Showing papers on "Molecule published in 2012"

Small molecule semiconductors for high-efficiency organic photovoltaics

Abstract: Organic photovoltaic cells (OPVs) are a promising cost-effective alternative to silicon-based solar cells, and possess light-weight, low-cost, and flexibility advantages. Significant progress has been achieved in the development of novel photovoltaic materials and device structures in the last decade. Nowadays small molecular semiconductors for OPVs have attracted considerable attention, due to their advantages over their polymer counterparts, including well-defined molecular structure, definite molecular weight, and high purity without batch to batch variations. The highest power conversion efficiencies of OPVs based on small molecular donor/fullerene acceptors or polymeric donor/fullerene acceptors are up to 6.7% and 8.3%, respectively, and meanwhile nonfullerene acceptors have also exhibited some promising results. In this review we summarize the developments in small molecular donors, acceptors (fullerene derivatives and nonfullerene molecules), and donor–acceptor dyad systems for high-performance multilayer, bulk heterojunction, and single-component OPVs. We focus on correlations of molecular chemical structures with properties, such as absorption, energy levels, charge mobilities, and photovoltaic performances. This structure–property relationship analysis may guide rational structural design and evaluation of photovoltaic materials (253 references).

Natural bond orbital methods

Abstract: Natural bond orbital (NBO) methods encompass a suite of algorithms that enable fundamental bonding concepts to be extracted from Hartree-Fock (HF), Density Functional Theory (DFT), and post-HF computations. NBO terminology and general mathematical formulations for atoms and polyatomic species are presented. NBO analyses of selected molecules that span the periodic table illustrate the deciphering of the molecular wavefunction in terms commonly understood by chemists: Lewis structures, charge, bond order, bond type, hybridization, resonance, donor–acceptor interactions, etc. Upcoming features in the NBO program address ongoing advances in ab initio computing technology and burgeoning demands of its user community by introducing major new methods, keywords, and electronic structure system/NBO communication enhancements. © 2011 John Wiley & Sons, Ltd.

Hydrogen bonding in the electronic excited state.

Abstract: Because of its fundamental importance in many branches of science, hydrogen bonding is a subject of intense contemporary research interest. The physical and chemical properties of hydrogen bonds in the ground state have been widely studied both experimentally and theoretically by chemists, physicists, and biologists. However, hydrogen bonding in the electronic excited state, which plays an important role in many photophysical processes and photochemical reactions, has scarcely been investigated.Upon electronic excitation of hydrogen-bonded systems by light, the hydrogen donor and acceptor molecules must reorganize in the electronic excited state because of the significant charge distribution difference between the different electronic states. The electronic excited-state hydrogen-bonding dynamics, which are predominantly determined by the vibrational motions of the hydrogen donor and acceptor groups, generally occur on ultrafast time scales of hundreds of femtoseconds. As a result, state-of-the-art femtos...

Universal energy-level alignment of molecules on metal oxides

Abstract: Transition-metal oxides improve power conversion efficiencies in organic photovoltaics and are used as low-resistance contacts in organic light-emitting diodes and organic thin-film transistors. What makes metal oxides useful in these technologies is the fact that their chemical and electronic properties can be tuned to enable charge exchange with a wide variety of organic molecules. Although it is known that charge exchange relies on the alignment of donor and acceptor energy levels, the mechanism for level alignment remains under debate. Here, we conclusively establish the principle of energy alignment between oxides and molecules. We observe a universal energy-alignment trend for a set of transition-metal oxides--representing a broad diversity in electronic properties--with several organic semiconductors. The trend demonstrates that, despite the variance in their electronic properties, oxide energy alignment is governed by one driving force: electron-chemical-potential equilibration. Using a combination of simple thermodynamics, electrostatics and Fermi statistics we derive a mathematical relation that describes the alignment.

