bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of Photosynthetic Electron Transfer from the Reaction Center to Electron Carriers of Photosystem II Studied by Fluorescence Induction
Authors: Malkin Shmuel
Published: November 2013

The relationships between the primary electron acceptor (Q) and the secondary pool (A1) are examined from fluorescence induction curves, at various illumination times and relaxation dark times. The fast‐phase in the fluorescence rise curve, obtained after insufficient relaxation time, indicates the occurrence of “unconnected” Q, i.e. the reaction between Q− and A1 is blocked. Various treatments bring about similar disconnection: high pH, ethylene glycol, low temperature (all reversible), trypsin and reduction of A1 by dithionite. All these treatments are similar to DCMU treatment. A scheme is suggested in which Q is mostly unconnected in the dark and becomes immediately connected as it is reduced by light. The above treatments inhibit the reconnection reaction in the light. The thermodynamic equilibrium between the Q populations that can or cannot be reconnected was analyzed from the fluorescence curves at various temperatures. The connection‐disconnection switching reaction is probably controlled by conformational changes of an associated protein. This scheme explains the difference of apparent redox equilibria of Q and A in the light or in the dark, as well as the IDP wave in the fluorescence induction of intact cells.
Energy and Electron Transfer in Photosynthetic Units
Authors: Mauzerall David
Published: November 2013

It is proposed that energy transfer by electron exchange is a likely alternative to that by electric‐dipole coupling for the case of chlorophyll and carotenoid proteins of the antennaes of photosynthetic systems. Biliproteins fit the criteria expected for the traditional Förster transfer. The criteria are fluorescence yield and lifetime of the pigments and structure and polarizability of their environment.
The Effect of Ring Strain on Ortho‐Annelated Aromatic Molecules
Authors: Thummel Randolph P.
Published: November 2013

This paper examines the effect of fusing a small carbocyclic ring onto the ortho positions of an aromatic nucleus. Benzene derivatives are considered to which have been fused one, two or three small rings. The effect of varying the size and orientation of the rings is discussed with respect to changes in the σ‐ and π‐bonding networks, the geometry of these molecules and their chemical reactivity. Other aromatic nuclei, such as pyridine, thiophene, naphthalene and the tropylium ion, are also described. Variations in physical properties appear to be best explained by a rehybridization theory which functions in the plane of the system. Perturbations of the π‐bonding framework are better manifested by changes in chemical reactivity.
cis‐ and trans‐Tris‐[2.2.2]‐σ‐Homobenzenes
Authors: McMullen Gabrielle , Lutterbeck Monika , Fritz Hans , Prinzbach Horst , Krüger Carl
Published: November 2013

The cis‐ and trans‐dicyano‐tris[2.2.2]‐σ‐homobenzenes 9/10 have been synthesized and characterized by spectroscopic methods and X‐ray structural analyses. From the relative ease of their transformations and from the products of their vapour phase pyrolyses, it is concluded that a pericyclic mechanism is no longer operative.
1,2‐Bridged Quadricyclanes
Authors: Hart Harold , Peng Cheng‐Tai
Published: November 2013

The readily available benzodihydropentalene 6 and dimethyl acetylene‐dicarboxylate react to give norbornadiene diester 8, with a three‐carbon bridge from C1 to C2. Inrradiation of 8 gives the corresponding C1‐C2 bridged quadricyclane diester 9, a new ring system. Diester 9 is quite stable, reverting to 8 with a t1/2 of 30 min at 170°C. The corresponding diacid 11, also prepared, reverts to its norbornadiene precursor at a considerably lower temperature, possibly as a consequence of acid catalysis.
On the Effect of Electron Relay Redox Potential on Electron Transfer Reactions in a Water Photoreduction Model System
Authors: Amouyal Edmond , Zidler Bertrand
Published: November 2013

The influence of electron relay redox potential (E1/2) on the electron‐transfer reactions occurring in the photo‐induced hydrogen generation from water has been investigated using the Ru(bipy)2+3/MV2+/EDTA/colloidal Pt model system. Quenching rate constants kq for electron transfer quenching of Ru(bipy)2+*3 by a series of 2,2′‐ and 4,4′‐bipyridinium ions and by a series of phenanthroline ions having different redox potential E1/2 have been determined by laser flash spectroscopy in deaerated aqueous solutions at pH 5. The rate constants kb of the back electron transfer following the quenching reaction have been obtained for five bipyridinium ions under the same experimental conditions. Our results show that: (1) for the same E1/2, the quencher molecular structure of the two homogeneous series does not affect kq significantly; (2) for the two series, kq increases with increasing E1/2 up to a value which is close to the diffusion‐controlled limit. The same correlation between kq and E1/2 is obtained for the two series. Such a correlation is satisfactorily interpreted in the frame of existing theories describing electron‐transfer reactions, particularly with the Rehm‐Weller treatment, provided that an intrinsic barrier ΔG*(0) = 5.2 kcal. M−1 is used; (3) kb is close to the diffusion‐controlled limit for E1/2 comprised between ‐ 0.33 and ‐ 0.65 V (vs NHE); (4) a correlation between H2 production rates and E1/2 is suggested, and a maximum H2 production is observed for E1/2 ≃ −0.45 V (vs. NHE) corresponding to compounds 1 and 14.
Solar Photoelectrochemical Cells Based on Photoinduced Hydrogen Atom Abstraction Reactions in Solution
Authors: Chandrasekaran K. , Whitten David G.
Published: November 2013

