribution density on the conformation at the isolated single‐polymer‐chain level was investigated with regiorandom (rra‐) poly(3‐hexylthiophene) (P3HT) and poly(3‐hexyl‐2,5‐thienylene vinylene) (P3HTV). Although pure P3HTV films are known to have low fluorescence quantum efficiencies, we observed a considerable increase in fluorescence intensity by dispersing P3HTV in poly(methyl methacrylate) (PMMA), which enabled a single‐molecule spectroscopy investigation. With single‐molecule fluorescence excitation polarization spectroscopy, we found that rra‐P3HTV single molecules form highly ordered conformations. In contrast, rra‐P3HT single molecules, display a wide variety of different conformations from isotropic to highly ordered, were observed. The experimental results are supported by extensive molecular dynamics simulations, which reveal that the reduced side‐chain‐distribution density, that is, the spaced‐out side‐chain substitution pattern, in rra‐P3HTV favors more ordered conformations compared to rra‐P3HT. Our results demonstrate that the distribution of side chains strongly affects the polymer‐chain conformation, even at the single‐molecule level, an aspect that has important implications when interpreting the macroscopic interchain packing structure exhibited by bulk polymer films.     

Fine structural analysis,formation of interfacial particle films,and accurate estimation of orientation in polyguanamine derivatives with a high refractive index

Precise analyses of the molecular arrangement of three‐dimensional crystals, two‐dimensional molecular films, and interfacial particle layers of polyguanamine derivatives with a high refractive index have been performed. The high refractive index of the polyguanamine derivatives is not due to the chemical structure of the molecule, but is based on the packing of molecular chains or the refraction of transmitted light due to the difference in electron density between the crystalline and amorphous regions. A highly crystalline polymer has been produced by polycondensation of guanamine derivatives bearing a triazine ring and phenyl rings. The packing models of molecular chains in the three‐dimensional crystal have been determined using wide‐angle X‐ray diffraction measurements and reciprocal lattice analysis. Highly hydrophobic polyguanamine derivatives undergo a transition from monolayer to single particle layer at the air/water interface. The π‐conjugated molecular plane in the two‐dimensional films is densely stacked. Multiparticle layers are formed with a highly ordered layered structure. Polymer nanoparticles are formed by the integration of units of the collapsed polymer monolayer folded along the height direction. Since this folding occurs within the amorphous region, formation of fine particles with a high refractive index and their integrated films with densely packed π‐conjugated planes is feasible. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 999–1009     

Rapid sampling of all‐atom peptides using a library‐based polymer‐growth approach

We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with a simple uniform dielectric solvent. The main novel feature of our approach is the use of precalculated statistical libraries of molecular fragments. A molecule is sampled by combining fragment configurations—of single residues in this study—which are stored in the libraries. Ensembles generated from the independent libraries are reweighted to conform with the Boltzmann‐factor distribution of the forcefield describing the full molecule. In this way, high‐quality equilibrium sampling of small peptides (4–8 residues) typically requires less than one hour of single‐processor wallclock time and can be significantly faster than Langevin simulations. Furthermore, approximate, clash‐free ensembles can be generated for larger peptides (up to 32 residues in this study) in less than a minute of single‐processor computing. We discuss possible applications of our growth procedure to free energy calculation, fragment assembly protein‐structure prediction protocols, and to “multi‐resolution” sampling. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

molSimplify: A toolkit for automating discovery in inorganic chemistry

We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.     

Direct Observation of Unstable Reaction Intermediates by Acid‐Base Complex Formation

The structures of several unstable or metastable reaction intermediates that were photoproduced in crystals were analyzed by using X‐ray techniques. The presence of enough void space around the reactive group(s) is an essential factor for the reaction to occur with retention of the single‐crystal form. To expand the void space, an acid group (COOH) was substituted onto the reactant molecule and acid‐base complex crystals were prepared with several amines, such as dibenzylamine and dicyclohexylamine. Following the formation of such acid‐base complexes in crystals, the metastable structures of nitrenes and red species of photochromic salicylideneanilines have been successfully analyzed by using X‐ray techniques. Moreover, the structure of a Pt complex anion in the excited state has been analyzed, which formed acid‐base complex crystals with various alkylammonium cations. The formation of acid‐base complexes will be a powerful tool for directly observing the structure of unstable or metastable reaction intermediates by using X‐ray techniques.     