Activation of remote meta -C–H bonds assisted by an end-on template

Abstract: Functionalization of unactivated carbon-hydrogen (C-H) single bonds is an efficient strategy for rapid generation of complex molecules from simpler ones. However, it is difficult to achieve selectivity when multiple inequivalent C-H bonds are present in the target molecule. The usual approach is to use σ-chelating directing groups, which lead to ortho-selectivity through the formation of a conformationally rigid six- or seven-membered cyclic pre-transition state. Despite the broad utility of this approach, proximity-driven reactivity prevents the activation of remote C-H bonds. Here we report a class of easily removable nitrile-containing templates that direct the activation of distal meta-C-H bonds (more than ten bonds away) of a tethered arene. We attribute this new mode of C-H activation to a weak 'end-on' interaction between the linear nitrile group and the metal centre. The 'end-on' coordination geometry relieves the strain of the cyclophane-like pre-transition state of the meta-C-H activation event. In addition, this template overrides the intrinsic electronic and steric biases as well as ortho-directing effects with two broadly useful classes of arene substrates (toluene derivatives and hydrocinnamic acids).

Non-basic high-performance molecules for solution-processed organic solar cells.

Abstract: A new small molecule, p-DTS(FBTTh(2))(2), is designed for incorporation into solution-fabricated high-efficiency organic solar cells. Of primary importance is the incorporation of electron poor heterocycles that are not prone to protonation and thereby enable the incorporation of commonly used interlayers between the organic semiconductor and the charge collecting electrodes. These features have led to the creation of p-DTS(FBTTh(2))(2)/PC(71)BM solar cells with power conversion efficiencies of up to 7%.

Recent advances in azaborine chemistry.

Abstract: The chemistry of organoboron compounds has been primarily dominated by their use as powerful reagents in synthetic organic chemistry. Recently, the incorporation of boron as part of a functional target structure has emerged as a useful way to generate diversity in organic compounds. A commonly applied strategy is the replacement of a CC unit with its isoelectronic BN unit. In particular, the BN/CC isosterism of the ubiquitous arene motif has undergone a renaissance in the past decade. The parent molecule of the 1,2-dihydro-1,2-azaborine family has now been isolated. New mono- and polycyclic B,N heterocycles have been synthesized for potential use in biomedical and materials science applications. This review is a tribute to Dewar's first synthesis of a monocyclic 1,2-dihydro-1,2-azaborine 50 years ago and discusses recent advances in the synthesis and characterization of heterocycles that contain carbon, boron, and nitrogen.

Stochastic sensing of proteins with receptor-modified solid-state nanopores

Abstract: Solid-state nanopores are capable of the label-free analysis of single molecules. It is possible to add biochemical selectivity by anchoring a molecular receptor inside the nanopore, but it is difficult to maintain single-molecule sensitivity in these modified nanopores. Here, we show that metallized silicon nitride nanopores chemically modified with nitrilotriacetic acid receptors can be used for the stochastic sensing of proteins. The reversible binding and unbinding of the proteins to the receptors is observed in real time, and the interaction parameters are statistically analysed from single-molecule binding events. To demonstrate the versatile nature of this approach, we detect His-tagged proteins and discriminate between the subclasses of rodent IgG antibodies.

Bond-order discrimination by atomic force microscopy.

Abstract: We show that the different bond orders of individual carbon-carbon bonds in polycyclic aromatic hydrocarbons and fullerenes can be distinguished by noncontact atomic force microscopy (AFM) with a carbon monoxide (CO)–functionalized tip. We found two different contrast mechanisms, which were corroborated by density functional theory calculations: The greater electron density in bonds of higher bond order led to a stronger Pauli repulsion, which enhanced the brightness of these bonds in high-resolution AFM images. The apparent bond length in the AFM images decreased with increasing bond order because of tilting of the CO molecule at the tip apex.

