Abstract: Realizing the extraordinary potential of unactivated sp3 C–H bond oxidation in organic synthesis requires the discovery of catalysts that are both highly reactive and predictably selective. We report an iron (Fe)–based small molecule catalyst that uses hydrogen peroxide (H2O2) to oxidize a broad range of substrates. Predictable selectivity is achieved solely on the basis of the electronic and steric properties of the C–H bonds, without the need for directing groups. Additionally, carboxylate directing groups may be used to furnish five-membered ring lactone products. We demonstrate that these three modes of selectivity enable the predictable oxidation of complex natural products and their derivatives at specific C–H bonds with preparatively useful yields. This type of general and predictable reactivity stands to enable aliphatic C–H oxidation as a method for streamlining complex molecule synthesis.

Abstract: Within a polymer film, free-volume elements such as pores and channels typically have a wide range of sizes and topologies This broad range of free-volume element sizes compromises a polymer's ability to perform molecular separations We demonstrated free-volume structures in dense vitreous polymers that enable outstanding molecular and ionic transport and separation performance that surpasses the limits of conventional polymers The unusual microstructure in these materials can be systematically tailored by thermally driven segment rearrangement Free-volume topologies can be tailored by controlling the degree of rearrangement, flexibility of the original chain, and judicious inclusion of small templating molecules This rational tailoring of free-volume element architecture provides a route for preparing high-performance polymers for molecular-scale separations

Abstract: Protein molecules have the ability to form a rich variety of natural and artificial structures and materials. We show that amyloid fibrils, ordered supramolecular nanostructures that are self-assembled from a wide range of polypeptide molecules, have rigidities varying over four orders of magnitude, and constitute a class of high-performance biomaterials. We elucidate the molecular origin of fibril material properties and show that the major contribution to their rigidity stems from a generic interbackbone hydrogen-bonding network that is modulated by variable side-chain interactions.

Abstract: Introducing a functional part into open-framework materials that tunes the pore size/shape and overall porous activity will open new routes in framework engineering and in the fabrication of new materials. We have designed and synthesized a bimodal microporous twofold interpenetrating network {[Ni(bpe)2(N(CN)2)](N(CN)2)(5H2O)}n (1), with two types of channel for anionic N(CN)2- (dicyanamide) and neutral water molecules, respectively. The dehydrated framework provides a dual function of specific anion exchange of free N(CN)2- for the smaller N3- anions and selective gas sorption. The N3-exchanged framework leads to a dislocation of the mutual positions of the two interpenetrating frameworks, resulting in an increase in the effective pore size in one of the counterparts of the channels and a higher accommodation of adsorbate than in the as-synthesized framework (1), showing the first case of controlled sorption properties in flexible porous frameworks.

Abstract: The concept of a chemical bond stands out as a major development in the process of understanding how atoms are held together in molecules and solids. Lewis’ classical picture of chemical bonds as shared-electron pairs1 evolved to the quantum-mechanical valence-bond and molecular-orbital theories2,3, and the classification of molecules and solids in terms of their bonding type: covalent, ionic, van der Waals and metallic. Along with the more complex hydrogen bonds4 and three-centre bonds5,6, they form a paradigm within which the structure of almost all molecules and solids can be understood. Here, we present evidence for hydrogen multicentre bonds—a generalization of three-centre bonds—in which a hydrogen atom equally bonds to four or more other atoms. When substituting for oxygen in metal oxides, hydrogen bonds equally to all the surrounding metal atoms, becoming fourfold coordinated in ZnO, and sixfold coordinated in MgO. These multicentre bonds are remarkably strong despite their large hydrogen–metal distances. The calculated local vibration mode frequency in MgO agrees with infrared spectroscopy measurements7. Multicoordinated hydrogen also explains the dependence of electrical conductivity on oxygen partial pressure, resolving a long-standing controversy on the role of point defects in unintentional n-type conductivity of ZnO (refs 8–10).

Abstract: Kohn–Sham density functional theory (KS-DFT) is nowadays the most widely used quantum chemical method for electronic structure calculations in chemistry and physics. Its further application in e.g. supramolecular chemistry or biochemistry has mainly been hampered by the inability of almost all current density functionals to describe the ubiquitous attractive long-range van der Waals (dispersion) interactions. We review here methods to overcome this defect, and describe in detail a very successful correction that is based on damped –C6·R–6 potentials (DFT-D). As examples we consider the non-covalent inter- and intra-molecular interactions in unsaturated organic molecules (so-called π–π stacking in benzenes and dyes), in biologically relevant systems (nucleic acid bases/pairs, proteins, and ‘folding’ models), between fluorinated molecules, between curved aromatics (corannulene and carbon nanotubes) and small molecules, and for the encapsulation of methane in water clusters. In selected cases we partition the interaction energies into the most relevant contributions from exchange-repulsion, electrostatics, and dispersion in order to provide qualitative insight into the binding character.

