Mostafa Baghbanzadeh

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions

Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate–thioester exchange, thiolate–disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov–Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving chemical systems.

Odd–Even Effects in Charge Transport across n-Alkanethiolate-Based SAMs

This paper compares rates of charge transport across self-assembled monolayers (SAMs) of n-alkanethiolates having odd and even numbers of carbon atoms (nodd and neven) using junctions with the structure M(TS)/SAM//Ga2O3/EGaIn (M = Au or Ag). Measurements of current density, J(V), across SAMs of n-alkanethiolates on Au(TS) and Ag(TS) demonstrated a statistically significant odd-even effect on Au(TS), but not on Ag(TS), that could be detected using this technique. Statistical analysis showed the values of tunneling current density across SAMs of n-alkanethiolates on Au(TS) with nodd and neven belonging to two separate sets, and while there is a significant difference between the values of injection current density, J0, for these two series (log|J0Au,even| = 4.0 ± 0.3 and log|J0Au,odd| = 4.5 ± 0.3), the values of tunneling decay constant, β, for nodd and neven alkyl chains are indistinguishable (βAu,even = 0.73 ± 0.02 Å(-1), and βAu,odd= 0.74 ± 0.02 Å(-1)). A comparison of electrical characteristics across junctions of n-alkanethiolate SAMs on gold and silver electrodes yields indistinguishable values of β and J0 and indicates that a change that substantially alters the tilt angle of the alkyl chain (and, therefore, the thickness of the SAM) has no influence on the injection current density across SAMs of n-alkanethiolates.

Characterizing the metal-SAM interface in tunneling junctions.

This paper investigates the influence of the interface between a gold or silver metal electrode and an n-alkyl SAM (supported on that electrode) on the rate of charge transport across junctions with structure Met(Au or Ag)(TS)/A(CH2)nH//Ga2O3/EGaIn by comparing measurements of current density, J(V), for Met/AR = Au/thiolate (Au/SR), Ag/thiolate (Ag/SR), Ag/carboxylate (Ag/O2CR), and Au/acetylene (Au/C≡CR), where R is an n-alkyl group. Values of J0 and β (from the Simmons equation) were indistinguishable for these four interfaces. Since the anchoring groups, A, have large differences in their physical and electronic properties, the observation that they are indistinguishable in their influence on the injection current, J0 (V = 0.5) indicates that these four Met/A interfaces do not contribute to the shape of the tunneling barrier in a way that influences J(V).

Introducing Ionic and/or Hydrogen Bonds into the SAM//Ga 2 O 3 Top- Interface of Ag TS /S(CH 2 ) n T//Ga 2 O 3 /EGaIn Junctions

Junctions with the structure Ag(TS)/S(CH2)nT//Ga2O3/EGaIn (where S(CH2)nT is a self-assembled monolayer, SAM, of n-alkanethiolate bearing a terminal functional group T) make it possible to examine the response of rates of charge transport by tunneling to changes in the strength of the interaction between T and Ga2O3. Introducing a series of Lewis acidic/basic functional groups (T = -OH, -SH, -CO2H, -CONH2, and -PO3H) at the terminus of the SAM gave values for the tunneling current density, J(V) in A/cm(2), that were indistinguishable (i.e., differed by less than a factor of 3) from the values observed with n-alkanethiolates of equivalent length. The insensitivity of the rate of tunneling to changes in the terminal functional group implies that replacing weak van der Waals contact interactions with stronger hydrogen- or ionic bonds at the T//Ga2O3 interface does not change the shape (i.e., the height or width) of the tunneling barrier enough to affect rates of charge transport. A comparison of the injection current, J0, for T = -CO2H, and T = -CH2CH3--two groups having similar extended lengths (in Å, or in numbers of non-hydrogen atoms)--suggests that both groups make indistinguishable contributions to the height of the tunneling barrier.

Anomalously Rapid Tunneling: Charge Transport across Self-Assembled Monolayers of Oligo(ethylene glycol)

