bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Electrochemical Techniques in the Synthesis, Characterization and Application of Molecular Conductors: Cation Effects in the Oxidation and Reduction of TTF[Ni(dmit)2]2 Electrodes
Authors: Valade L. , Legros J‐P. , De Montauzon D. , Cassoux P. , Interrante L. V.
Published: November 2013

The use of various electrochemical techniques in the synthesis, characterization and applications of molecular conductors derived from transition metal complexes of the dmit2− ligand, is reviewed (H2dmit = 4,5‐dimercapto‐1,3‐dithia‐2‐thione). Cyclic voltammetry can be used for the detection of the formation of conductive species derived from the concerned complexes. The use of the TTF[Ni(dmit)2]2 compound1 as electrode material and its electrochemical behaviour with various supporting electrolytes, is extensively studied.
The 1:1 Mixed Stack Complex of Tetrathiafulvalene and 2,5‐Dibenzyltetracyanoquinodimethane (TTF:DBTCNQ) at 115 K
Authors: Aharon‐Shalom E. , Becker J. Y. , Bernstein J. , Bittner S. , Shaik S. S.
Published: November 2013

Crystallographic constants for the title compound are as follows: Mr = 384.5 + 204.3, triclinic, PĪ, a = 6.878 (2), b = 10.309 (4), c = 11.159 (7) Å, α = 109.94 (4), β = 100.91 (4), γ = 105.64 (3)°, Z = 1, V = 680.8 Å3, Dc = 1.46 g cm−3, Dm= 1.40 g cm−3 (flotation, aqueous KI), λ(MoKα) = 0.71069 Å, μ = 3.27 cm−1, F(000) = 304, RF = 0.085 for 1948 data with |F0| > 2.5 σ(F0). The complex crystallizes in mixed stacks of alternating donors and acceptors with a maximum of intrastack overlap and a minimum of interstack interactions. The degree of charge transfer is shown by a number of criteria to be essentially zero, in stark contrast to the complex of TTF with unsubstituted TCNQ. Comparison is made with the relatively few other complexes of derivatives of TTF and TCNQ which form mixed stack complexes.
Charge Transfer Interactions in Micelles and Vesicles. Inter‐ and Intramolecular Probes of Solubilization Site Polarity
Authors: Shin Dong M. , Schanze Kirk S. , Otruba Joseph P. , Brown Patti E. , Whitten David G.
Published: November 2013

A study of intra‐ and intermolecular charge transfer interactions with organic reagents which can be solubilized in micelles and vesicles is reported. The first part of the paper details the study on the formation of intermolecular charge transfer complexes between aromatic hydrocarbons (“enes”) and the methyl viologen dication; these complexes show a weak charge transfer transition which is dependent on solvent polarity. A study of the charge transfer transition in homogeneous solutions and microheterogeneous media shows that the complexes occur for micelles at a reasonably polar “interfacial” site. A quantitative study of complex formation for several different substrates and different surfactant media reveals that the precise micropolarity for various combinations varies and hence indicates that the solubilization site provided for a given set of reagents in a given detergent is variable and cannot be too precisely defined. Studies of two polyenes containing electron donor and electron acceptor substituents within the same molecule have also been carried out. In the case of 4‐nitro‐4′‐methoxystilbene (NMS) it has been found that the triplet‐triplet absorption spectrum observed following laser flash excitation is sensitive to both solvent polarity and viscosity; in micelles, NMS exhibits a single moderately polar solubilization site in good agreement with that reported for the aforementioned charge transfer complexes. In contrast, it has been found that vesicles solubilize NMS in two distinctively different solubilization sites. One of the solubilization sites is attributed to an “interfacial” location while the other appears less polar but more viscous. Studies of the analogous diene, NND, have focused on its fluorescence and indicate the presence once again of a site which is sensitive to the hydrocarbon chains in bilayer vesicles. The hydrocarbon‐sensitive site in vesicles for both NMS and NND could be associated with a “wedge”‐shaped or cleft site in the vesicles which exists most prominently below the phase transition temperature of the vesicle.
NAD(P)+‐NADPH Models. 60. Induction of Double Asymmetry in the Reduction of α‐Keto Esters
Authors: Ohno Atsuyoshi , Yasuma Tsuneo , Nakamura Kaoru , Oka Shinzaburo
Published: November 2013