Abstract: The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule.

Abstract: Neutron diffraction data with hydrogen isotope substitution on aqueous solutions of NaCl and KCl at concentrations ranging from high dilution to near-saturation are analyzed using the Empirical Potential Structure Refinement technique. Information on both the ion hydration shells and the microscopic structure of the solvent is extracted. Apart from obvious effects due to the different radii of the three ions investigated, it is found that water molecules in the hydration shell of K+ are orientationally more disordered than those hydrating a Na+ ion and are inclined to orient their dipole moments tangentially to the hydration sphere. Cl- ions form instead hydrogen-bonded bridges with water molecules and are readily accommodated into the H-bond network of water. The results are used to show that concepts such as structure maker/breaker, largely based on thermodynamic data, are not helpful in understanding how these ions interact with water at the molecular level.

Abstract: Nanoparticles can be used as the building blocks for materials such as supracrystals or ionic liquids. However, they lack the ability to bond along specific directions as atoms and molecules do. We report a simple method to place target molecules specifically at two diametrically opposed positions in the molecular coating of metal nanoparticles. The approach is based on the functionalization of the polar singularities that must form when a curved surface is coated with ordered monolayers, such as a phase-separated mixture of ligands. The molecules placed at these polar defects have been used as chemical handles to form nanoparticle chains that in turn can generate self-standing films.

Abstract: A molecular origin of the striking rate increase observed in a reaction on water is studied theoretically. A key aspect of the on-water rate phenomenon is the chemistry between water and reactants that occurs at an oil-water phase boundary. In particular, the structure of water at the oil-water interface of an oil emulsion, in which approximately one in every four interfacial water molecules has a free ("dangling") OH group that protrudes into the organic phase, plays a key role in catalyzing reactions via the formation of hydrogen bonds. Catalysis is expected when these OH's form stronger hydrogen bonds with the transition state than with the reactants. In experiments more than a 5 orders of magnitude enhancement in rate constant was found in a chosen reaction. The structural arrangement at the "oil-water" interface is in contrast to the structure of water molecules around a small hydrophobic solute in homogeneous solution, where the water molecules are tangentially oriented. The latter implies that a breaking of an existing hydrogen-bond network in homogeneous solution is needed in order to permit a catalytic effect of hydrogen bonds, but not for the on-water reaction. Thereby, the reaction in homogeneous aqueous solution is intrinsically slower than the surface reaction, as observed experimentally. The proposed mechanism of rate acceleration is discussed in light of other on-water reactions that showed smaller accelerations in rates. To interpret the results in different media, a method is given for comparing the rate constants of different rate processes, homogeneous, neat and on-water, all of which have different units, by introducing models that reduce them to the same units. The observed deuterium kinetic isotope effect is discussed briefly, and some experiments are suggested that can test the present interpretation and increase our understanding of the on-water catalysis.

Abstract: Single-molecule chemical reactions with individual single-walled carbon nanotubes were observed through near-infrared photoluminescence microscopy. The emission intensity within distinct submicrometer segments of single nanotubes changed in discrete steps after exposure to acid, base, or diazonium reactants. The steps were uncorrelated in space and time and reflected the quenching of mobile excitons at localized sites of reversible or irreversible chemical attack. Analysis of step amplitudes revealed an exciton diffusional range of about 90 nanometers, independent of nanotube structure. Each exciton visited about 10,000 atomic sites during its lifetime, providing highly efficient sensing of local chemical and physical perturbations.

Abstract: The very large breathing effect of a metal-organic framework during CO 2 adsorption is discussed. An experiment was conducted for the case of CO2 adsorption at room temperature for porous chromium (III) terephthalate MIL-53. The structural topology of MIL-53 consists of a 4 4 net with tilted chains of CrIIIO4(OH) 2 octahedra sharing trans hydroxyl groups solid. These chains are linked through the carboxylate groups of the terephthalate ions forming a 3D framework. An in situ solid-state NMR study of the hydration of MIL-53HT showed that the shrinkage that occurred upon insertion of water molecules resulted from the onset of two types of strong hydrogen bonds. The first type involves the hydrogen atoms of water molecules and the oxygen atoms of the bridging carboxylate groups. The second type, which seems to be more energetically favorable, links OH groups to inserted water molecules.