This paper describes charge transport by tunneling across self-assembled monolayers (SAMs) of thiol-terminated derivatives of oligo(ethylene glycol) (HS(CH2CH2O)nCH3; HS(EG)nCH3); these SAMs are positioned between gold bottom electrodes and Ga2O3/EGaIn top electrodes. Comparison of the attenuation factor (β of the simplified Simmons equation) across these SAMs with the corresponding value obtained with length-matched SAMs of oligophenyls (HS(Ph)nH) and n-alkanethiols (HS(CH2)nH) demonstrates that SAMs of oligo(ethylene glycol) have values of β (β(EG)n = 0.29 ± 0.02 natom-1 and β = 0.24 ± 0.01 Å-1) indistinguishable from values for SAMs of oligophenyls (β(Ph)n = 0.28 ± 0.03 Å-1), and significantly lower than those of SAMs of n-alkanethiolates (β(CH2)n = 0.94 ± 0.02 natom-1 and 0.77 ± 0.03 Å-1). There are two possible origins for this low value of β. The more probable involves hole tunneling by superexchange, which rationalizes the weak dependence of the rate of charge transport on the length of the molecules of HS(EG)nCH3 using interactions among the high-energy, occupied orbitals associated with the lone-pair electrons on oxygen. Based on this mechanism, SAMs of oligo(ethylene glycol)s are good conductors (by hole tunneling) but good insulators (by electron and/or hole drift conduction). This observation suggests SAMs derived from these or electronically similar molecules are a new class of electronic materials. A second but less probable mechanism for this unexpectedly low value of β for SAMs of S(EG)nCH3 rests on the possibility of disorder in the SAM and a systematic discrepancy between different estimates of the thickness of these SAMs.

Charge Tunneling along Short Oligoglycine Chains

This work examines charge transport (CT) through self-assembled monolayers (SAMs) of oligoglycines having an N-terminal cysteine group that anchors the molecule to a gold substrate, and demonstrate that CT is rapid (relative to SAMs of n-alkanethiolates). Comparisons of rates of charge transport-using junctions with the structure Au(TS)/SAM//Ga2O3/EGaIn (across these SAMs of oligoglycines, and across SAMs of a number of structurally and electronically related molecules) established that rates of charge tunneling along SAMs of oligoglycines are comparable to that along SAMs of oligophenyl groups (of comparable length). The mechanism of tunneling in oligoglycines is compatible with superexchange, and involves interactions among high-energy occupied orbitals in multiple, consecutive amide bonds, which may by separated by one to three methylene groups. This mechanistic conclusion is supported by density functional theory (DFT).

The Rate of Charge Tunneling in EGaIn Junctions Is Not Sensitive to Halogen Substituents at the Self-Assembled Monolayer//Ga2O3 Interface

This paper describes experiments that are designed to test the influence of terminal groups incorporating carbon-halogen bonds on the current density (by hole tunneling) across self-assembled monolayer (SAM)-based junctions of the form MTS/S(CH2)9NHCOCH nX3- n//Ga2O3/EGaIn (where M = Ag and Au and X = CH3, F, Cl, Br, I). Within the limits of statistical significance, these rates of tunneling are insensitive to the nature of the terminal group at the interface between the SAM and the Ga2O3. The results are relevant to the origin of an apparent inconsistency in the literature concerning the influence of halogen atoms at the SAM//electrode interface on the tunneling current density.

Nanocatalysis and continuous-flow processing: Towards greener and more sustainable chemistry