A layer-structured Eu-MOF as a highly selective fluorescent probe for Fe3+ detection through a cation-exchange approach

Abstract: A new series of lanthanide metal–organic frameworks, LnL (Ln = La, Y, Eu, Tb, and Gd), were prepared under hydrothermal conditions. The five compounds are all isostructural as confirmed by the analyses of single crystal and powder X-ray diffractions. The compounds exhibit layer-like structures with the [H2NMe2]+ cations being located in the interlayer channels, which can be easily replaced by a number of metal ions. Most interestingly, compound EuL performs as a rare example of a highly selective and sensitive luminescence sensor for Fe3+ ions based on total quenching of the Eu-luminescence via cation-exchange. The possible sensing mechanism was further explored in detail. Remarkably, it is the first Eu-MOF luminescent material to exhibit an excellent ability for the detection of Fe3+ ions in a biological system.

A Chiral Porous Metal–Organic Framework for Highly Sensitive and Enantioselective Fluorescence Sensing of Amino Alcohols

Abstract: A highly porous and fluorescent metal–organic framework (MOF), 1, was built from a chiral tetracarboxylate bridging ligand derived from 1,1′-bi-2-naphthol (BINOL) and a cadmium carboxylate infinite-chain secondary building unit The fluorescence of 1 can be effectively quenched by amino alcohols via H-bonding with the binaphthol moieties decorating the MOF, leading to a remarkable chiral sensor for amino alcohols with greatly enhanced sensitivity and enantioselectivity over BINOL-based homogeneous systems The higher detection sensitivity of 1 is due to a preconcentration effect by which the analytes are absorbed and concentrated inside the MOF channels, whereas the higher enantioselectivity of 1 is believed to result from enhanced chiral discrimination owing to the cavity confinement effect and the conformational rigidity of the BINOL groups in the framework 1 was quenched by four chiral amino alcohols with unprecedentedly high Stern–Volmer constants of 490–31200 M–1 and enantioselectivity ratios of 11

Stability and Hydrolyzation of Metal Organic Frameworks with Paddle-Wheel SBUs upon Hydration

Abstract: Instability of most prototypical metal organic frameworks (MOFs) in the presence of moisture is always a limita- tion for industrial scale development. In this work, we examine the dissociation mechanism of microporous paddle wheel frameworks M(bdc)(ted)0.5 [M=Cu, Zn, Ni, Co; bdc= 1,4-benzenedicarboxylate; ted= triethylenediamine] in controlled humidity environments. Combined in-situ IR spectroscopy, Raman, and Powder x-ray diffraction measurements show that the stability and modification of isostructual M(bdc)(ted)0.5 compounds upon exposure to water vapor critically depend on the central metal ion. A hydrolysis reaction of water molecules with Cu-O-C is observed in the case of Cu(bdc)(ted)0.5. Displacement reactions of ted linkers by water molecules are identified with Zn(bdc)(ted)0.5 and Co(bdc)(ted)0.5. In contrast,. Ni(bdc)(ted)0.5 is less suscept- ible to reaction with water vapors than the other three compounds. In addition, the condensation of water vapors into the framework is necessary to initiate the dissociation reaction. These findings, supported by supported by first principles theoretical van der Waals density functional (vdW-DF) calculations of overall reaction enthalpies, provide the necessary information for de- termining operation conditions of this class of MOFs with paddle wheel secondary building units and guidance for developing more robust units.

Three-dimensional chiral plasmonic oligomers.

Abstract: The living world is chiral. Chirality or the handedness of a structure or molecule is at the heart of life itself. Recently, it has been shown that plasmonic structures exhibit unprecedented and gigantic chiral optical responses. Here we show that truly three-dimensional arrangements of plasmonic "meta-atoms" only exhibit a chiral optical response if similar plasmonic "atoms" are arranged in a handed fashion as we require resonant plasmonic coupling. Moreover, we demonstrate that such particle groupings, similarly to molecular systems, possess the capability to encode their three-dimensional arrangement in unique and well-modulated spectra making them ideal candidates for a three-dimensional chiral plasmon ruler. Our results are crucial for the future design and improvement of plasmonic chiral optical systems, for example, for ultrasensitive enantiomer sensing on the single molecule level.

