Reactions Of Organic Molecules Research Articles

Monooxygenation of small hydrocarbons catalyzed by bacterial cytochrome p450s.

Cytochrome P450s (P450s) catalyze the NAD(P)H/O2-dependent monooxygenation of less reactive organic molecules under mild conditions. The catalytic activity of bacterial P450s is very high compared with P450s isolated from animals and plants, and the substrate specificity of bacterial P450s is also very high. Accordingly, their catalytic activities toward nonnative substrates are generally low especially toward small hydrocarbons. However, mutagenesis approaches have been very successful for engineering bacterial P450s for the hydroxylation of small hydrocarbons. On the other hand, "decoy" molecules, whose structures are very similar to natural substrates, can be used to trick the substrate recognition of bacterial P450s, allowing the P450s to catalyze oxidation reactions of nonnative substrates without any substitution of amino acid residues in the presence of decoy molecules. Thus, the hydroxylation of small hydrocarbons such as ethane, propane, butane and benzene can be catalyzed by P450BM3, a long-alkyl-chain hydroxylase, using substrate misrecognition of P450s induced by decoy molecules. Furthermore, a number of H2O2-dependent bacterial P450s can catalyze the peroxygenation of a variety of nonnative substrates through a simple substrate-misrecognition trick, in which catalytic activities and enantioselectivity are dependent on the structure of decoy molecules.

Redox-Induced Photoluminescence of Metal–Organic Coordination Polymer Gel

In this study, we have prepared a redox-active and intrinsically nonphotoluminescent metal–organic gel comprised of iron ions and terephthalic acid. In the presence of small reactive organic molecules like pyrrole, aniline, and bithiophene, the gelation process was unaffected and at the same time it led to the formation of highly photoluminescent hybrid materials. The photoluminescence turn-on response was primarily attributed to the redox reaction between iron ions and the small organic molecules generating oxidized oligomers in the porous gel matrix. A remarkable morphological transformation of the metal–organic gel from spindle-like to nanofibers, induced by the redox reaction, was detected. The adopted synthetic approach is very simple and the ease of tailor-making photoluminescence in the materials by varying the combinations of redox system and reactive small organic molecule will open up new perspective in the field of coordination polymers, specifically, for sensors, photonics, and photovoltaic ap...

Bitz, Ginoux, Jacobson, Nizkorodov, and Yang Receive 2013 Atmospheric Sciences Ascent Awards: Citation for Sergey Nizkorodov

The Atmospheric Sciences section of AGU awards one of the five Ascent Awards to Professor Sergey Nizkorodov of the Department of Chemistry at the University of California, Irvine (UCI) for elucidating at the molecular level the formation, growth, and reactions of organic molecules in the atmosphere.

Modeling adsorption and reactions of organic molecules at metal surfaces.

ConspectusThe understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials.Here we show that the recently developed DFT+vdWsurf method that accurately accounts for the collective electronic response effects enables reliable modeling of structure and stability for a broad class of organic molecules adsorbed on metal surfaces. This method was demonstrated to achieve quantitative accuracy for aromatic hydrocarbons (benzene, naphthalene, anthracene, and diindenoperylene), C60, and sulfur/oxygen-containing molecules (thiophene, NTCDA, and PTCDA) on close-packed and stepped metal surfaces, leading to an overall accuracy of 0.1 Å in adsorption heights and 0.1 eV in binding energies with respect to state-of-the-art experiments. An unexpected finding is that vdW interactions contribute more to the binding of strongly bound molecules on transition-metal surfaces than for molecules physisorbed on coinage metals. The accurate inclusion of vdW interactions also significantly improves tilting angles and adsorption heights for all the studied molecules, and can qualitatively change the potential-energy surface for adsorbed molecules with flexible functional groups. Activation barriers for molecular switches and reaction precursors are modified as well.

Peroxygenase reactions catalyzed by cytochromes P450

Cytochromes P450 (P450s) catalyze monooxygenation of a wide range of less reactive organic molecules under mild conditions. By contrast with the general reductive oxygen activation pathway of P450s, an H2O2-shunt pathway does not require any supply of electrons and protons for the generation of a highly reactive intermediate (compound I). Because the low cost of H2O2 allows us to use it in industrial-scale synthesis, the H2O2-shunt pathway is an attractive process for monooxygenation reactions. This review focuses on the P450-catalyzed monooxygenation of organic molecules using H2O2 as the oxidant.