Abstract: The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. The authors investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles. A "partial radical" concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules. In addition, the uniqueness of the zigzag-edged graphene nanoribbon is further demonstrated by comparing it with other forms of sp2 carbons, including a graphene sheet, nanotubes, and an armchair-edged graphene nanoribbon.

Abstract: All molecules of up to 11 atoms of C, N, O, and F possible under consideration of simple valency, chemical stability, and synthetic feasibility rules were generated and collected in a database (GDB). GDB contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds. By comparison, only 63 857 compounds of up to 11 atoms were found in public databases (a combination of PubChem, ChemACX, ChemSCX, NCI open database, and the Merck Index). A total of 538 of the 1208 ring systems in GDB are currently unknown in the CAS Registry and Beilstein databases in any carbon/heteroatom/multiple-bond combination or as a substructure. Over 70% of GDB molecules are chiral. Because of their small size, all compounds obey Lipinski's bioavailability rule. A total of 13.2 million compounds also follow Congreve's “Rule of 3” for lead-likeness. A Kohonen map trained with autocorrelation descriptors organizes GDB according to compound classes and shows that leadlike compou...

Abstract: Using the difference Fourier analysis of neutron powder diffraction data along with first-principles calculations, we reveal detailed structural information such as methyl group orientation, hydrogen adsorption sites, and binding energies within the nanopore structure of ZIF8 (Zn(MeIM)2). Surprisingly, the two strongest adsorption sites that we identified are both directly associated with the organic linkers, instead of the ZnN4 clusters, in strong contrast to classical MOFs, where the metal-oxide clusters are the primary adsorption sites. These observations are important and hold the key to optimizing this new class of ZIF materials for practical hydrogen storage applications. Finally, at high concentration H2-loadings, ZIF8 structure is capable of holding up to 28 H2 molecules (i.e., 4.2 wt %) in the form of highly symmetric novel three-dimensional interlinked H2-nanoclusters with relatively short H2−H2 distances compared to solid H2. Hence, ZIF compounds with robust chemical stability can be also an id...

Abstract: A novel one step synthesis of water soluble Au and Ag nanoparticles has been reported at room temperature using a naturally occurring bifunctional molecule, namely, gallic acid. The mechanistic details of nanoparticle formation were elucidated by carrying out control experiments using a variety of model compounds. The newly synthesized nanoparticles are extremely stable in the pH range of 4.5−5.0, due to (i) the strong electrostatic interaction of the carboxylate anion of the capping agent with the surface of the nanoparticle and (ii) a very high ζ potential (−45 mV). Under these pH conditions, it is difficult to bring nanoparticles in proximity due to strong interparticle electrostatic repulsion. However, the unique coordination behavior of Pb2+ ions (coordination number up to 12, flexible bond length and geometry) allows the formation of a stable supramolecular complex resulting in plasmon coupling and a visual color change. Because of the rigid coordination geometry, other metal cations (Ca2+, Cu2+, Cd...

Abstract: The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state hydrogen-bonding dynamics of fluorenone (FN) in hydrogen donating methanol (MeOH) solvent. The infrared spectra of the hydrogen-bonded FN-MeOH complex in both the ground state and the electronically excited states are calculated using the TDDFT method, since the ultrafast hydrogen-bonding dynamics can be investigated by monitoring the vibrational absorption spectra of some hydrogen-bonded groups in different electronic states. We demonstrated that the intermolecular hydrogen bond C=O...H-O between fluorenone and methanol molecules is significantly strengthened in the electronically excited-state upon photoexcitation of the hydrogen-bonded FM-MeOH complex. The hydrogen bond strengthening in electronically excited states can be used to explain well all the spectral features of fluorenone chromophore in alcoholic solvents. Furthermore, the radiationless deactivation via internal conversion (IC) can be facilitated by the hydrogen bond strengthening in the excited state. At the same time, quantum yields of the excited-state deactivation via fluorescence are correspondingly decreased. Therefore, the total fluorescence of fluorenone in polar protic solvents can be drastically quenched by hydrogen bonding.

