Molecular and Crystal Structure Diversity,and Physical Properties of Tetrathiafulvalene Derivatives Substituted with Various Aryl Groups through Sulfur Bridges

A library of tetrathiafulvalene (TTF) derivatives ( TTF‐1 – TTF‐47 ) bearing aryl groups attached through sulfur bridges has been created. The peripheral aryl groups exert a significant influence on both the electronic and crystallographic properties of the resulting TTFs. These TTFs display broad absorption bands at 400–500 nm caused by intramolecular charge‐transfer transitions between the aryl groups and central TTF core, and their first redox potentials increase with increasing electron‐withdrawing ability of the aryl groups. In their crystal structures (22 examples), the central TTF cores adopt various conformations, including chair, half‐chair, boat, and planar conformations. Moreover, the peripheral aryl groups exhibit multiple alignment modes with respect to the central TTF core, caused by their rotation about the two C? S bonds of the sulfur bridges. The packing motifs of these TTFs depend on both the nature of the aryl groups and their spatial alignment modes. Driven by intermolecular van der Waals forces and π–π interactions between the aryl groups and between the aryl groups and the TTF core, these TTFs adopt various packing structures. As a typical example, TTF‐14 , an achiral molecule, adopts a helical chain stack through intermolecular atomic close contacts. Moreover, the molecular geometries and packing motifs of these TTFs are sensitive to environmental variation, as exemplified by TTF‐28 , which adopts three distinct crystal modifications with diverse molecular geometries and stacking modes under different crystallization conditions. This work indicates that these TTFs are potential candidates as electronic materials, as well as functional building blocks for supramolecular assembly.     

Computational study on the ring distortions of 1,4-dicyanobenzene in the gas phase and in the crystal

A molecular mechanics software enhanced to perform empirical energy calculations on crystals (KESSHOU) was further developed to handle intermolecular electrostatic interactions as well. The packing of the molecules of 1,4-dicyanobenzene and 1,4-diisocyanobenzene in the crystal was studied. The role of the van der Waals and the electrostatic interactions in the balance of nonbonded atom-atom interactions is analyzed. The packing forces are dominated by van der Waals forces. The electrostatic interactions have higher stabilizing contribution for the dicyano isomer than for the diisocyano form. The dependence of the results on the size of the crystal, the molecular mechanics force field (MM2 vs MM3), and the dielectric constant are also assessed. Ab initio MP2/6–311G** geometries of the isolated molecules are in accordance with the observed benzene ring distortions determined by electron diffraction.     

Mechano‐fluorochromic PtII Luminogen and Its Cysteine Recognition

A new triphenylamine‐based organometallic Pt^II luminogen ( 1 ) and its analogous organic compound ( 2 ) are reported. The molecules are decorated with aldehyde functionality to improve their photophysical properties by utilising donor–acceptor interactions. The single crystal X‐ray structure analysis of Pt^II analogue 1 revealed that the neighbouring molecules were loosely organised by weak intermolecular C?H???π interactions. Because of the twisted nature of the triphenylamine backbone the compounds showed aggregation‐induced emission enhancement in THF/water mixture. Due to their loose crystal packing, upon application of external stimuli these luminogens exhibited mechano‐fluorochromic behaviour. The crystalline forms of the compounds displayed a more superior emission efficiency than the grinded samples. Moreover, the compounds showed crystallization‐induced emission enhancement (CIEE) and exhibited chemodosimetric response towards cysteine under physiological condition.     

[1‐(Pyrazin‐2‐yl)ethylidene]hydrazine: a new multitopic ligand for the design of hybrid molecular frameworks

Hydrazones and their derivatives are closely related to imine compounds and are potential antimicrobial agents. They have also found application in supramolecular chemistry as multitopic ligands to link multiple metal centres for the design of hybrid molecular frameworks. The molecule of the title compound, C₆H₈N₄, consists of an imine linkage with an N—N bond length of 1.3540 (14) Å. This asymmetric compound is nearly planar and adopts an E configuration about the azomethine C=N double bond. In the solid state, there are two intermolecular N—H…N interactions that interconnect the molecules into a two‐dimensional network. The three‐dimensional arrangement of the crystal packing is further stabilized by intermolecular π–π interactions interconnecting the centroids of the heterocyclic rings.     

New Fluorescence Domain “Excited Multimer” Formed upon Photoexcitation of Continuously Stacked Diaroylmethanatoboron Difluoride Molecules with Fused π‐Orbitals in Crystals

The crystal‐packing structures of seven derivatives of diaroylmethanatoboron difluoride ( 1 a – gBF₂ ) are characterized by no overlap of the π‐conjugated main units of two adjacent molecules (type I), overlap of the benzene ring π‐orbitals of two adjacent molecules (type II), and overlap of the benzene and dihydrodioxaborinine rings π‐orbitals of adjacent molecules (type III). The crystal‐packing structures govern the fluorescence (FL) properties in the crystalline states. The FL domain that is present in type I crystals, in which intermolecular orbital interactions are absent, leads to excited monomer‐like FL properties. In the case of the type II crystals, the presence of intermolecular overlap of the benzene rings π‐orbitals generates new FL domains, referred to as “excited multimers”, which possess allowed S₀–S₁ electronic transitions and, as a result, similar FL lifetimes at longer wavelengths than the FL of the type I crystals. Finally, intermolecular overlap of the benzene and dihydrodioxaborinine ring π‐orbitals in the type III crystals leads to “excited multimer” domains with forbidden S₀–S₁ electronic transitions and longer FL lifetimes at similar wavelengths as that in type I crystals.     