Using a chiral 1,4‐dihydronicotinamide derivative, N‐α‐methylbenzyl‐1‐propyl‐2,4‐dimethyl‐1,4‐dihydronicotinamide (Me2PNPH), we have studied the reduction of various α‐keto esters that have a chiral center in the acid‐moiety. All of the four possible diastereomers of the corresponding α‐hydroxy esters were afforded. A detailed investigation into the diastereomeric composition of the product has revealed that the molecular arrangement and the conformations of the substrate at the transition state of the reduction are controlled by the polarity and/or the polarizability of the substituents. The 2R,3R‐isomer is the most predominant product when 4R,9R‐Me2PNPH is employed as the reductant.
Photoaccumulation in Photosystem I Does Not Produce a Phylloquinone Radical
Authors: Barry Bridgette A. , Bender Christopher J. , Mcintosh Lee , Ferguson‐Miller Shelagh , Babcock Gerald T.
Published: November 2013

A characteristic EPR spectrum is observed from Photosystem I (PS I) particles that are illuminated under reducing conditions. This signal is thought to arise from the secondary electron acceptor of PS I, A1. This EPR spectrum, along with data from other spectroscopic methods, has been taken as evidence that A1 is phylloquinone. In the work reported here, we have used a methionine auxotroph of Anabaena to deuterate specifically the 2‐methyl group on the phylloquinone ring. Mass spectrometry of the isolated quinone shows 65% yield in the labeling procedure. The photoaccumulated A1 EPR spectra in protonated and deuterium‐labeled cells are indistinguishable, from which we conclude that the photoaccumulated radical is not phylloquinone.
Towards a New Taxonomy of Photosynthetic Bacteria: ADMR‐Monitored Triplet Difference Spectroscopy of Reaction Center Pigment–Protein Complexes
Authors: Antonie Dijkman J. , Den Blanken Hubert J. , Hoff Arnold J.
Published: November 2013

Low‐temperature (1.2 K) triplet‐minus‐singlet absorbance difference spectra of a number of photosynthetic bacteria, including members of almost all genera with the exception of Heliobacteriaceae, have been recorded by absorbance‐detected magnetic resonance (ADMR). The spectra of the purple bacteria fall into two distinct classes. It is argued that these classes reflect the extent of delocalization of the primary donor triplet state over its two bacteriochlorophylls. The spectra from the green sulfur bacteria form a third class. In some cases, the bleaching of the long‐wavelength primary donor absorption is split, or shows a strong shoulder at lower energy. This phenomenon is attributed to an intrinsic heterogeneity of the reaction center with regard to the precise configuration of the primary donor dimer. It is argued that the zero‐field splitting parameters and the triplet‐minus‐singlet difference spectra may be used as a taxonomic tool.
Photocleavage of Water in Organized Molecular Systems
Authors: YA. Shafirovich Vladimir , Shilov Alexander E.
Published: November 2013

Photocleavage of water by solar light in molecular systems is discussed. The advantages of organized molecular photosystems are demonstrated for the main steps of the photocleavage process: charge photoseparation, stabilization of the separated charges, and catalytic production of hydrogen and oxygen under the action of one‐electron reductants and oxidants, respectively.
Electronic Energy Transfer in Photosynthetic Bacterial Reaction Centers
Authors: Jean John M. , Chan Chi‐Kin , Fleming Graham R.
Published: November 2013

We present simulations of energy transfer in reaction centers of the purple bacteria Rhodopseudomonas viridis and Rhodobacter sphaeroides. Calculations using a weak coupling model based on Förster's theory give transfer rates that are at least an order of magnitude slower than the results from recent femtosecond transient absorption studies. The discrepancy between experimental and theoretical results is discussed in terms of the various assumptions upon which the model is based.
Mechanisms of the Early Steps in Bacterial Photosynthesis and Their Implications for Experiment
Authors: Marcus Rudolph A.
Published: November 2013

The current situation on experiment and theory as regards the early electron transfer steps in bacterial photosynthesis is discussed. Recent experiments have limited the mechanistic possibilities, while an internal consistency test has limited the values of some parameters in the superexchange mechanism. The partitioning method has provided a useful and unified way of treating superexchange and other properties in these systems. The alternative reaction mechanisms have a number of consequences, and various experimental tests are considered or suggested.
Studies of Liquid Crystalline Solutions Using NMR Spectroscopy
Authors: Emsley J.W.
Published: November 2013

The form of the NMR spectra obtained from liquid crystalline samples is discussed. It is shown how orientational order parameters can be derived from quadrupolar splittings and dipolar couplings, and their use in investigating possible forms for potentials of mean torque is illustrated for rigid solute molecules. For non‐rigid molecules, the observed partially‐averaged quadrupolar and dipolar couplings depend upon the nature of the internal rotations about bonds, as well as on the orientational order; it is shown how both of these factors can be investigated by NMR for both mesogenic molecules and for non‐rigid solutes. Finally, it is shown how deuterium NMR is being used to study field‐induced orientational order in the isotropic phase of mesogenic molecules.
Electron Spin Echo Modulation Studies of Dipolar Hyperfine Interactions of Catalytic Reaction Intermediates Involving Transition Metal Ions on Oxide Surfaces
Authors: Kevan Larry
Published: November 2013