Abstract: The molecules presented here provide a test-bed for competitive supramolecular chemistry, and on the basis of five crystal structures a ranking of the relative structural importance and influence of competing weak/strong hydrogen bonds and weak/strong halogen bonds has been achieved.

Abstract: The electrostatic potentials computed on the surfaces of a series of molecules R3X, where X is a Group V atom, show that some of these atoms have regions of positive potential on their outer surfaces, approximately on the extensions of the RX bonds. This suggests the likelihood of weak, directional noncovalent interactions between such atoms and nucleophiles, paralleling what has already been established for Groups VI and VII. The origins and relative strengths of the positive regions are explained in terms of the σ-hole concept, supported by natural bond orbital analyses. MP2/6-311++G(3df,2p) calculations confirm the formation of stable complexes between five such Group V molecules and the model nucleophile HCN. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Abstract: Non-classical behaviour, brought about by a confinement that imposes spatial constraints on molecules, is opening avenues to novel applications. For example, carbon nanotubes, which show rapid and selective transport of small molecules across the nanotubes, have significant potential as biological or chemical separation materials for organic solvents or gaseous molecules1,2,3,4,5. With polymers, when the dimensions of a confining volume are much less than the radius of gyration, a quantitative understanding of perturbations to chain dynamics due to geometric constraints remains a challenge6,7,8,9,10 and, with the development of nanofabrication processes, the dynamics of confined polymers have significant technological implications11,12,13,14,15,16,17. Here, we describe a weak molecular-weight-dependent mobility of polymers confined within nanoscopic cylindrical pores having diameters smaller than the dimension of the chains in the bulk. On the basis of the chain configuration along the pore axis, the measured mobility of polymers in the confined geometry is much higher than the mobility of the unconfined chain. With the emergence of nanofabrication processes based on polymer flow, the unexpected enhancement in flow and reduction in intermolecular entanglements are of significant importance in the design and execution of processing strategies.

Abstract: There has been considerable speculation about the role of water and water complexes in chemical gas-phase reactions, including the conjecture that water may act as a molecular catalyst through its ability to form hydrogen bonds. Here, we present kinetic studies in which the effect of water on the rate of the reaction between hydroxyl radicals and acetaldehyde has been measured directly in Laval nozzle expansions at low temperatures. An increasing enhancement of the reaction rate by added water was found with decreasing temperatures between 300 and 60 kelvin. Quantum chemical calculations and statistical rate theory support our conclusions that this observation is due to the reduction of an intrinsic reaction barrier caused by specific water aggregation. The results suggest that even single water molecules can act as catalysts in radical-molecule reactions.

Abstract: Part I: The Hydrogen Bond Chapter 1. The hydrogen bond: formation, thermodynamic properties, classification Chapter 2. Geometrical properties of H-bonds and H-bonded organized supramolecular structures Chapter 3. Methods to observe and describe H-bonds Calorimetry Chapter 4. Infrared spectroscopy of H-bonded systems: experimental point of view Chapter 5. Infrared spectroscopy of H-bonded systems: theoretical descriptions Chapter 6. Reactivity of H-bonds: transfers of protons and of H-atoms Chapter 7. H/D isotopic substitution in H-bonds Part II: The Water Molecule Chapter 8. The H2O molecule in water vapour and ice Chapter 9. The H2O molecule in liquid water Chapter 10. The water molecule in (bio)macromolecules Chapter 11. Observing the water molecule Part III: General Conclusion Chapter 12. Conclusion: the H-bond, the water molecule and life

Abstract: Liquid-phase adsorption of tetracene and phenanthrene on a single-walled carbon nanotube (SWCNT) was examined. Tetracene adsorption was more than six times greater than that of phenanthrene. X-ray photoelectron spectroscopic examination clearly showed that tetracene and phenanthrene molecules efficiently coated the SWCNT external surfaces. The remarkable difference between the adsorption amounts of tetracene and phenanthrene was caused by the nanoscale curvature effect of the tube surface, resulting in a difference in the amount of contact between the molecule and the tube surface. The adsorption of tetracene and phenanthrene caused a significant higher frequency shift in the radial breathing mode (RBM) of the Raman band of the SWCNT, indicating an intensive π−π interaction between these polycyclic aromatic hydrocarbons and the external SWCNT surface.