Solar irradiation of a two‐component photoelectrochemical cell containing aqueous alcohol (2‐propanol, ethanol or methanol) solutions of a “mediator,” such as methyl viologen or diquat, and benzophenone in the photoanode compartment and aqueous acid in the cathode leads to the generation of moderately stable photocurrents in the 400–1500 μA range. Similar results are obtained, but with generally lower currents, when benzophenone‐free solutions are irradiated. The reactions in the photoanode compartment all originate with an excited state hydrogen atom abstraction from the alcohol to generate two reducing free radicals; the ketyl radicals formed are rapidly oxidized by the mediator to give an electrochemically active but relatively stable semi‐reduced mediator species which is oxidized at the electrode surface. The basic photochemical and subsequent dark reactions are reasonably efficient and well‐understood; the overall peak efficiencies of the present cell system are relatively low (1–2%) reflecting the low fraction of the solar spectrum absorbed by the photochemically reactive reagents. The net chemical change occurring is endothermic and the products are in principle readily recyclable. The solutions are photochromic due to transient generation of the semi‐reduced mediator. A primary advantage of this system is that the use of a mediator to avert radical combination or other energy‐wasting processes provides the system with a directionality analogous to that obtained via band bending in semiconductors.
Modified P‐Type Si Photocathodes for Photochemical Hydrogen Generation: Surface Texturing, Molecular Derivatizing Reagents, and Noble Metal Catalysts for Multi‐Electron Processes
Authors: Bruce James A. , Wrighton Mark S.
Published: November 2013

Modification of single‐crystal (100), p‐type Si photocathode material to improve photoelectrochemical H2 generation from H2O is reported. The (100) surface has been first modified by chemical etching to reveal pyramids (1–5 μM in height) having (111) sides to give a “textured” surface having lower specular reflection losses than polished (100) or (111) single‐crystal Si. Second, the textured surface has been derivatized with {N,Nî‐bis‐[3‐trimethoxysilyl)propyl]‐4,4′‐bipyridinium}dibromide, I, to yield large coverages (0.5–5 × 10−8 mol/cm2) of redox centers [PQ2+/+]surf in a polysiloxane network. The surface redox polymer is a fast electron acceptor and can be reduced photoelectrochemically, [PQ2+]surf → [PQ+]surf, by ≥ Eg = 1.1 eV light at ∼0.0 to ‐ 0.1 V vs. SCE in aqueous electrolyte solution, or ∼ 500 mV more positive than on a reversible electrode such as Pt. Third, the surface polymer is then further modified by depositing Pd(O) or Pt(O) onto the outermost surface to catalyze the reaction 2[PQ+]surf + 2H+ → 2[PQ2+]surf + H2. Energy conversion efficiency from the modified photocathodes for 632.8 nm (∼ 10 mW/cm2) light‐driven H2 evolution is ∼ 5% at pH = 4, representing significant improvement compared to polished, (100) or (111) p‐type Si‐based photoelectrochemical devices where the surface of the p‐type Si is not modified.
A Study of Lineshapes in Selective Adsorption in Atom—Surface Scattering
Authors: Celli V. , Evans D.
Published: November 2013

Calculations are presented involving the scattering of low energy4 He atoms from LiF(001), and compared with experiment. Resonant scattering theory is briefly reviewed, and a prescription for determining the shapes and signatures of resonant features is presented. Inelastic effects are included by means of a Debye—Waller scaling.
Quantum‐Mechanical Treatments of Rotationally Inelastic Molecule‐Surface Scattering
Authors: Kouri D. J. , Gerber R. B.
Published: November 2013

Quantum‐mechanical approximation methods and calculations for rotational transitions in molecule‐surface collisions are reviewed. The methods are analyzed with regard to predictions of several observable effects: (1) Large ΔJ (rotational quantum number) transitions, and rotational rainbow scattering. (2) The relation between rotational and diffractive transitions. (3) Scaling properties of the rotationally‐inelastic scattering amplitudes. (4) Trapping and resonances induced by rotational‐translational energy transfer. The methods examined with regard to some of these effects include: coupled‐channel calculations; the Sudden approximation with regard to both the rotational and the diffractive transitions, and the hard corrugated wall model. It is concluded that whilst available methods provide a qualitative description of the effects mentioned, quantitative treatment of real systems remains an open problem. The main difficulties in formulating a satisfactory quantitative model are examined. Finally, the article presents new results on molecular reorientation processes (ΔMJ transitions) in molecule‐surface collisions. It is shown, using the Sudden approximation, that molecular reorientation probabilities should reflect sensitively on surface structural corrugation.
The Auger Parameter of Adsorbed Xenon as a Probe of Surface Polarizability
Authors: Stair P. C.
Published: November 2013

The change in Auger parameter, α (α = Auger kinetic energy minus photoelectron kinetic energy from core levels) between gas phase and adsorbed phase xenon provides an unambiguous measure of final state electronic relaxation in the surface toward the xenon ion. For many surfaces this relaxation is purely electronic polarization in the surface so that the Auger parameter provides a measure of the surface polarizability. Moreover, the Auger parameter for adsorbed xenon can be related to the relaxation energy in core level photoemission with high accuracy. Measurement of the xenon Auger parameter and its sensitivity to surface dielectric properties is illustrated by experiments on a series of oxygen treated Mo(100) surfaces.
A Theoretical Discrimination of Active Regions of Molecules in Chemical Reactions
Authors: Fujimoto Hiroshi , Koga Nobuaki , Endo Masayuki , Hataue Itaru , Fukui Kenichi
Published: November 2013