Periodic mesoporous silica‐supported Ni(II) organometallic complex as an active and reusable nanocatalyst for water‐medium Sonogashira coupling reaction

Phenyl‐bridged periodic mesoporous organosilicas (PMOs) functionalized with diphenylphosphino (PPh2‐) ligands were synthesized via a surfactant‐directed self‐assembly approach, and were used as a support to immobilize Ni(II) organometallic complex by coordination interaction. In comparison with Ni‐PPh2‐SBA‐15 and Ni‐PPh2‐PMOs(Et) catalysts, the as‐prepared Ni‐PPh2‐PMOs(Ph) exhibited superior catalytic reactivity and selectivity in water‐medium Sonogashira reaction. A control experiment demonstrated that its high activity could be attributed to the high dispersion of Ni(II) active sites and ordered mesopore channels, which effectively diminished diffusion limitation. Meanwhile, the phenyl organic groups in the support wall enhanced surface hydrophobicity, which promoted the adsorption for organic reactant molecules. Moreover, it displayed almost the same catalytic efficiency with the corresponding homogeneous Ni(PPh3)2Cl2 catalyst and could be used repetitively, which was considered as a more environmentally friendly catalytic process since it simultaneously avoided the use of noble metal active species and toxic organic solvents. Copyright © 2013 John Wiley & Sons, Ltd.

Amine-bridged periodic mesoporous organosilica nanospheres as an active and reusable solid base-catalyst for water-medium and solvent-free organic reactions

An amine-bridged periodic mesoporous organosilica catalyst in uniform nanospheres (∼85nm) (NH-PMO-NS) was synthesized by surfactant-directed co-condensation between amine-bridged silane and tetraethoxysilane (TEOS). As-prepared NH-PMO-NS contained short and straight mesoporous channels with amine-groups integrally incorporated into silica walls. In water-medium Knoevenagel condensation and solvent-free Henry reactions, this catalyst exhibited much higher activity and selectivity than both the common amine-bridged PMO (NH-PMO-com) with irregular shape synthesized by traditional method and the amine-functionalized MCM-41 in nanospheres (NH-MCM-NS) prepared by grafting amine-groups onto the pore surface. In addition, it displayed comparable catalytic efficiencies with the homogeneous base-catalyst (diethylamine), and could also be easily recovered and used repetitively. Based on the structural characterizations and kinetic studies, the high catalytic activity and selectivity were ascribed to the short and straight mesoporous channels in nanospheres with amine-groups incorporated into silica walls. The accessible basic catalytic sites may facilitate the diffusion and thus, promoted the adsorption of organic reactant molecules, leading to the enhanced activity and selectivity.

Gas uptake and chemical aging of semisolid organic aerosol particles.

Organic substances can adopt an amorphous solid or semisolid state, influencing the rate of heterogeneous reactions and multiphase processes in atmospheric aerosols. Here we demonstrate how molecular diffusion in the condensed phase affects the gas uptake and chemical transformation of semisolid organic particles. Flow tube experiments show that the ozone uptake and oxidative aging of amorphous protein is kinetically limited by bulk diffusion. The reactive gas uptake exhibits a pronounced increase with relative humidity, which can be explained by a decrease of viscosity and increase of diffusivity due to hygroscopic water uptake transforming the amorphous organic matrix from a glassy to a semisolid state (moisture-induced phase transition). The reaction rate depends on the condensed phase diffusion coefficients of both the oxidant and the organic reactant molecules, which can be described by a kinetic multilayer flux model but not by the traditional resistor model approach of multiphase chemistry. The chemical lifetime of reactive compounds in atmospheric particles can increase from seconds to days as the rate of diffusion in semisolid phases can decrease by multiple orders of magnitude in response to low temperature or low relative humidity. The findings demonstrate that the occurrence and properties of amorphous semisolid phases challenge traditional views and require advanced formalisms for the description of organic particle formation and transformation in atmospheric models of aerosol effects on air quality, public health, and climate.