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

Abstract: Magnesium ions have an important role in the structure and folding mechanism of ribonucleic acid systems. To properly simulate these biophysical processes, the applied molecular models should reproduce, among other things, the kinetic properties of the ions in water solution. Here, we have studied the kinetics of the binding of magnesium ions with water molecules and nucleic acid systems using molecular dynamics simulation in detail. We have validated the parameters used in biomolecular force fields, such as AMBER and CHARMM, for Mg2+ ions and also for the biologically relevant ions Na+, K+, and Ca2+ together with three different water models (TIP3P, SPC/E, and TIP5P). The results show that Mg2+ ions have a slower exchange rate than Na+, K+, and Ca2+ in agreement with the experimental trend, but the simulated value underestimates the experimentally observed Mg2+–water exchange rate by several orders of magnitude, irrespective of the force field and water model. A new set of parameters for Mg2+ was develop...

Catalytic functionalization of unactivated primary C-H bonds directed by an alcohol

Abstract: The combination of an iridium-phenanthroline catalyst and a dihydridosilane reagent leads to the site-selective functionalization of primary C–H bonds that are proximal to a hydroxyl group. The development of new synthetic methods for the selective functionalization of C–H bonds is extremely important, because this chemical transformation has the potential to revolutionize the synthesis of complex molecules. Here, Eric Simmons and John Hartwig show that the combination of an iridium-phenanthroline catalyst and a dihydridosilane reagent leads to the site-selective functionalization of primary C–H bonds situated close to a hydroxyl group. The scope of the reaction encompasses alcohols and ketones, suggesting that this methodology will be suitable for the selective functionalization of C–H bonds in complex natural products. New synthetic methods for the catalytic functionalization of C–H bonds have the potential to revolutionize the synthesis of complex molecules1,2,3,4. However, the realization of this synthetic potential requires the ability to functionalize selectively one C–H bond in a compound containing many such bonds and an array of functional groups. The site-selective functionalization of aliphatic C–H bonds is one of the greatest challenges that must be met for C–H bond functionalization to be used widely in complex-molecule synthesis1,3,5,6, and processes catalysed by transition-metals provide the opportunity to control selectivity7,8. Current methods for catalytic, aliphatic C–H bond functionalization typically rely on the presence of one inherently reactive C–H bond9,10, or on installation and subsequent removal of directing groups that are not components of the desired molecule8. To overcome these limitations, we sought catalysts and reagents that would facilitate aliphatic C–H bond functionalization at a single site, with chemoselectivity derived from the properties of the catalyst and site-selectivity directed by common functional groups11 contained in both the reactant and the desired product. Here we show that the combination of an iridium-phenanthroline catalyst and a dihydridosilane reagent leads to the site-selective γ-functionalization of primary C–H bonds controlled by a hydroxyl group, the most common functional group in natural products12. The scope of the reaction encompasses alcohols and ketones bearing many substitution patterns and auxiliary functional groups; this broad scope suggests that this methodology will be suitable for the site-selective and diastereoselective functionalization of complex natural products.

Direct Catalytic Anti-Markovnikov Hydroetherification of Alkenols

Abstract: A direct intramolecular anti-Markovnikov hydroetherification reaction of alkenols is described. By employing catalytic quantities of commercially available 9-mesityl-10-methylacridinium perchlorate and 2-phenylmalononitrile as a redox-cycling source of a H-atom, we report the anti-Markovnikov hydroetherification of alkenes with complete regioselectivity. In addition, we present results demonstrating that this novel catalytic system can be applied to the anti-Markovnikov hydrolactonization of alkenoic acids.