Pairwise orbital transformations in reagents and in reactants indicate which parts of molecules participate actively in chemical reactions. Similar orbitals are obtained for different molecules, demonstrating common features of the relevant reaction, and different orbitals are obtained for the same molecule, reflecting multiple types of reactivities of organic compounds. The possibility of analyzing the roles of orbital interactions along a reaction pathway is demonstrated.
Application of Molecular Orbital‐Valence Bond Theory to Geometric Isomerism
Authors: Epiotis Nicolaos D. , Larson J. R.
Published: November 2013

The Molecular Orbital‐Valence Bond (MOVB) method is briefly outlined and it is subsequently applied to the problem of geometric isomerism of molecules having eight and ten sigma valence electrons such as bent HC≡CH and HN=≡NH. It is shown that orbital symmetry dictates a trans bending tendency for HCCH and in the hypothetical absence of nonbonded repulsion, a cis geometry for XNNY and XOOY.
Strain Energies of Small Ring Alkenes
Authors: Wiberg Kenneth B. , Bonneville George , Dempsey Richard
Published: November 2013

The energies of hydrogenation of a series of alkenes have been calculated using both the 4‐31G and 6‐31G* basis sets. The inclusion of polarization functions leads to only a small change in calculated energy for simple alkenes but a large change is found with the more highly strained compounds. The calculated enthalpies of hydrogenation have been compared with experimental values and show that the error in the calculation is essentially constant (6 ± 2 kcal/mol). This makes it possible to estimate the enthalpies of formation and strain energies of the small ring alkenes for which experimental data are not available. The calculated structures of the compounds also are discussed.
Ab Initio CI Calculations of the Energy Difference between Trimethylenemethane and Butadiene
Authors: Feller David , Davidson Ernest R. , Borden Weston Thatcher
Published: November 2013

Ab initio configuration interaction (CI) calculations have been carried out in order to determine the energy difference between 3A î2 trimethylenemethane (TMM) and 1Ag butadiene. The pi CI value of 38.3 kcal/mol is very similar to the CI values obtained when excitations of the sigma electrons are permitted. This finding suggests that correlation effects involving sigma orbitals make at most a small contribution to the energy differences between non‐Kekulé hydrocarbon diradicals and their closed‐shell isomers. Possible complications in the experimental measurement of this energy difference are discussed. It is pointed out that methylenecyclopropane might be formed in attempts to deprotonate the 2‐methallyl cation, without the involvement of TMM. From the experimental heats of formation of methylenecyclopropane and butadiene, an energy difference of 14–16 kcal/mol between 3A î2 TMM and methylenecyclopropane is estimated. This is in excellent agreement with a previous energy difference obtained by direct calculation.
Electrophilic Attack on Tetrahedral Metal Complexes
Authors: Silvestre Jerome , Albright Thomas A.
Published: November 2013

A number of ML4Lî complexes exist where Lî contains an electropositive atom connected to the transition metal. The structures of these compounds are very distorted; they do not correspond to a trigonal bipyramid, square pyramid or somewhere between these two extremes. An electronic rationale for these alternative structures is presented with the aid of molecular orbital calculations of the extended Hückel type. It is shown that in these compounds the M‐Lî bond is quite ionic in the sense of Lî+ML−4. The deformation is then due, in part, to the tendency of ML−4 to adopt a tetrahedral arrangement. Furthermore, it is shown that an electrophile (Lî+) may attack a three‐fold face, two‐fold edge, or somewhere intermediate at the tetrahedral ML−4 group yielding an alternative structure for these five‐coordinate complexes.
Circular Dichroism of Phytochromobilin and Related Compounds
Authors: Thümmler F. , Rüdiger W.
Published: November 2013

Absorption and circular dichroism (CD) spectra are recorded for partially denatured phytochrome, Pfr chromopeptide as well as (ZZZ)‐ and (ZZE)‐configurated phycocyanin chromopeptides. Solvent induced circular dichroism (SICD) spectra are included for (ZZZ)‐ and (ZZE)‐octaethylbilindione. Irradiation of Pr in 4 M urea yields a bleached chromophore with weak absorption and Δϵ values. On acidification in the dark it shows the known absorption and CD spectra of the Pfr chromophore. Subsequent irradiation of the acidified solution leads to absorption and CD spectra of the Pr chromophore. The red shift of absorption and CD bands obtained during this Pfr ŕ Pr chromophore transformation is observed in both absorption and CD or SICD spectra of Pfr peptides, (E)‐configurated phycocyanin peptides and (E)‐configurated octaethylbilindione during irradiation in acid solution. The shift may be coupled with inversion of the sign of CD or SICD bands, e.g., in fraction 5, phycocyanin peptide and octaethylbilindione. Several fractions of phycocyanin peptides with almost identical absorption spectra show significant differences in their CD spectra. Differences are also found in the pH dependency of CD or SICD spectra of the various fractions of phycocyanin peptides and of octaethylbilindione.
On the Orientation Mechanism of Small Molecules in Liquid‐Crystalline Environments
Authors: Snijders J. G. , De Langea C. A. , Burnell E. E.
Published: November 2013

A general molecular theory for the description of the orientation of small molecules in anisotropic environments is presented. Assuming a second‐order tensorial interaction between some solute property βij and the anisotropy in a liquid‐crystal “field” Fij rigid and non‐rigid contributions to the dipolar and quadrupolar couplings observable by NMR are evaluated. The behaviour of the solutes hydrogen, methane and their deuterated analogues in nematic phases can be described by special cases of this general theory and excellent agreement between observed and calculated anisotropic couplings is obtained. The present results suggest that the coupling between the solute molecular quadrupole moment and the anisotropy in the liquid‐crystal electric field gradient plays a significant role in the orienting process in the case of hydrogen.
The Orientational Ordering of Some Non‐cylindrically Symmetric Solutes in Nematic Solvents
Authors: Catalano D. , Forte C. , Veracini C. A. , Zannoni C.
Published: November 2013