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.     

Unilaterally Fluorinated Acenes: Synthesis and Solid‐State Properties

The rapid development of organic electronics is closely related to the availability of molecular materials with specific electronic properties. Here, we introduce a novel synthetic route enabling a unilateral functionalization of acenes along their long side, which is demonstrated by the synthesis of 1,2,10,11,12,14‐hexafluoropentacene ( 1 ) and the related 1,2,9,10,11‐pentafluorotetracene ( 2 ). Quantum chemical DFT calculations in combination with optical and X‐ray absorption spectroscopy data indicate that the single‐molecule properties of 1 are a connecting link between the organic semiconductor model systems pentacene (PEN) and perfluoropentacene (PFP). In contrast, the crystal structure analysis reveals a different packing motif than for the parent molecules. This can be related to distinct F???H interactions identified in the corresponding Hirshfeld surface analysis and also affects solid‐state properties such as the exciton binding energy and the sublimation enthalpy.     

Bulk chemical shifts in hydrogen-bonded systems from first-principles calculations and solid-state-NMR

We present an analysis of bulk (1)H NMR chemical shifts for a series of biochemically relevant molecular crystals in analogy to the well-known solvent NMR chemical shifts. The term bulk shifts denotes the change in NMR frequency of a gas-phase molecule when it undergoes crystallization. We compute NMR parameters from first-principles electronic structure calculations under full periodic boundary conditions and for isolated molecules and compare them to the corresponding experimental fast magic-angle spinning solid-state NMR spectra. The agreement between computed and experimental lines is generally very good. The main phenomena responsible for bulk shifts are packing effects (hydrogen bonding and pi-stacking) in the condensed phase. By using these NMR bulk shifts in well-ordered crystalline model systems composed of biologically relevant molecules, we can understand the individual spectroscopic signatures of packing effects. These local structural driving forces, hydrogen bonding, pi-stacking, and related phenomena, stand as a model for the forces that govern the assembly of much more complex supramolecular aggregates. We show to which accuracy condensed-phase ab initio calculations can predict structure and structure-property relationships for noncovalent interactions in complex supramolecular systems.     

From crystal structure prediction to polymorph prediction: interpreting the crystal energy landscape

Many organic molecules are emerging as having many crystalline forms, including polymorphs and solvates, as more techniques are being used to generate and characterise the organic solid state. The fundamental scientific and industrial interest in controlling crystallisation is inspiring the development of computational methods of predicting which crystal structures are thermodynamically feasible. Sometimes, computing this crystal energy landscape will reveal that a molecule has one way of packing with itself that is sufficiently more favourable than any other so only this crystal structure will be observed. More frequently, there will be many energy minima that are energetically feasible, showing approximately equi-energetic compromises between the various intermolecular interactions allowed by the conformational flexibility. Such cases generally lead to multiple solid forms. At the moment, we usually calculate the lattice energy landscape, an approximation to the real crystal energy landscape at 0 K. Despite its limitations, many studies show that this is a valuable complement to solid form screening, which helps in discovering new structures as well as rationalising the solid forms that are found in experimental searches. The range of factors that can determine which of the thermodynamically feasible crystal structures are observed polymorphs, shows the many further challenges in developing crystal energy landscapes as a tool for control of the organic solid state.     

Direct Identification of Protein–Protein Interactions by Single‐Molecule Force Spectroscopy

Single‐molecule force spectroscopy based on atomic force microscopy (AFM‐SMFS) has allowed the measurement of the intermolecular forces involved in protein‐protein interactions at the molecular level. While intramolecular interactions are routinely identified directly by the use of polyprotein fingerprinting, there is a lack of a general method to directly identify single‐molecule intermolecular unbinding events. Here, we have developed an internally controlled strategy to measure protein–protein interactions by AFM‐SMFS that allows the direct identification of dissociation force peaks while ensuring single‐molecule conditions. Single‐molecule identification is assured by polyprotein fingerprinting while the intermolecular interaction is reported by a characteristic increase in contour length released after bond rupture. The latter is due to the exposure to force of a third protein that covalently connects the interacting pair. We demonstrate this strategy with a cohesin–dockerin interaction.     

