Determination of an organic crystal structure with the aid of topochemical and related considerations: correlation of the molecular and crystal structures of α-benzylidene-γ-butyrolactone and 2- benzylidenecyclopentanone with their solid state photoreactivity

The crystal structure of α-benzylidene-γ-butyrolactone 2, can be determined with the aid of atom-atom pairwise energy evaluation procedures, because its (previously reported) solid state photoreactivity coupled with topochemical principles, greatly restricts the number of possible orientations of the molecule in the unit cell. Crystals of lactone 2 are monoclinic with space group P2$_1$/n and with Z = 4, a = 11.014(2), b = 5.959(1), c = 14.286(5), β = 108.05(2). Refinement on 846 non-zero reflections led to an R (reliability) of 0.046. In contrast, the isoelectronic ketone 2-benzylidenecyclopentanone (3) is photostable, and crystallizes in the same space group with Z = 4, a = 7.466(4), b = 6.821(4), c = 19.005(1), β = 94.14(1). The structure of 3 was solved by direct methods and refined on 1037 non-zero reflections to an R of 0.036. The difference between the two structures can be rationalized in terms of intramolecular conformation and weak C-H$\cdots$O hydrogen bonding. Differences in the solid state photoreactivities of the two compounds can be related to the extent of orbital overlap between 'potentially reactive' double bonds on nearest neighbour molecules that are related by inversion. Compound 2 reacts in the solid state topochemically but not topotactically showing directional preference, while 3, which has reduced orbital overlap, is photostable

Comparison Between Hydrogen and Halogen Bonds in Complexes of 6-OX-Fulvene with Pnicogen and Chalcogen Electron Donors

Quantum chemical calculations are applied to complexes of 6‐OX‐fulvene (X=H, Cl, Br, I) with ZH3/H2Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H‐bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order

Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation

Selective ion separation is a major challenge with far-ranging impact from water desalination to product separation in catalysis. Recently introduced ferrocene (Fc)/ferrocenium (Fc⁺) polymer electrode materials have been demonstrated experimentally and theoretically to selectively bind carboxylates over perchlorate through weak C–H···O hydrogen bond (HB) interactions that favor carboxylates, despite the comparable size and charge of the two species. However, practical application of this technology in aqueous environments requires further selectivity enhancement. Using a first-principles discovery approach, we investigate the effect of Fc/Fc⁺ functional groups (FGs) on the selectivity and reversibility of formate–Fc⁺ adsorption with respect to perchlorate in aqueous solution. Our wide design space of 44 FGs enables identification of FGs with higher selectivity and rationalization of trends through electronic energy decomposition analysis or geometric hydrogen bonding analysis. Overall, we observe weaker, longer HBs for perchlorate as compared to formate with Fc⁺. We further identify Fc⁺ functionalizations that simultaneously increase selectivity for formate in aqueous environments but permit rapid release from neutral Fc. We introduce the materiaphore, a 3D abstraction of these design rules, to help guide next-generation material optimization for selective ion sorption. This approach is expected to have broad relevance in computational discovery for molecular recognition, sensing, separations, and catalysis.National Science Foundation (U.S.) (ECCS-1449291

Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

<p>Abstract</p> <p>Background</p> <p>Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint.</p> <p>Results</p> <p>Reaction of cytosine (Cyt) and 5-fluorocytosine (5Fcyt) with 5-nitrouracil (Nit) in aqueous solution yielded two new products, which have been characterized by single-crystal X-ray diffraction. The products include a dihydrated molecular salt (CytNit) having both ionic and neutral hydrogen-bonded species, and a dihydrated cocrystal of neutral species (5FcytNit). In CytNit a protonated and an unprotonated cytosine form a triply hydrogen-bonded aggregate in a self-recognition ion-pair complex, and this dimer is then hydrogen bonded to one neutral and one anionic 5-nitrouracil molecule. In 5FcytNit the two neutral nucleobase derivatives are hydrogen bonded in pairs. In both structures conventional N-H^...O, O-H^...O, N-H^+...N and N-H^...N^-intermolecular interactions are most significant in the structural assembly.</p> <p>Conclusion</p> <p>The supramolecular structure of the molecular adducts formed by cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit and 5FcytNit, respectively, have been investigated in detail. CytNit and 5FcytNit exhibit widely differing hydrogen-bonding patterns, though both possess layered structures. The crystal structures of CytNit (D<it>p</it>k_a= -0.7, molecular salt) and 5FcytNit (D<it>p</it>k_a= -2.0, cocrystal) confirm that, at the present level of knowledge about the nature of proton-transfer process, there is not a strict correlation between the D<it>p</it>k_avalues and the proton transfer, in that the acid/base <it>p</it>k_astrength is not a definite guide to predict the location of H atoms in the solid state. Eventually, the absence in 5FcytNit of hydrogen bonds involving fluorine is in agreement with findings that covalently bound fluorine hardly ever acts as acceptor for available Brønsted acidic sites in the presence of competing heteroatom acceptors.</p