The problem of obtaining information on the molecular properties of non‐cylindrically symmetric solute molcules in liquid crystals is examined. Nitrobenzene, tetrafluoro‐p‐benzoquinone and pyridine have been investigated in various nematic solvents at a series of temperatures using proton, fluorine and deuterium NMR where relevant. The ordering matrices for these essentially rigid molecules have been determined as a function of temperature. The predictions of a mean field theory for solutes deviating from cylindrical symmetry are considered. The relative importance of polarizability, steric forces and specific interactions in determining orientational ordering is discussed.
Deuterium NMR Studies of Discotic Liquid Crystals
Authors: Goldfarb D. , Luz Z. , Zimmermann H.
Published: November 2013

Deuterium Nuclear Magnetic Resonance studies in discotic mesophases are reviewed. The studies include NMR measurements on neat compounds as well as deuterated probe molecules dissolved in the mesophase. The discotic compounds discussed include derivatives of benzene, triphenylene and truxene which exhibit a variety of mesophases. Particular emphasis is placed on comparing axially symmetric and biaxial phases, and on analyzing the various orientational order parameters required to characterize their NMR spectra. The conformation of side chains as derived from the deuterium resonance of the methylene and methyl deuterons is also reviewed. Finally, the properties of discotic mesophases as ordering solvents for solute probe molecules are discussed.
The Study of Bilayers in the Micelles of Lyotropic Nematic Mesophases
Authors: Reeves Leonard W.
Published: November 2013

Nematic micellar liquid crystals based on rod and disk shaped bilayers can be prepared with both signs of the magnetic susceptibility anisotropy giving 4 subclassifications, II DM, II CM, I DM and ICM. These bilayer systems, because they spontaneously align in magnetic fields, are especially useful as media for the study of the bilayer chemistry of the constituent micelles. The deuterium magnetic resonance of specific and perdeuterated hydrocarbon chains yield degree of order profiles, which contain information about whole chain movements and segmental motion within the chains. The degree of order ratios within a given chain for different segments only contain information about the segmental trans / gauche rotations in the carbon–carbon bonds. The order profile, in ratio form, can be used as a discriminating tool for detecting physical and chemical changes in the bilayers. Solubilisation of solutes in the bilayers can be studied either from the effect on motions in the host surfactants or directly in the solutes themselves. The disk‐micelle bilayers do not differ detectably from those of multi‐lamellar phases in thermodynamic equilibrium. Changes in trans / gauche equilibria in the chains can explain the accommodation of single chain amphiphiles to a host bilayer thickness in terms of changes in the probability of isolated gauche rotations near the non‐polar tail. Acid/base equilibria of guest amphiphiles may be investigated. In the particular case of an optically active guest, the non‐equivalence of the αCD2 group may be titrated because the non‐equivalence in quadrupole splitting is a function of the pH of the water used to prepare the mesophase. The use of α,ω amphiphiles as guests in the mesophase bilayer is instructive in revealing the presence of U‐shaped and spanning conformations of the intervening hyrocarbon chain. For short chain α,ω amphiphiles, the constraint angle effect on segmental motions is a function of the chemical nature of the bilayer matrix and the pH of the water.
Concerning the Radical Character of Superoxide. The H—O Bond Energy of HO−2
Authors: Liebman Joel F. , Valentine Joan S.
Published: November 2013

The strength of the H‐O bond in H−O2 should be a good indicator of the chemical reactivity of superoxide, O−2, as a hydrogen atom abstractor. This quantity can be calculated if the electron affinity of HO2 is known. A recent experimental determination of the electron affinity of HO2 [V. M. Bierbaum, R. J. Schmitt and C. H. DePuy, J. Am. Chem. Soc., 103, 6262–6263 (1981)] gave that value as 27.4 ± 0.2 kcal mol−1. The H‐O bond energy of HO−−2 can then be calculated from that value to be approximately 66 kcal mol−1. Various theoretical methods may also be used to approximate the value of the electron affinity of HO2. These methods generally give values in accord with the experimental result. Based on the low H—O bond energy of 66 kcal mol−1 for HO−2, superoxide is expected to be relatively unreactive, comparable to iodine atoms but less reactive than bromine atoms or HO2 and much less reactive than chlorine atoms or hydroxyl radicals. Based on our analysis, we predict that superoxide can only react as a hydrogen atom abstractor with substrates that contain relatively weak bonds to hydrogen such as hydroxylamine or hydroquinones.
H2O2‐Diffusion Through Liposomes
Authors: Frimer Aryeh A. , Forman Arthur , Borg Donald C.
Published: November 2013

The toxicity of H2O2 suggests that it readily diffuses through cell membranes. The present paper demonstrates via a chromogenic peroxidase reaction that H2O2 can cross the lipid bilayer membrane without affecting the cell wall's integrity. In this demonstration, the chromogen ABTS was encapsulated with horseradish peroxidase into ovolecithin multilamellar liposomes. Upon the addition of dilute H2O2, the color was generated exclusively within the intact liposomes. Related results were observed with the AAP/DHBS chromogenic couple; however, this system is complicated by the small holes created by the phenol DHBS in the liposomal wall.
Reactions of Alkoxy Radicals in Aqueous Solutions
Authors: Bors Wolf , Tait David , Michel Christa , Saran Manfred , Erben‐Russ Michael
Published: November 2013