C Nanocrystals (NCs) are solution-grown, nanometer-sized, inorganic particles that are stabilized by a Self-Assembled Monolayer (SAM) of surfactants attached to their surface. NCs possess useful properties that are controlled by their composition, size and shape, and the SAM coating ensures that these structures are easy to fabricate and process further into more complex structures. This combination of features makes colloidal NCs attractive and promising building blocks for advanced materials, green chemistry, and specifically in catalysis. Colloidal NCs are potentially able to blend the many advantages of heterogeneous catalysis with the versatility of homogeneous catalysts. This presentation will focus on: (i) Advantages of continuous-flow processing in in-situ preparation of Fe3O4 NCs from a Fe (e.g., FeCl2·4H2O, FeCl3·6H2O, and Fe(OAc)2) precursor using hydrazine hydrate as the reducing agent to catalyze the organic reactions (e.g., reduction of nitroarenes) and (ii) Shape-selective synthesis of TiO2 colloidal NCs and their application in a continuous-flow photocatalytic transformation.P have evolved bioactive metabolites of great complexity and potency, however the compounds found in the wild-type plant representonly a fraction of the genomic capability of the species, If we could only “tell” plants what bioactivity we required from them, this would open a new chapter in plant drug discovery. Naprogenix’ novel technology achieves this by “evolving” plant biosynthesis, via mutation and selection, toward metabolites targeted on specific proteins. This can increase yields of known compounds, or generate active metabolites which are not detectable in the wild-type plant. Proof of concept has used several plant species and several targets, but this example describes the production of inhibitors of the human dopamine transporter (DATa molecular target in Parkinson’s disease) in cell cultures of a native Lobelia species. This plant contains small amounts of lobinaline, a previously uninvestigated inhibitor of the DAT, which would be a conventional lead compound except that it is a complex binitrogenous alkaloid with 5 chiral centers and no known chemical synthesis. However, this complexity makes it an excellent example of the value of target-directed biosynthesis. First, we expressed the human DAT target protein in cells of this species, making them susceptible to a cytotoxin which is accumulated intra cellularly by the DAT. Mutants which are overproducing inhibitors of the DAT now have a survival advantage when exposed to the toxin. About 1/300 gain-of-function mutants survived selection, providing 120 toxin-resistant individual clones. Extracts from 41 of these showed greatly increased levels of DAT inhibition, and 16 of these were overproducing lobinaline. However, the other 25 clones were overproducing other metabolites, 8 of which were not detectable in the wild-type plant. Several of these showed chemical similarity to lobinaline and putatively represent a biosynthetic active compound library. In this way it is possible to tell a plant species to synthesize metabolites with a specific bioactivity and, by selection, the plant cell also does the initial pharmacological screening. Mankind can become the orchestrator of plant biosynthetic evolution rather than its passive beneficiary.T chemical fixation and activation of CO2 by metal complexes may lead to certain devices that can eliminate the CO2 present in the air and hence controlling its concentration and reducing the environmental problems due to the greenhouse effect and global warming. This can be achieved by designing “inexpensive inorganic compounds” that rapidly and effectively catalyze the atmospheric CO2 fixation. In slightly basic solutions, the atmospheric fixation of CO2 by metal complexes, through hydroxo-species, afford the carbonato metal complexes. A number of simple N-donor ligands and multi-dentate Schiff bases containing two or three N-atoms, phenolic and alkoxy groups are to used synthesize a series of 3d(M(II) = Ni, Cu, Zn) and 4f(Ln(III) = lanthanides) complexes. The incorporation of lanthanide (III) ion into the skeleton of3d complexes to produce 3d-4f heteronuclear metal complexes should increase the affinity of the compounds for CO2 fixation into the Ln (III) pocket (Ln3+ ion is a hard Lewis acid which strongly bound to hard Lewis bases; O-donor species such as CO32ion). The carbonato complexes are not only interesting from the structural and geometrical points of view, but alsomay result in the discovery of interesting Single Molecular Magnets (SMM’s) which can be used to increase the memory of the computers. The resulting carbonato-bridged compounds can also be used to prepare some useful organic compounds. Recent developments concerning synthesis and structure characterization of different coordination carbonato-bridged compounds, magnetic properties and their potential applications will be addressed.T global drive towards the reduction of energy consumption, emissions and minimisation of waste are increasingly important and becoming major technological, political and societal issues. A promising approach to address the current challenges is to adopt green chemistry and sustainability during process design, innovation, integration and optimisation. The use of green chemistry and process intensificationin the processing of polymeric, inorganic and composite materials will be described. The emerging of eco-friendly and sustainable non vacuum chemical processing technologies will be presented for the production of nanostructured materials and high value added superthin/thin films and thick coatings. These processes that are not only low cost, less polluting, conserve energy, reduce waste but also increase efficiency and enhance product performance. Case studies leading to sustainable products and increasing profits for a variety of applications, including fine chemicals, clean energy, engineering, and biomedical sectors will be presented.S succinate, a pharmaceutical used in industry is an organic contaminant that has the potential to create environmental toxicity and pollution problems and cause health risks for humans as well as biota. Natural organic matters, such as humic acid, HA in aquatic environments can increase the stability of nanoparticles. In this work, solifenacin succinate in wastewater was removed by a biosorption method using HA-coated TiO2 nanoparticles. The FTIR, EDX and FESEM studies were used to characterize the fabricated nanosorbents. Mathematical adsorption and kinetics models representing the biosorption processes were formulated, supporting the Langmuir isotherm and pseudo-second order rate equation for the adsorption of aqueous solifenacin succinate using batch mode experiments. All