Inorganic Double‐Helix Nanotoroid of Simple LithiumPhosphorus Species

A theoretical study of Li₉₀P₉₀, which possesses a circular double‐helix structure that resembles the Watson–Crick DNA structure, is reported. This is a new bonding motif in inorganic chemistry. The calculations show that the molecule might become synthesized and that it could be a model for other inorganic species which possess a double‐helix structure.     

The energies of some isomers of C60F8: the use of experimental and theoretical considerations to limit candidate structures

A survey of possible structures for the C60F8 molecule has been carried out, using both experimental (19F NMR data) and theoretical (structure-energy correlation) considerations to limit the number of isomers to be regarded as candidates for the previously isolated species. Several isomers are suggested as likely, with one low-energy structure in particular appearing to fulfill all the criteria better than the literature suggestion. Both this predicted isomer and that previously suggested have in common a sub-structure of a single fluorinated carbon atom surrounded by three vicinal fluorine neighbours together with a further pair of fluorine atoms added so as to generate a T-shaped motif.     

X-ray absorption spectroscopies: useful tools to understand metallorganic frameworks structure and reactivity

The large unit cells, the enormous flexibility and variation in structural motifs of MOFs represent a big challenge in the characterization of MOF materials, particularly in cases where single crystal diffraction data are not available. In this critical review it is shown that in cases where only powder diffraction data are available additional structural information, particularly regarding local coordination within the inorganic cluster, are often mandatory in order to solve the structure. There are also cases where the inorganic cluster does not follow the symmetry of the overall structure. In such cases diffraction techniques will just "see" an average structure, missing the local structure: a lack that may be critical for understanding the specific properties of the material. In both cases, EXAFS spectroscopy is the tool that provides complementary structural information on the inorganic cluster and the way it binds to the ligand. Selected examples will show how EXAFS will be relevant in: (i) confirming the structure obtained from diffraction refinements; (ii) highlighting that the inorganic cornerstone has a lower symmetry with respect to that of the organic framework; (iii) obtaining the local structure of the inorganic cluster in the desolvated material when desolvation causes a partial loss of long range order; (iv) obtaining the local structure of the inorganic cluster in the desolvated material after coordination of a probe (or reactant) molecule, including cluster deformation upon molecule coordination and metal-molecule binding distance; (v) evidencing the presence of impurities in the form of amorphous extra-phases (339 references).     

Zigzag‐Helix Transformation of Expanded Polyvaline Induced by Racemization

Biological macromolecules are essentially homochiral. For example, proteins mostly consist of l ‐amino acids. What happens when a chiral molecule meets itself in a mirror? For expanded polyvaline, zigzag‐helix transformation occurs. In this study, expanded polyvalines containing bis(pyridine)silver(I) moieties were synthesized and isolated as single crystals. The molecular structures were determined by X‐ray analysis, which revealed that chiral expanded poly(l ‐valine) and poly(d ‐valine) form zigzag chains. However, racemic mixture of these molecules form left‐ and right‐handed 4₁ helices that retain the original sequences. These secondary structures can be transformed by only flipping the C‐terminal amide plane for each unit, which is reminiscent of the relationship between an α‐helix and a β‐strand. Such expanded polypeptides can be built up into expanded protein, forming a tailor‐made three‐dimensional structure, which will lead to new functions.     

RGB Small Molecules Based on a Bipolar Molecular Design for Highly Efficient Solution‐Processed Single‐layer OLEDs

In this paper, we describe a bipolar molecular design for small molecule solution‐processed organic light emitting diodes (OLEDs). Combining the rigidity of the conjugated emissive cores and the flexibility of the peripheral alkyl‐linked carbazole groups, two series of highly efficient bipolar RGB (red, green, blue) emitters have been synthesized and characterized. The emissive cores are composed of electron‐withdrawing groups; the carbazole groups endow the materials electron‐donating units. Such bipolar structures are advantageous for the carrier injection and balance. Four peripheral carbazole groups are introduced in T‐series materials (TCDqC, TCSoC, TCBzC, TCNzC), and another four in O‐series materials (OCDqC, OCSoC, OCBzC, OCNzC). With the single‐layer device configuration of ITO/PEDOT:PSS/emitting layer/CsF/Al, two green devices exhibited excellent performance with a maximum luminescence efficiency of over 6.4 cd A^?1, and a high maximum luminance of more than 6700 cd m^?2. In addition, compared with the T‐series, the luminescence efficiency of blue and red devices based on O‐series materials increased from 1.6 to 2.8 cd A^?1 and 0.2 to 1.3 cd A^?1, respectively. To our knowledge, the performance of the blue device based on OCSoC is among the best of the blue small‐molecule solution‐processed single‐layer devices reported so far.