The kinetic and mechanistic properties of alkoxy radicals in organic solvents are briefly reviewed. Owing to the scarcity of such data in aqueous solutions and since reactions at the membrane/water interface may be also biologically important, we have studied the reactivity of these radicals in water and the results of our investigations are reported. Alkoxy radicals were generated by photolytic or radiolytic cleavage of peroxide precursors (tert‐butyl hydroperoxide and di‐tert‐butyl peroxide as well as hydroperoxides of polyunsaturated fatty acids). A quantitative correlation between the structure of various substances, in particular phenolic antioxidants, and their activity in inhibiting the alkoxy radical‐induced bleaching of the water‐soluble carotenoid crocin will be discussed. Rate constants for intermolecular reactions of t‐BuO radicals were determined by pulse radiolysis. The diffusion‐controlled reaction with the catechol antioxidant nordihydroguaiaretic acid demonstrates an effective competition with the very rapid intra molecular β‐fragmentation in water. The results support the view that a considerable amount of alkoxy radicals interact with substrates before they can rearrange intramolecularly.
Trimetalation of a Methallyl‐Thioether and Amine
Authors: Klein Joseph , Weiler Larry
Published: November 2013

Methallylphenyl sulfide 2 undergoes trimetalation on treatment with n‐butyllithium and TMEDA. The trilithiated product gives with chlorotrimethylsilane the trisilyl derivative 3. A similar reaction of the tertiary amine 4 leads to a mixture of the trisilyl 7 and two disilyl derivatives 5 and 6.
Highly Chemoselective Allylic Reductions with Silicon Hydrides and Palladium Catalyst
Authors: Keinan Ehud , Greenspoon Noam
Published: November 2013

Novel reducing systems, comprising various silicon hydrides and a soluble palladium(0) catalyst, allow very mild and chemoselective reductive cleavage of allylic heterosubstituents. Other easily‐reducible functionalities such as ketones, aldehydes and Michael‐acceptors are not affected under these conditions. The relative reactivities of twelve commercially available silanes towards allylic reduction were determined using 1H NMR techniques. Similarly, the role of various reaction parameters such as temperature, solvent and concentration of reactants, and the effect of added water and zinc chloride on the reduction rate have been studied.
Molybdenum Catalyzed Reactions Selectivity in Oxidations with Hydrogen Peroxide and Ammonium Molybdate
Authors: Trost Barry M. , Masuyama Yoshiro
Published: November 2013

Hydrogen peroxide in conjunction with ammonium molybdate effects the epoxidation of olefins, the oxidation of secondary alcohols to ketones, and the oxidation of aldehydes to acids. By controlling pH olefin epoxidation can be suppressed in favor of alcohol oxidation. Secondary alcohols are cleanly oxidized in the presence of primary alcohols. Sterically more hindered alcohols are oxidized more rapidly than less hindered alcohols. The latter rate preference permitted selective conversion of a 17‐hydroxyl group of several steroids into a.ketone in the presence of a 3‐hydroxyl group. The chemoselective oxidation of aldehydes to carboxylic acids is another use of this inexpensive oxidation system. A rate acceleration by addition of the lanthanide salt cerium chloride is noted and attributed to enhanced rates of hydration of the aldehyde. Potential mechanisms are discussed.
Infrared Multiphoton Excitation of Small Molecules
Authors: Bloembergen N. , Burak I. , Mazur E. , Simpson T. B.
Published: November 2013

The collisionless infrared multiphoton excitation of small molecules, OCS, SO2, NO2 and DN3 is discussed. Despite the small absorbance of IR photons by these molecules, evidence for the population of highly excited vibronic levels below the dissociation threshold is obtained. Multiphoton dissociation is observed, as well. The average number of photons absorbed and dissociation yields depend predominately on the laser intensity. High order multiphoton processes couple the ground vibrational level with the quasicontinuum of excited levels below and above the dissociation threshold.
Stark Shifting and Double Resonance Decomposition in IR MPD Pump‐and‐Probe Experiments
Authors: Rayner D. M. , Hackett P. A.
Published: November 2013

We report upon the dynamics of the IR MPD of perfluoroalkyl iodides using visible laser induced multiphoton ionization of free iodine atoms in their ground state (2P3/2) as the probe technique. Stark shifting of an atomic MPI line by an intense infrared field was observed for the first time. The importance of an IR/visible double resonance dissociation through an excited electronic state was demonstrated and monitored through MPI of the excited spin‐orbit state (2P1/2) which is produced uniquely through this pathway. The consequences of the complications caused by these two effects for pump‐and‐probe experiments are discussed and methods to minimise their effect are suggested.
Conformation, Coordination and Ion Selectivity of the Ionophore X206
Authors: van Roey Patrick , Duax William L. , Strong Phyllis D. , David Smith G.
Published: November 2013

The conformation and the cation coordination of the ionophore X206, which selectively transports potassium over sodium, are evaluated in an effort to correlate the structural features of the ionophore with its ion selectivity. For this purpose, the crystal structure of the Na+‐complex of X206 has been determined by X‐ray diffraction and is compared with those of the free acid form of X206, its Ag+‐complex and the K+‐complex of the closely related ionophore alborixin. The ionophore conformation is very similar in all four structures. The carboxylic acid end is essentially invariant, but small changes in torsion angles of up to 26° at the other end of the molecule, combined with differences in the positions of the cations, result in very different coordination geometries for the cations. The conformations of the Ag+‐ and K+‐complexes resemble the free acid conformation more closely than does that of the Na+‐complex. The K+ ion is 8 coordinate while the Ag+ and Na+ ions are 6 and 5 coordinate, respectively. Empirical calculations of the bond strength on the basis of the coordination bond lengths show a stronger binding of K+ than of Na+ which is consistent with the greater selectivity for binding of the former.
Heavy Metal Ionophores: Correlations Among Structural Parameters of Complexed Nonpeptide Polyamino Acids
Authors: Stezowski J. J. , Hoard J. L.
Published: November 2013