Synthesis, characterization, and in vitro biological evaluation of highly stable diversely functionalized superparamagnetic iron oxide nanoparticles

In this article, we report the design and synthesis of a series of well-dispersed superparamagnetic iron oxide nanoparticles (SPIONs) using chitosan as a surface modifying agent to develop a potential T 2 contrast probe for magnetic resonance imaging (MRI). The amine, carboxyl, hydroxyl, and thiol functionalities were introduced on chitosan-coated magnetic probe via simple reactions with small reactive organic molecules to afford a series of biofunctionalized nanoparticles. Physico-chemical characterizations of these functionalized nanoparticles were performed by TEM, XRD, DLS, FTIR, and VSM. The colloidal stability of these functionalized iron oxide nanoparticles was investigated in presence of phosphate buffer saline, high salt concentrations and different cell media for 1 week. MRI analysis of human cervical carcinoma (HeLa) cell lines treated with nanoparticles elucidated that the amine-functionalized nanoparticles exhibited higher amount of signal darkening and lower T 2 relaxation in comparison to the others. The cellular internalization efficacy of these functionalized SPIONs was also investigated with HeLa cancer cell line by magnetically activated cell sorting (MACS) and fluorescence microscopy and results established selectively higher internalization efficacy of amine-functionalized nanoparticles to cancer cells. These positive attributes demonstrated that these nanoconjugates can be used as a promising platform for further in vitro and in vivo biological evaluations.

Hyperconjugation

AbstractThis review outlines the ubiquitous nature of hyperconjugative interactions and their role in the structure and reactivity of organic molecules. After defining the common hyperconjugative patterns, we discuss the main factors controlling the magnitude of hyperconjugative effects, including orbital symmetry, energy gap, electronegativity, and polarizibility. The danger of underestimating the magnitude of hyperconjugative interactions are illustrated by a number of spectroscopic, conformational, and structural effects. Through the use of advanced computational techniques, the true role of hyperconjugative effects, as it pertains to their influence on stereoelectronics, conformational equilibria, and reactivities relative to other electronic effects, continue to be uncovered. © 2011 John Wiley & Sons, Ltd.WIREs Comput Mol Sci2011 1 109–141 DOI: 10.1002/wcms.6This article is categorized under:Structure and Mechanism > Molecular Structures

Periodic mesoporous organosilica grafted palladium organometallic complex: efficient heterogeneous catalyst for water‐medium organic reactions

AbstractWater‐medium organic reactions were studied over periodic mesoporous silica (PMO) containing Pd(II) organometallic complex. This heterogeneous catalyst was achieved by Pd(II) compound coordinated with the PPh2‐ligand onto the pore surface of phenylene‐bridged PMO support. This catalyst displayed ordered mesoporous channels, which ensured the high dispersion of Pd(II) active sites and the convenient diffusion of reactant molecules into the pore channels. Meanwhile, the phenyl group in the pore wall of PMO could enhance the surface hydrophobicity which promoted the adsorption of organic reactant molecules on the catalyst in aqueous environment. As a result, this elaborated catalyst exhibited comparable activity and selectivity with the corresponding PdCl2(PPh3)2 homogeneous catalyst in the water‐medium organic reactions, and could be used repeatedly, showing a good potential in industrial applications. Copyright © 2010 John Wiley & Sons, Ltd.

ChemInform Abstract: The Effect of Heteroatoms on the Reactions of Organic Molecules with Caesium Fluoroxysulfate.

ChemInform Abstract: The Effect of Heteroatoms on the Reactions of Organic Molecules with Caesium Fluoroxysulfate.

Ozonation of ethinylestradiol in aqueous-methanolic solution: direct monitoring by electrospray ionization mass spectrometry