Abstract: The novel functional electron localizability indicator is a useful tool for investigating chemical bonding in molecules and solids. In contrast to the traditional electron localization function (ELF), the electron localizability indicator is shown to be exactly decomposable into partial orbital contributions even though it displays at the single-determinantal level of theory the same topology as the ELF. This approach is generally valid for molecules and crystals at either the single-determinantal or the explicitly correlated level of theory. The advantages of the new approach are illustrated for the argon atom, homonuclear dimers N 2 and F 2 , unsaturated hydrocarbons C 2 H 4 and C 6 H 6 , and the transition-metal-containing molecules Sc 2 2+ and TiF 4 .

Abstract: A proton shared between two closed-shell molecules, [A·H + ·B], constitutes a ubiquitous soft binding motif in biological processes. The vibrational transitions associated with the shared proton, which provide a direct probe of this interaction, have been extensively studied in the condensed phase but have yielded only limited detailed information because of their diffuse character. We exploited recent advances in gas-phase ion spectroscopy to identify sharp spectral features that can be assigned to both the shared proton and the two tethered molecules in a survey of 18 cold, isolated [A·H + ·B] ions. These data yield a picture of the intermolecular proton bond at a microscopic scale, facilitating analysis of its properties within the context of a floppy polyatomic molecule.

Abstract: A significant improvement in molecular hydrogen uptake properties is revealed by our ab initio calculations for Li-decorated metal–organic framework 5. We have found that two Li atoms are strongly adsorbed on the surfaces of the six-carbon rings, one on each side, carrying a charge of +0.9e per Li atom. Each Li can cluster three H2 molecules around itself with a binding energy of 12 kJ (mol H2)−1. Furthermore, we show from ab initio molecular dynamics simulations with a hydrogen loading of 18 H2 per formula unit that a hydrogen uptake of 2.9 wt % at 200 K and 2.0 wt % at 300 K is achievable. To our knowledge, this is the highest hydrogen storage capacity reported for metal–organic framework 5 under such thermodynamic conditions.

Abstract: A predictive group-contribution statistical associating fluid theory (SAFT-γ) is developed by extending the molecular-based SAFT-VR equation of state [A. Gil-Villegas et al. J. Chem. Phys. 106, 4168 (1997)] to treat heteronuclear molecules which are formed from fused segments of different types. Our models are thus a heteronuclear generalization of the standard models used within SAFT, comparable to the optimized potentials for the liquid state OPLS models commonly used in molecular simulation; an advantage of our SAFT-γ over simulation is that an algebraic description for the thermodynamic properties of the model molecules can be developed. In our SAFT-γ approach, each functional group in the molecule is modeled as a united-atom spherical (square-well) segment. The different groups are thus characterized by size (diameter), energy (well depth) and range parameters representing the dispersive interaction, and by shape factor parameters (which denote the extent to which each group contributes to the overal...

Abstract: To systematically explore the higher-dimensional network structures with mixed connectivity, a series of two-dimensional (2D) and three-dimensional (3D) metal-organic frameworks (MOFs) with unusual (3,6)-connected net topologies are presented. These crystalline materials include [{[Mn(btza)2(H2O)2].2 H2O}n] (1), [{[Zn(btza)2(H2O)2].2 H2O}n] (2), [{[Cu(btza)2].H2O}n] (3), and [{[Cd(btza)2].3 H2O}n] (4), which have been successfully assembled through a predesigned three-connected organic component bis(1,2,4-triazol-1-yl)acetate (btza) with a variety of octahedral metal cores based on the modular synthetic methodology. The topological paradigms shown in this work cover the 2D CdCl2, 3D (4(2).6)2(4(4).6(2).8(7).10(2)), and pyrite (pyr) types. That is, when properly treated with the familiar first-row divalent metal ions, btza may perfectly furnish the coordination spheres for effective connectivity to result in diverse (3,6)-connected nets. Beyond this, a detailed analysis of network topology for all known 3D (3,6)-connected frameworks in both inorganic and inorganic-organic hybrid materials is described. Specific network connectivity of these MOFs indicates that the metal centers represent the most significant and alterable factor in structural assembly, although they show reliable and similar geometries. In this context, the combination of the distinct d10 AgI ion with btza in different solvents affords two isomorphous MOFs [{[Ag(btza)].glycol}n] (5) and [{[Ag(btza)]CH3OH}n] (6) with a binodal 4-connected 3D SrAl2 (sra) topology. The network structures of MOFs 1-3 and 5 turn out to be more complicated and interesting if one considers the hydrogen bonding between the host coordination frameworks and the intercalated solvent molecules. Furthermore, the role of the included solvents in the generation and stabilization of MOFs 1-6 is also investigated.