Oxycodone N‐oxide

The title compound, (5R,9R,13S,14S,17R)‐14‐hydroxy‐3‐methoxy‐17‐methyl‐4,5‐epoxymorphinan‐6‐one N‐oxide, C₁₈H₂₁NO₅, has been prepared in a diastereomerically pure form by the reaction of oxycodone with 3‐chloroperbenzoic acid and subsequent crystallization of the product from chloroform. The crystal packing shows that the molecule exhibits intramolecular O—H...O [D...A = 2.482 (2) Å] hydrogen bonding. In addition, there are weak intermolecular C—H...O interactions which, along with van der Waals forces, stabilize the structure. The new chiral center at the 17‐position is demonstrated to be R.     

Molecular Pair Analysis: C?H⋅⋅⋅F Interactions in the Crystal Structure of Fluorobenzene? And Related Matters

The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.     

From Intramolecular (Circular) in an Isolated Molecule to Intermolecular Hole Delocalization in a Two‐Dimensional Solid‐State Assembly: The Case of Pillarene

To achieve long‐range charge transport/separation and, in turn, bolster the efficiency of modern photovoltaic devices, new molecular scaffolds are needed that can self‐assemble in two‐dimensional (2D) arrays while maintaining both intra‐ and intermolecular electronic coupling. In an isolated molecule of pillarene, a single hole delocalizes intramolecularly via hopping amongst the circularly arrayed hydroquinone ether rings. The crystallization of pillarene cation radical produces a 2D self‐assembly with three intermolecular dimeric (sandwich‐like) contacts. Surprisingly, each pillarene in the crystal lattice bears a fractional formal charge of +1.5. This unusual stoichiometry of oxidized pillarene in crystals arises from effective charge distribution within the 2D array via an interplay of intra‐ and intermolecular electronic couplings. This important finding is expected to help advance the rational design of efficient solid‐state materials for long‐range charge transfer.     

Characterization of force fields for lipid molecules: Applications to crystal structures

The nonbonded portion of a force field for lecithins was characterized by application to the study of the crystal packing geometry and energetics of eight different molecules. The molecules were either lecithin fragments or chosen to isolate particular intermolecular features to test the accuracy of the force field specifically for those interactions. In particular, the hydrocarbon interactions, hydrogen bonding, electrostatics, and phosphate interactions were critiqued. The results support previous findings that indicated that this force field is reasonably accurate for lecithins. For all molecules, a minimum was found near the experimentally determined crystal structure. Using D-glucitol as an example, it is shown that the structural effect of hydrogen bonding is better represented by a nonelectrostatic force-field model than by a purely electrostatic model. Results obtained with glycerylphosphocholine and four smaller organic phosphate molecules suggest that further study of nonbonded interactions of phosphate groups is needed. © John Wiley & Sons, Inc.     

Calculation of vibrational frequencies of α para-dichlorobenzene crystal

Vibrational frequencies of an α para-dichlorobenzene crystal are calculated. By solving an inverse spectral problem, the series of force constants of an isolated p-C₆H₄Cl₂ molecule were found. It was shown that this series can be carried over to the crystal model. This means that during crystallization, the electronic structure of a p-C₆H₄Cl₂ molecule stays constant. Intermolecular interaction was modeled upon pseudo-bonds. Force constants were estimated from the calculation of intermolecular interaction energy, by the way of a Monte-Carlo simulation. Vibrational dynamics of the crystal and isolate molecule were analyzed. Absorption bands sensitive to the crystallization of the molecule were found.     

Three-dimensional six-connecting organic building blocks based on polychlorotriphenylmethyl units--synthesis, self-assembly, and magnetic properties

The synthesis of a three-dimensional, six-connecting, organic building block based on a robust, rigid, and open-shell polychlorotriphenylmethyl (PTM) unit (radical 1) is reported, and its self-assembly properties are described in detail. The tendencies of this highly polar molecule and its hydrogenated precursor, compound 4, to form hydrogen bonds with oxygenated solvents ([1THF(6)] and [4THF(6)]) were reduced by replacing THF with diethyl ether in the crystallization process to yield two-dimensional (2D) hydrogen-bonded structures ([1(Et(2)O)(3)] and [4(Et(2)O)(3)]). The presence of direct hydrogen bonds between the radicals in the latter phase of 1 gives rise to very weak ferromagnetic intermolecular interactions at low temperatures, whereas when the radicals are isolated by THF molecules these interactions are antiferromagnetic and very weak. The role played by the carboxylic groups not only in the self-assembly properties but also in the transmission of the magnetic interactions has been illustrated by determination of the crystal structure and measurement of the magnetic properties of the corresponding hexaester radical 6, in which the close packing of molecular units gives rise to weak antiferromagnetic intermolecular interactions. Attempts to avoid solvation of the molecules in the solid state and to increase the structural and magnetic dimensionality were pursued by recrystallization of both compounds 1 and 4 from concentrated nitric acid, affording two three-dimensional (3D) robust hydrogen-bonded structures. While the structure obtained with compound 4 is characterized by the presence of polar channels and boxes containing water guest molecules along the c axis, radical 1 was oxidized to the corresponding fuchsone 10, which presented a completely different close-packed, guest-free structure.