The ozonolysis of ethinylestradiol (1), a synthetic steroidal estrogen, in an aqueous-methanolic solution was investigated. HPLC-UV analyses revealed that 1 was completely consumed after a 20 min reaction time either at pH 5 or 8. ESI(-)-MS (electrospray ionization mass spectrometry in the negative ion mode) monitoring also revealed the continuous consumption of 1 (detected as [1 – H]- of m/z 295) concomitantly with the emergence of oxidation products. Chemical structures were proposed for these products based on the data of MS and MS/MS (the m/z values and fragmentation profiles of the anionic specie, respectively). These data, in conjunction with the well-established knowledge about the reactivity of organic molecules toward ozone in aqueous solution, were evaluated and an unprecedented reaction route for the ozonation of 1 could thus be suggested. Hence, the first step in this reaction sequence was ascribed to involve a 1,3-dipolar cycloaddition of ozone at the phenolic ring of 1 yielding the di-hydroxylated product 2 (detected as [2 – H]- of m/z 311). The loss of acetylene as the unique dissociation channel for [2 – H]- thus confirmed that such hydroxylation occurred at the phenolic ring rather than the acetylenic moiety of 1. Subsequent oxidations were proposed to be the origin of a number of other products, all of them bearing the COOH functionally (this was verified by the characteristic loss of CO2 during the dissociation of the related deprotonated molecules). The ESI(-)-MS records also revealed notable differences between the reaction conducted at pH 5 and 8, i.e. at slightly acid or basic media, respectively.

Fabrication of Organic Thin Films for Copper Diffusion Barrier Layers Using Molecular Layer Deposition

AbstractDevice scaling predicts that copper barrier layers of under 3 nm in thickness will soon be needed in back-end processing for integrated circuits, motivating the development of new barrier layer materials. In this work, nanoscale organic thin films for use as possible copper diffusion barrier layers are deposited by molecular layer deposition (MLD) utilizing a series of self-limiting reactions of organic molecules. MLD can be used to tailor film properties to optimize desirable barrier properties, including density, copper surface adhesion, thermal stability, and low copper diffusion. Three systems are examined as copper diffusion barriers, a polyurea film deposited by the reaction of 1,4-phenylene diisocyanate (PDIC) and ethylenediamine (ED), a polyurea film with a sulfide-modified backbone, and a polythiourea films using a modified coupling chemistry. Following deposition of the MLD films, copper is sputter deposited. The copper diffusion barrier properties of the film are tested through adhesion and annealing tests, including 4-point bend testing and TEM imaging to examine the level of copper penetration. The promise and challenges of MLD-formed organic copper diffusion barriers will be discussed.

Luminescence for Grafting Organic Molecules on γ-Alumina via the Reaction of Alumina and Organic Compounds

Scheme 1. Reaction of organic molecules with γ-alumina under microwave irradiation or reflux. The grafting of organic moieties onto the surface of inorganic compounds is an important in numerous applications such as organic synthesis on solid phases and the modification of the surface properties of solids. Alumina is one of the most interesting inorganic materials for grafting organic moieties. Alumina has pore structure for ease diffusion of organic compounds and excellent properties as high melting point, low electrical conductivity, thermal and chemical stability and oxidation and corrosion resistance. However there are not many reports on preparing methods and optical properties of organic-alumina hybrid materials. Here we report the preparation of hybrid material grafting organic moieties on alumina and investigation of their photoluminescence (PL) properties. Although several reactions of phosphoric or phosphonic derivatives with alumina have been reported, the other organic functional groups do not have been used for grafting organic moieties on alumina. We have prepared the hybrid materials which used to graft organic moieties on alumina through the microwave irradiation or reflux, and investigated their PL properties. To prepare the hybrid materials with organic moieties on alumina, the readily available commercial γ-alumina 2 (surface area is 132 m/g) is used, and benzoyl chloride (1a), hexanoyl chloride (1b), heptyl bromide (1c), naphthoic acid (1d) were used as organic compounds. Benzoylalumina hybrid material 3aM was prepared from the reaction of benzoyl chloride (1a) and γ-alumina 2 without solvent in microwave irradiation for 15 minutes. On the other hand, benzoylalumina hybrid material 3aR was prepared in the reflux condition for 12 hours. After cooling to room temperature, the crude products were washed with dichloromethane (3 × 50 mL), ethylacetate (3 × 50 mL), hexane (3 × 50 mL), and methanol (3 × 50 mL). Hexanoylalumina 3bM, 3bR and heptylalumina 3cM, 3cR were prepared using hexanoyl chloride (1b) and heptyl bromide (1c) with γ-alumina 2 on microwave irradiation or reflux conditions. The toluene solution of naphthoic acid (1d) and γalumina 2 was irradiated by microwave at 150 W for 15 minutes and same solution was refluxed for 12 hours to get naphthoicalumina 3dM and 3dR. Each washed material, 3aM, 3aR, 3bM, 3bR, 3cM, 3cR, 3dM, 3dR was dried in vacuum as well as in oven, each for 24 hours to remove the organic solvent in porous site (Scheme 1) and (Table 1). Each organic grafting alumina was characterized by elemental analysis and IR. Graft densities (δ) of the covalently attached organic molecules (1a-d) in γ-alumina 2 were determined by carbon elemental analysis (eq 1), where gE is the C content, ME is the molecular weight of C, Z is the number of C atoms per organic group.