parameters influencing the removal efficiency such as: Adsorbent dose, medium pH, initial adsorbate concentration and temperature were considered for optimizing the experimental conditions. Thermodynamic study was carried out to describe the feasibility, thermic and entropic behaviors of the investigated biosorption process. The results showed that the method developed here is very effective for the removal of solifenacin succinate from an aqueous environment.C is one of the most powerful tools of green chemistry, enabling reactions with lower energy consumption and providing new pathways for bond formation. Catalytic C-H functionalizations, in particular, are powerful methodologies for installing functional groups in previously non-functionalized positions of a molecule and the use of catalyst directing groups has enabled a wide variety of exciting bond formations with remarkable selectivities and broad applicability. One of the greatest current challenges in this research area is how to catalyze analogous C-H functionalization reactivity without the presence of catalyst directing groups. Such transformations often suffer from the lack of a strong catalyst pre-coordination, which can lead to lower reactivities. The research described in this presentation will showcase basic principles of catalyst and methodology design to achieve non-directed C-H functionalizations and provide insights into reactivity and selectivity-determining factors for the C-H aminations of arenes and the alpha-C H oxidation of tertiary amines.P synthesis has received significant recent research interest in the context of ideal synthesis and green sustainable chemistry. In general, organolithium species react with electrophilic functional groups very rapidly, and therefore such functional groups should be protected before an organolithium reaction, if they are not involved in the desired transformation. If organolithium chemistry could be free from such a limitation, its power would be greatly enhanced. A flow microreactor enables such protecting-group-free organolithium reactions by choosing the appropriate residence time and the reaction temperature. Organolithium species bearing alkoxycarbonyl, nitro, and ketone carbonyl groups can be generated and reacted with various electrophiles using a flow-microreactor system. In addition, asymmetric carbolithiation of conjugate enzymes can be also achieved without the epimerization of a configurationally unstable chiral organolithium intermediate based on precise control of the residence time using a flow microreactor. In this presentation, we report that a flow microreactor system enables the generation of various unstable organolithium compounds.D green catalysts is the key for the development of next-generation technologies to convert biomass molecules into liquid fuels or other value-added chemicals. Recently, a few hydrogenation catalysts have been developed to effectively drive biomass conversions. However, designing hydrogenation catalysts that can work under mild conditions such as low pressure, low temperature, and green solvent remains a challenge. To provide the insights for designing greener hydrogenation catalysts, we explored the thermodynamics conditions (e.g., temperature, pressure, and solvents) for various hydrogenation or hydrogenolysis reaction based on biomass model compounds, by combining the Ab initio quantum chemistry calculations and experimental explorations. Our results show that thermodynamically it is indeed possible to design greener catalysts (e.g., robust and economic catalysts that work under mild conditions) for converting biomass molecules into value-added chemicals. In addition, we showed that optimal hydrogenation catalysts could be sought under the guidance of inverse design methods.We report densities, ijk ρ and speeds of sound, ijk u of 1-ethyl-3-methylimidazolium tetrafluoroborate (i) + water (j) + formamide or N,N- dimethylformamide (k) ternary mixtures over entire composition range at 293.15, 298.15, 303.15, 308.15 K. The heat capacities, Cpof 1-ethyl-3-methylimidazolium tetrafluoroborate, water, formamideand N,N- dimethylformamide have also been measured at 293.15, 298.15, 303.15, 308.15 K using micro differential scanning calorimeter (Model -µDSC 7 Evo). The measured ijk ρ and ijk u data have been utilized to determine their excess molar volumes, E ijk V andThe presence of bark in wood can constitute a serious limitation for the bioconversion of forest residues into bioethanol, especially due to the presence of high content of extractives, which may inhibit ethanol fermentation. However, a perfectly debarked wood chip may not represent an economical source of carbohydrates for industrial applications. An option is to utilise bark as a source of renewable energy and chemicals, within a biorefinery platform. In this study, enzymatic hydrolysis and bioethanol fermentation of Douglas-fir bark were studied before and after organosolv and diluted acid pre-treatments performed at 150°C and 180°C. The recovery of valuable platforms molecules was also determined after pre-treatment. Results showed that an organosolv-free acid pre-treatment performed at 150°C gave the best results in terms of platforms molecules recovery (40% w/w) and bioethanol yield (2 g.100g-1 total solids). However, the low glucose and ethanol yields obtained (6% and 16% of the theoretical values, respectively) confirmed that enzymatic hydrolysis remains the limiting step of bioethanol fermentation from bark. Interestingly, ethanol was produced without inhibition of fermentation from the untreated and pretreated substrates.W have studied in the last 15 years the efficiency of oxime-derived palladacycles as pre-catalysts in carbon-carbon forming reactions such as, Heck, Suzuki, Stille, Hiyama, Ullmann, Sonogashira and Glaser reactions by in situ generation of palladium nanoparticles. Interestingly, they exhibit increasing catalytic activity when water is used as solvent due to the formation of threeand four-palladium atom clusters as has been recently found out by Corma and col. In this talk recent challenge applications of these palladacycles working in aqueous media will be presented. Matsuda-Heck reactions have been performed efficiently in water at rt. In the case of the Suzuki-Miyaura reaction, deactivated aryl chlorides and imidazolylsulfonates can be cross-coupled with boronic acids or potassium trifluoroborates using water as solvent. The copper-free Sonogashira reaction has been also performed with deactivated aryl chlorides and with aryl imidazolylsulfonates under copper-free conditions using water as solvent. The head to head dimerization of terminal alkynes in water allows the steroselective preparation of (E)-1, 4-enynes in the presence of an imidazolinium salt.