Bis(4-fluoro­anilinium) sulfate

In the crystal of the title molecular salt, 2C6H7FN+·SO4 2−, the cations and anions are linked by N—H⋯O and C—H⋯O hydrogen bonds into sheets parallel to the ab plane. The crystal studied was found to be a racemic twin with a 0.50 (10):0.50 (10) domain ratio

Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

Modular and predictable assembly of porous organic molecular crystals

Nanoporous molecular frameworks are important in applications such as separation, storage and catalysis. Empirical rules exist for their assembly but it is still challenging to place and segregate functionality in three-dimensional porous solids in a predictable way. Indeed, recent studies of mixed crystalline frameworks suggest a preference for the statistical distribution of functionalities throughout the pores rather than, for example, the functional group localization found in the reactive sites of enzymes. This is a potential limitation for 'one-pot' chemical syntheses of porous frameworks from simple starting materials. An alternative strategy is to prepare porous solids from synthetically preorganized molecular pores. In principle, functional organic pore modules could be covalently prefabricated and then assembled to produce materials with specific properties. However, this vision of mix-and-match assembly is far from being realized, not least because of the challenge in reliably predicting three-dimensional structures for molecular crystals, which lack the strong directional bonding found in networks. Here we show that highly porous crystalline solids can be produced by mixing different organic cage modules that self-assemble by means of chiral recognition. The structures of the resulting materials can be predicted computationally, allowing in silico materials design strategies. The constituent pore modules are synthesized in high yields on gram scales in a one-step reaction. Assembly of the porous co-crystals is as simple as combining the modules in solution and removing the solvent. In some cases, the chiral recognition between modules can be exploited to produce porous organic nanoparticles. We show that the method is valid for four different cage modules and can in principle be generalized in a computationally predictable manner based on a lock-and-key assembly between modules

Identification of a new cocrystal of citric acid and paracetamol of pharmaceutical relevance

Cocrystals have been increasingly recognized as an attractive alternative delivery form for solid drug products. In this work, Raman spectroscopy, X-ray powder diffraction/X-ray crystallography, and differential scanning calorimetry have been used to study the phenomenon of cocrystal formation in stoichiometric mixtures of citric acid with paracetamol. Raman spectroscopy was particularly useful for the characterization of the products and was used to determine the nature of the interactions in the cocrystals. It was observed that little change in the vibrational modes associated with the phenyl groups of the respective reactants took place upon cocrystal formation but changes in intensities of the vibrational modes associated with the amide and the carboxylic acid groups were observed upon cocrystal formation. Several new vibrational bands were identified in the cocrystal which were not manifest in the raw material and could be used as diagnostic features of cocrystal formation. An understanding of the effects of cocrystal formation on the vibrational modes was obtained by the complete assignment of the spectra of the starting materials and of the cocrystal component. The results show that the cocrystals was obtained in a 2:1 molar ratio of paracetamol to citric acid. The asymmetric unit of the crystal contains two paracetamol molecules hydrogen-bonded to the citric acid; one of these acts as a phenolic-OH hydrogen bond donor to the carbonyl of a carboxylic acid arm of citric acid. In contrast, the other phenolic-OH acts as a hydrogen bond acceptor from the quaternary C-OH of citric acid. © 2011 The Royal Society of Chemistry

Redox-controlled potassium intercalation into two polyaromatic hydrocarbon solids

Alkali metal intercalation into polyaromatic hydrocarbons (PAHs) has been studied intensely after reports of superconductivity in a number of potassium- and rubidium-intercalated materials. There are, however, no reported crystal structures to inform our understanding of the chemistry and physics because of the complex reactivity of PAHs with strong reducing agents at high temperature. Here we present the synthesis of crystalline K2Pentacene and K2Picene by a solid–solid insertion protocol that uses potassium hydride as a redox-controlled reducing agent to access the PAH dianions, and so enables the determination of their crystal structures. In both cases, the inserted cations expand the parent herringbone packings by reorienting the molecular anions to create multiple potassium sites within initially dense molecular layers, and thus interact with the PAH anion π systems. The synthetic and crystal chemistry of alkali metal intercalation into PAHs differs from that into fullerenes and graphite, in which the cation sites are pre-defined by the host structure