Nonpeptide polyamine acid ligands such as ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) are members of a family of nonspecific heavy metal ionophores. Drawing upon the Cambridge Crystallographic Data Files and the results of a crystal structure determination for BaNd(III)DTPA·3H2O, we have looked for correlations between structural parameters and the physical and chemical properties of the metal ions complexed. Good correlations were found for primary metal‐ligand (PMtL) interaction parameters (parameters involving only atoms interacting directly with the metal). Meaningful correlations were also found for secondary metal–ligand (SMtL) interaction parameters and for parameters involving only ligand atoms (L parameters). The correlations observed are interpreted as indicating that (a) contact distances between oxygen atoms in the metal ion coordination sphere are important to the determination of average Mt–O bond distances, (b) the Mt–ethylenediamine rings display considerably less sensitivity to contact distances in the coordination polyhedron than do Mt–amino acid rings and (c) there appears to be a meaningful correlation between the Mt–O bond distance and the amount of single bond character in the associated CO (carboxylate) bond.
Biomimetic Systems for the “Visible” Copper‐Site CuA in Cytochrome c Oxidase
Authors: Toftlund Hans , Becher Jan , Olesen Preben H. , Pedersen Jens Z.
Published: November 2013

Recent work on the structure of the CuA site of cytochrome c oxidase is described. Synthetic model systems containing two thiolate sulfur and two nitrogen donors are reviewed. The electronic model of CuA is discussed and a new dynamic model, which accounts for the atypical ESR properties of this enzyme, is suggested.
Stereoselective Hydrolysis of Amino Acid Esters Catalyzed by β‐Cyclodextrin‐L(or D)‐histidine Compounds
Authors: Ohkubo Katsutoshi , Nagamura Hiroo
Published: November 2013

The catalytic activity of β‐cyclodextrin‐L(or D)‐histidine compounds, β‐CD‐D‐His(e) (2a), β‐CD‐L‐His(e) (2b), and β‐CD‐D‐D‐His(a) (2c), for the stereoselective hydrolysis of N‐acyl‐amino acid esters (3a‐f) was examined at 25° C (pH 7.90). The ability of 2a‐c to bind the ester substrate into the cyclodextrin cavity and to attack the bound substrate by the nucleophilic imidazolyl group of the histidine moiety resulted in extremely high activity for those catalysts. However, the stereoselection of the enantiomeric esters during the inclusion of the substrate by 2a‐c was found to be opposite, in terms of chiral specificity, to that during the esterolysis of 2a‐c in the molecular cavity: that is, the stereoselective activity of 2a‐c is very small. The catalytic activities of 2a‐c are also influenced by the structural differences in 3a‐f, which result in the different modes of substrate inclusion by the catalyst through hydrophobic forces.
Preparation and Electrochemical Properties of bis‐2.2′‐(4.5‐Dimethyl‐1.3‐dithiolium)‐1.4‐phenylene‐bis‐perchlorate
Authors: Fabre J.M. , Giral L. , Harms R.H. , Heinze J. , Mortensen J.
Published: November 2013

The title compound C16H16S4(ClO4)2, hereafter called (TMCHDT) (ClO4)2, has been synthesized by a simple two‐step reaction sequence. Its electrochemical behaviour was studied by cyclic volammetry under superdry conditions. Different results were obtained depending on the nature of the solvent. In propionitrile, the voltammograms showed an irreversible two‐electron transfer wave at Ep = +0.050 V vs. Ag/AgCl. In methylenechloride, however, two separate, reversible one‐electron transfer waves were observed at half wave potentials of EI1/2 = −0.107 V and EII1/2 = −0.321 vs. Ag/AgCl, respectively.
Micellar‐Promoted Stereospecific Hydrolysis of Amino Acid Esters Catalyzed by Peptide‐Like Nucleophiles
Authors: Ohkubo Katsutoshi , Hirayama Kazuyuki , Yamaki Kazuhiro
Published: November 2013

The efficiency of peptide‐type nucleophiles (Z‐L‐Leu‐L‐His (2a), Z‐D‐Leu‐L‐His (2b, Z‐L‐His‐L‐Leu (2c), Z‐L‐Ala‐L‐His‐OMe (2d), Z‐L‐Leu‐L‐His‐OMe (2e), Z‐L‐Phe‐L‐His‐OMe (2f), Z‐L‐Leu‐L‐His‐L‐Leu (3a), Z‐D‐Leu‐L‐His‐L‐Leu (3b), and Z‐L‐Leu‐L‐Leu‐L‐His (3c)) in the stereospecific hydrolysis of p‐nitrophenyl N‐acyl‐phenylalanates (4a‐b) was examined at 10–30°C (pH 7.68) in an solution of hexadecyltrimethylammonium bromide (5). The hydrophobic and chiral amino acid group which is adjacent to the nucleophilic L‐histidine part in 2a‐f (or 3a‐c) was found to play an important role in determining the closeness of approach between the reactive nucelophile and substrate. The nucleophiles 2a and 3a gave high reactivity and stereospecificity in the hydrolysis of 4b possessing a long N‐acyl chain, and the maximum enantiomer rate ratio (L/D), 16.1 (25°C) or 26.2 (10°C), was obtained with mixed micelles of 3a and 5. The structural effect of the nucleophiles on the stereospecific esterolysis of 4a‐b is also discussed in detail on the basis of kinetic parameters (Kb/N, km, ΔH‡, and ΔS‡).
X‐Ray Analysis of trans‐9, 10‐Dihydroxy‐9,10‐diphenyl‐9,10‐dihydroanthracene and Its 1:2 Molecular Complex with Methanol, and Structural Comparison with the Related 1:1 Ethanol and 1:1 1,4‐Butanediol Adducts
Authors: Toda Fumio , Tanaka Koichi , Nagamatsu Shinji , Mak Thomas C.W.
Published: November 2013