Periodic mesoporous silica-immobilized palladium(II) complex as an effective and reusable catalyst for water-medium carbon–carbon coupling reactions

Ethyl-bridged periodic mesoporous organosilicas (PMOs) functionalized with diphenylphosphino (PPh 2) ligands were synthesized by one-step evaporation-induced self-assembly (EISA), which were used as a support to immobilize Pd(II) organometallic catalyst by coordination reaction. The as-prepared Pd(II)–PPh 2–PMO(Et) exhibited high activity in water-medium C–C coupling reactions and could be used repetitively. The high activity could be attributed to the high dispersion of Pd(II) active sites and ordered mesopore channels which effectively diminished the steric hindrance and thus, diffusion limit. Meanwhile, the ethyl-fragments and the PPh 2-ligands in the support wall could synergic enhance surface hydrophobicity, which promoted the adsorption for organic reactant molecules.

Conformationally Complex π‐Conjugated Molecular and Polymeric Materials: New Challenges for Organic Synthesis

Conformational influences profoundly impact the performance of organic electronic materials and the reactivity of organic molecules. We recently found that the expected former consideration was uniquely accompanied by the latter. This report describes a surprisingly regioselective bromination that suggests the general use of conformation as a protecting group during complex molecule synthesis.

Organic Chemistry: Synthesis and Study of Reactive Intermediates Found in Interstellar Space

This Today’s Science for Tomorrow’s Scientists (TSTS) tutorial introduces current scientific research to synthesize and study the structure, photochemistry, and spectroscopy of reactive organic molecules, many of which are thought to play a role in the chemistry of interstellar space.

Adsorption and reaction of organic molecules on solid surfaces – ab-initio density functional investigations

The state-of-the-art of density-functional studies of the adsorption and reaction of organic molecules on solid surfaces is illustrated at three examples chosen to cover different aspects of the field. The first concerns the adsorption and subsequent hydrogenation of benzene on nickel surfaces. Here the essential points are the description of the adsorption geometry and the determination of the barriers and heats of reaction for the hydrogenation to cyclohexene. It is shown that although in the gas-phase, the energy differences between the different cyclic hydrocarbon species are correctly described only at the level of a meta-generalized-gradient-approximation (meta-GGA) to the exchange-correlation functional (providing an improved description of electron localization in double bonds), for the adsorbed species a conventional GGA leads to accurate geometries and energetics. The second example serves to study the interplay between surface reconstruction and the molecular geometry of the adsorbate. It is demonstrated that the buckling of the Si–Si dimers in the Si(100) surface (and the associated charging of the surface Si atoms) has a decisive influence on the energetically most favorable adsorption configuration of acrylonitrile, based on the resonant form of the molecule with cumulative C=C and C=N double bonds. As the formation of the energetically most favorable configuration involves a complex rearrangement of the adsorbate, it is argued that kinetic effects are also essential for interpreting the experimental information. The third case study describes the Beckmann rearrangement of cyclohexanone oxime to ɛ-caprolactam catalyzed by an acid zeolite. It is shown that, in combination with harmonic transition-state theory, the DFT calculations allow to uniquely identify Bronsted acid sites as the catalytically active center. Finally we discuss briefly the current status of the implementation of the hierarchy of DFT functionals and their application to the interaction between molecules and solids (with particular reference to the performance of hybrid functionals) and attempts to include entropic effects in the ab-initio modeling of catalyzed molecular reactions.

Study of the Influence of Supramolecular Structures of Glycyrrhizic Acid on the Reactivity of Organic Molecules by 1H NMR and CIDNP

Study of the Influence of Supramolecular Structures of Glycyrrhizic Acid on the Reactivity of Organic Molecules by 1H NMR and CIDNP