In-situ plasmon-driven chemical reactions revealed by high vacuum tip-enhanced Raman spectroscopy

Abstract: With strong surface plasmons excited at the metallic tip, tip-enhanced Raman spectroscopy (TERS) has both high spectroscopic sensitivity and high spatial resolution, and is becoming an essential tool for chemical analysis. It is a great challenge to combine TERS with a high vacuum system due to the poor optical collection efficiency. We used our innovatively designed home-built high vacuum TERS (HV-TERS) to investigate the plasmon-driven in-situ chemical reaction of 4-nitrobenzenethiol dimerizing to dimercaptoazobenzene. The chemical reactions can be controlled by the plasmon intensity, which in turn can be controlled by the incident laser intensity, tunneling current and bias voltage. The temperature of such a chemical reaction can also be obtained by the clearly observed Stokes and Anti-Stokes HV-TERS peaks. Our findings offer a new way to design a highly efficient HV-TERS system and its applications to chemical catalysis and synthesis of molecules, and significantly extend the studies of chemical reactions.

Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials.

Abstract: We develop a nonempirical atoms-in-molecules (AIM) method for computing net atomic charges that simultaneously reproduce chemical states of atoms in a material and the electrostatic potential V(r) outside its electron distribution. This method gives accurate results for a variety of periodic and nonperiodic materials including molecular systems, solid surfaces, porous solids, and nonporous solids. This method, called DDEC/c3, improves upon our previously published DDEC/c2 method (Manz, T. A.; Sholl, D. S. J. Chem. Theory Comput. 2010, 6, 2455–2468) by accurately treating nonporous solids with short bond lengths. Starting with the theory all AIM charge partitioning functionals with spherically symmetric atomic weights must satisfy, the form of the DDEC/c3 functional is derived from first principles. The method is designed to converge robustly by avoiding conditions that lead to nearly flat optimization landscapes. In addition to net atomic charges, the method can also compute atomic multipoles and atomic s...

The curious case of the hydrated proton.

Abstract: Understanding the hydrated proton is a critically important problem that continues to engage the research efforts of chemists, physicists, and biologists because of its involvement in a wide array of phenomena. Only recently have several unique properties of the hydrated proton been unraveled through computer simulations. One such process is the detailed molecular mechanism by which protons hop between neighboring water molecules, thus giving rise to the anomalously high diffusion of protons relative to other simple cations. Termed Grotthuss shuttling, this process occurs over multiple time and length scales, presenting unique challenges for computer modeling and simulation. Because the hydrated proton is in reality a dynamical electronic charge defect that spans multiple water molecules, the simulation methodology must be able to dynamically readjust the chemical bonding topology. This reactive nature of the chemical process is automatically captured with ab initio molecular dynamics (AIMD) simulation me...

Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules.

Abstract: We present a set of 40 noncovalent complexes of organic halides, halohydrides, and halogen molecules where the halogens participate in a variety of interaction types. The set, named X40, covers electrostatic interactions, London dispersion, hydrogen bonds, halogen bonding, halogen−π interactions, and stacking of halogenated aromatic molecules. Interaction energies at equilibrium geometries were calculated using a composite CCSD(T)/CBS scheme where the CCSD(T) contribution is calculated using triple-ζ basis sets with diffuse functions on all atoms but hydrogen. For each complex, we also provide 10 points along the dissociation curve calculated at the CCSD(T)/CBS level. We use this accurate reference to assess the accuracy of selected post-HF methods.

Bispecific t cell activating antigen binding molecules

Abstract: The present disclosure generally relates to novel bispecific antigen binding molecules for T cell activation and re-direction to specific target cells. In addition, the present disclosure relates to polynucleotides encoding such bispecific antigen binding molecules, and vectors and host cells comprising such polynucleotides. The disclosure further relates to methods for producing the bispecific antigen binding molecules of the invention, and to methods of using these bispecific antigen binding molecules in the treatment of disease.

Dynamics of water interacting with interfaces, molecules, and ions.

Abstract: Water is a critical component of many chemical processes, in fields as diverse as biology and geology. Water in chemical, biological, and other systems frequently occurs in very crowded situations: the confined water must interact with a variety of interfaces and molecular groups, often on a characteristic length scale of nanometers. Water’s behavior in diverse environments is an important contributor to the functioning of chemical systems. In biology, water is found in cells, where it hydrates membranes and large biomolecules. In geology, interfacial water molecules can control ion adsorption and mineral dissolution. Embedded water molecules can change the structure of zeolites. In chemistry, water is an important polar solvent that is often in contact with interfaces, for example, in ion-exchange resin systems.Water is a very small molecule; its unusual properties for its size are attributable to the formation of extended hydrogen bond networks. A water molecule is similar in mass and volume to methane,...