trans‐9,10‐Dihydroxy‐9,10‐diphenyl‐9,10‐dihydroanthracene (2) and its 1:2 molecular complex (3) with methanol have been subjected to X‐ray analysis. The crystal structure of 2 is built of discrete molecules held by π interactions between neighboring parallel phenyl rings and van der Waals forces, whereas that of 3 features virtually rhombic hydrogen‐bonded (OH)4 rings, each comprising two methanol fragments and two hydroxy groups, linking the molecular moieties into a chain‐and‐layer arrangement. The molecular stereochemistry, hydrogen bonding, and packing modes in these two compounds are compared with those in the 1:1 adducts of 2 with ethanol and 1,4‐butanediol. Crystal data: for 2, space group P1, a = 6.814(1), b = 8.119(1), c = 9.053(1)Å, α = 103.66(1), β = 96.30(1), γ = 106.55(1)°, and Z = 1 : for 3, space group C2/c, a = 12.165(3), b = 12.484(3), c = 16.349(4)Å, β = 110.33(2)° and Z = 4. Based on observed MoKα data, the structures of 2 and 3 have been refined to RF = 0.069 for 1139 reflections and RF = 0.070 for 1412 reflections, respectively.
Anion Exchange Kinetics in Resins of High Selectivity. Part I. Analysis of Theoretical Models
Authors: Helfferich F.G. , Liberti L. , Petruzzelli D. , Passino R.
Published: November 2013

This paper reviews five kinetic models potentially applicable to ion exchange with resins of high selectivity: liquid‐phase mass transfer control with linear driving force; solid‐phase diffusion control; chemical reaction control with SN2 mechanism; chemical reaction control with shrinking core mechanism; and solid‐phase diffusion with irreversible equilibrium reaction. The parameters affecting the rate are analyzed.
Synthesis and Thermal Rearrangement of 4‐Heterohepta‐1,2,5,6‐tetraenes
Authors: Cheng Y.S. Patrick , Garratt Peter J. , Neoh Soon Bin , Rumjanek Victor M.
Published: November 2013

4‐Heterohepta‐1,6‐diynes can be rearranged by base catalysis under carefully controlled conditions to the corresponding 4‐heterohepta‐1,2,5,6‐tetraenes. Thermal rearrangment of these tetraenes gives the corresponding dimers by a process in which the rate‐determining step is first order. The rate constants for these reactions have been determined and the relative rates accounted for in terms of an aromatic contribution afforded to the presumed diradical intermediates. In the two cases investigated it was found that when the thermolyses were conducted in the presence of 3O2 then cyclic peroxides were formed.
The SN2 Transition State. 6: Breakdown of the Reactivity–Selectivity Principle in the SN2 Reaction of α‐Halocarbonyl Compounds. A Molecular Orbital Analysis [1]
Authors: Kost Daniel , Aviram Kalman
Published: November 2013

A molecular orbital (MO) analysis of the SN2 transition state (TS) of α‐carbonyl derivatives is described with various nucleophile leaving group pairs. On the basis of this analysis it is shown that the enhanced selectivity toward nucleophiles observed in α‐halocarbonyl compounds is directly associated with SN2 rate enhancement. Both observations result from a stabilizing frontier orbital interaction between a high lying π‐type three center orbital along the reaction coordinate axis and the carbonyl π‐system. The magnitude of interaction is greater for more powerful nucleophiles, resulting in both greater reactivity as well as additional selectivity relative to simple alkyl halides.
Using Macromolecular Dynamics Simulations to Interpret Experiments
Authors: Levy Ronald M.
Published: November 2013

The use of molecular dynamics simulations to study the internal motions and structural flexibility of proteins and nucleic acids has received a great deal of attention in recent years. The attraction of the method is, in part, its potential for studying detailed properties of biological macromolecules that are only indirectly accessible to experiment. Equally important is the use of the method to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques are emphasized: (1) nuclear magnetic resonance relaxation spectroscopy; (2) refinement of macromolecular X‐ray structures; and (3) vibrational spectroscopy.
Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J‐coupling and from Presence and Absence of NOE's
Authors: De Vlieg J. , Boelens R. , Scheek R. M. , Kaptein R. , van Gunsteren W. F.
Published: November 2013

In recent years a procedure has been developed by which the three‐dimensional (3D) structure of biomolecules can be derived from 2D NMR data. This procedure combines model building with restrained energy minimization (EM) and molecular dynamics (MD) techniques. Distance information from NOE's is incorporated in the form of an upper limit distance restraining term that is added to the interatomic potential function.

Here, two improvements of the refinement procedure are introduced. First, the information that is contained in empty parts of 2D‐NOE spectra is transformed into, so‐called, non‐NOE's which are modelled by adding a lower limit distance restraining term to the potential function for each non‐NOE proton pair. Secondly, the information that is contained in the occurrence of large J‐coupling constants for specific dihedrals is modelled by adding a sinusoidal dihedral angle restraining term to the potential function for each dihedral angle with a large J‐value.

The improved refinement procedure is tested by application of the lac repressor headpiece. Both the inclusion of non‐NOE data and the inclusion of J‐coupling information markedly improve the result of the restrained MD refinement of headpiece. In the refinement procedure MD simulation is used for searching configuration space. Energy barriers which are too high to be crossed by MD are surmounted by manually changing the model structures on a picture system. The resulting close non‐bonded contacts are relaxed by EM.

The final structure of headpiece satisfies essentially all 169 NOE and 9529 non‐NOE distance constraints as well as the 6Cα – Cβ dihedral angle values corresponding to the measured J‐coupling values.
Chemistry of Organic Polyheterocyclic Conductors
Authors: Wudl Fred
Published: November 2013

The synthesis and some properties of polymeric heterocycles as well as the latest results in the area of soluble conducting polymers are reviewed. Polyheterocycles with long chain substituents exhibit unusual properties in solution while retaining a relatively high conductivity in the solid state. All known methods for the preparation of conducting polymers are presented and their merits discussed. Among the insoluble polymers, the electrochemical methods are still the best because they afford films on a large variety of substrates.
Chemical and Physical Properties of Capped and Uncapped Alkylthio Substituted Tetrathiafulvalenes and Their Charge Transfer Complexes
Authors: Saito Gunzi , Kumagai Hiroaki , Katayama Chuji , Tanaka Chizuko , Tanaka Jiro , Wu Peiji , Mori Takehiko , Imaeda Kenichi , Enoki Toshiaki , Inokuchi Hiroo , Higuchi Yoshiki , Yasuoka Noritake
Published: November 2013

A series of tetrakis(n‐alkylthio)tetrathiafulvalene (alkyl‐methyl to octadecyl; TTCn‐TTF (n = 1‐18) has been synthesized. Synthesis, structure, and some physical properties of these uncapped analogues of bis(ethylenedithiolo)tetrathiafulvalene (BEDT‐TTF) are described and compared with those of BEDT‐TTF. Several charge transfer complexes of TTC1‐TTF are presented in terms of their electrical conductivities, ionicity, structures, and intermolecular interactions and compared with those of BEDT‐TTF compounds. Molecular conformation, mode of the sulfur‐to‐sulfur atomic contacts, and requirements for an organic metal are discussed from the viewpoint of the molecular design.
[FeII(MeCN)4]2+(ClO4−)2 and [FeIIICl33] as Mimics for the Catalytic Centers of Peroxidase, Catalase and Cvtochrome P‐450
Authors: Sawyer Donald T. , Spencer Lee , Sugimoto Hiroshi
Published: November 2013

Addition of [FeII(MeCN)24+(ClO−4)2 to solutions of hydrogen peroxide in dry acetonitrile (MeCN) catalyzes a rapid disproportionation of H2O2 via the initial formation of an adduct, [FeII(HOOH)↔Fe(O)(OH2)]2+, which oxidizes a second H2O2 to dioxygen. This intermediate also cleanly oxidizes substituted hydrazines, alcohols, aldehydes, and thioethers by a two‐electron process. The products for these H2O2 oxidations are consistent with those that result from catalase‐ and some peroxidase‐catalyzed processes. In the same aprotic medium (MeCN) anhydrous FeIIICl3 catalyzes the demethylation of N,N‐dimethylaniline, the epoxidation of olefins, and the oxidative cleavage of 1‐phenyl‐1,2‐ethanediol (and other 1,2‐diols) by hydrogen peroxide. A mechanism is proposed in which an initial Lewis acid‐base interaction of FeIIICl3 with H2O2 generates a highly electrophilic FeIII‐oxene species as the reactive intermediate. For each class of substrate the products closely parallel those that result from their enzymatic oxidation by cytochrome P‐450. Because of (a) the close congruence of products, (b) the catalytic nature of the FeIIICl3/H2O2 reaction mimic, and (c) the similarity of the dipolar aprotic solvent (acetonitrile) to the proteinaceous lipid matrix of the biomembrane, the form of the reactive intermediate may be the same in each case. This is in contrast to the prevailing view that cytochrome P‐450 acts as a redox catalyst to generate an Fe(V)‐oxo species or an Fe(IV)‐oxo cation radical as the reactive intermediate.
Optical Nuclear Spin Polarization (ONP) Studies of Short‐Lived Excited Triplet States in Anthracene Crystals Doped with Phenazine. Structure and Mechanism of Reversible Photochemical H‐Transfer
Authors: Buntkowsky G. , Nack M. , Stehlik D. , Vieth H.‐M.
Published: November 2013

In anthracene crystals doped with phenazine two types of ONP active triplet states are identified: delocalized triplet excitons of anthracene and localized triplet states with small zero‐field splitting and characteristic hyperfine interaction (hfi). All three basic ONP mechanisms can be demonstrated in one system with transfer of the photoinduced electron polarization (OEP) to the nuclear spins by (a) static hfi in the level crossing region (LAC‐ONP), (b) time modulated hfi inducing electron‐nuclear cross relaxation (Overhauser effect) and (c) rf saturation of forbidden transitions (RF‐ONP, solid effect). The localized triplet states are identified as a radical pair product of a H‐transfer photoreaction, in which an H atom is abstracted from an anthracene X‐trap to the neighboring phenazine guest molecule, between two translationally equivalent lattice sites along the crystalline b‐axis. Kinetic rates determined with RF‐ONP techniques indicate a cyclic reaction with slow radical pair product formation and faster, spin selective, triplet product decay. Analogies are discussed with similar H‐transfer reactions in doped fluorene. Whereas anthracene acts as H‐acceptor when doped in fluorene, it becomes H‐donor in the anthracene crystal doped with phenazine.