Adsorption of organic molecules on rutile TiO2 and anatase TiO2 single crystal surfaces.

Abstract: The interaction of organic molecules with titanium dioxide surfaces has been the subject of many studies over the last few decades. Numerous surface science techniques have been utilised to understand the often complex nature of these systems. The reasons for studying these systems are hugely diverse given that titanium dioxide has many technological and medical applications. Although surface science experiments investigating the adsorption of organic molecules on titanium dioxide surfaces is not a new area of research, the field continues to change and evolve as new potential applications are discovered and new techniques to study the systems are developed. This tutorial review aims to update previous reviews on the subject. It describes experimental and theoretical work on the adsorption of carboxylic acids, dye molecules, amino acids, alcohols, catechols and nitrogen containing compounds on single crystal TiO2 surfaces.

Cytotoxicity and slow release of the anti-cancer drug doxorubicin from ZIF-8

Abstract: Metal–organic frameworks are emerging as a powerful platform for the delivery and controlled release of several drug molecules. Herein, we report the incorporation of the anti-cancer drug doxorubicin into the zeolitic imidazolate framework (ZIF-8) with high-load and progressive release. Adsorption measurements show that doxorubicin is incorporated into ZIF-8 with a load of 0.049 g doxorubicin g−1 dehydrated ZIF-8. Doxorubicin is released in a highly controlled and progressive fashion with 66% of the drug released after 30 days. We also characterize the antitumoral potential and cytotoxicity of the doxorubicin-ZIF-8 (DOXO-ZIF-8) complex towards the mucoepidermoid carcinoma of human lung (NCI-H292), human colorectal adenocarcinoma (HT-29), and human promyelocytic leukemia (HL-60) cell lines. It is shown that the complex doxorubicin-ZIF-8 exhibits lower cytotoxicity than pure doxorubicin for the tested cells, possibly due to the slower release of the incorporated drug. Furthermore, host–guest interactions have been addressed from a microscopic perspective through molecular docking simulations. In conjunction with our experimental characterization, the calculations suggest that doxorubicin binds preferentially to the surface rather than into the pores of ZIF-8, whose entry diameter is at least half the size of the shortest axis of the drug. These findings are also consistent with high-resolution X-ray crystallography and NMR spectroscopy studies of ZIF-8 which shows that this framework is very rigid under constant pressure in contrast to previous experimental and theoretical studies of ZIF-8 under gas pressure.

Nonlinear Light Scattering and Spectroscopy of Particles and Droplets in Liquids

Abstract: Nano- and microparticles have optical, structural, and chemical properties that differ from both their building blocks and the bulk materials themselves. These different physical and chemical properties are induced by the high surface-to-volume ratio. As a logical consequence, to understand the properties of nano- and microparticles, it is of fundamental importance to characterize the particle surfaces and their interactions with the surrounding medium. Recent developments of nonlinear light scattering techniques have resulted in a deeper insight of the underlying light-matter interactions. They have shed new light on the molecular mechanism of surface kinetics in solution, properties of interfacial water in contact with hydrophilic and hydrophobic particles and droplets, molecular orientation distribution of molecules at particle surfaces in solution, interfacial structure of surfactants at droplet interfaces, acid-base chemistry on particles in solution, and vesicle structure and transport properties.

Palladium-Mediated Cell-Surface Labeling

Abstract: Benign C–C bond formation at various sites in cell-surface channels has been achieved through Suzuki–Miyaura coupling of genetically positioned unnatural amino acids containing aryl halide side chains. This enabled site-selective cell surface manipulation of Escherichia coli; the phosphine-free catalyst caused no cell death at required Pd loadings, suggesting future in vivo application of catalytic metal-mediated bond formation in more complex organisms.