The application of electron spin echo modulation (ESEM) pulsed electron spin resonance methods to detect dipolar hyperfine interactions of catalytic reaction intermediates involving transition metal ions on oxide surfaces is described. This provides a method to determine critical aspects of the geometrical structure of such intermediates. One example involves catalysis of ethylene dimerization by paramagnetic Ni+ on silica. ESEM results show direct coordination of two and three ethylene molecules to Ni+ as reaction intermediates in ethylene dimerization, depending on the activation temperature of the catalyst pretreatment. A second example involves catalysis of ethylene dimerization by paramagnetic Pd+ in X—zeolite. ESEM results show direct coordination of successively one and two molecules of ethylene to Pd+ prior to dimerization. Thus ESEM methods provide a powerful tool to develop a molecular picture of the course of catalytic reactions on surfaces.
EPR Study of Cation Radicals of Short Chain Polyenes
Authors: Prasad L. Sreeramachandra , Ding Ruisong , Bradford Eric G. , Kispert Lowell D. , Wang Hanqing
Published: November 2013

Short chain polyene cation diene and triene radicals generated by X‐ray irradiation of different polyenes diluted in a CFCl3 matrix have been detected by EPR and the magnitudes of the g and isotropic hyperfine coupling constants have been obtained. The structure of the resulting cation radicals were deduced by comparing the experimental coupling constants to those derived from an INDO calculation. An estimate was obtained of the unpaired spin density as a function of chain length, suggesting that resolved hyperfine structure in the EPR spectra of long chain carotenoid cation radicals should not be observed.
1H and 2H ENDOR Investigations of Flavin Radicals Bound to Riboflavin Binding Protein from Egg White
Authors: Bretz Norbert H. , Henzel Norbert , Kurreck Harry , Müller Franz
Published: November 2013

Riboflavin‐binding apoprotein isolated from egg white has been used as a protein matrix for a variety of substituted and/or deuterated flavins. The neutral radical states of the reconstituted flavoproteins were studied by ENDOR (electron nuclear double resonance) spectroscopy in disordered solids. For the first time all major hyperfine coupling constants of a flavin cofactor embedded within a protein could be measured and unambiguously assigned to molecular positions. Some conclusions about the geometrical arrangement of the flavin within the protein pocket and about molecular motions could be drawn.
Medium‐Ring Compounds 30. cis‐1,6‐Cyclodecanediol: Molecular Compounds with the trans Isomer and with Itself
Authors: Ermer Otto , Vincent Beverly R. , Dunitz Jack D.
Published: November 2013

The crystal structures of cis‐1,6‐cyclodecanediol (1) and of the molecular compound formed between cis and trans‐1,6‐cyclodecanediol in the ratio 2:1 (2) have been established by X‐ray diffraction. The two substances are closely isostructural. (Crystal data: both monoclinic, P21/c, Z = 6; (1) a = 6.665(6), b = 18.074(3), c = 14.351(8) Å, β = 119.77(6)°, V = 1500(2) Å3; (2) a = 6.679(8), b = 18.074(4), c = 14.314(10) Å, β = 119.64(8)°, V = 1502(3) Å3). The asymmetric unit of the molecular compound contains one cis molecule in a general position and one trans molecule at a center of symmetry. In the crystal of the pure cis diol a set of disordered cis molecules mimics the corresponding centrosymmetric trans molecules in the molecular compound. The molecules have the stable BCB cyclodecane ring conformation, except for the disordered cis molecules, which have a conformation about 2 kJ mol−1 higher in energy (molecular mechanics calculations). The intricate three‐dimensional hydrogen‐bond network found in both crystals is presumably especially favorable from an energetic viewpoint.
Electronic Interactions of Cyclopropyl Groups: Synthesis and Photoelectron Spectra of Model Compounds Derived from Triasterane, Nortricyclane and Norbornane
Authors: De Meijere Armin , Michelsen Klaus , Gleiter Rolf , Spanget‐Larsen Jens
Published: November 2013

The syntheses of the new hydrocarbons trimethylenetriasterane12, trispirocyclopropanetriasterane3, trispirocyclopropanenortricyclane4, and of the trispirocyclopropanenorbornanes5, 6, and7are reported.12contains six vinylcyclopropane units rigidly held in an antiperiplanar (ap) conformation in aD3hsymmetric framework.3and4are the first model compounds with bicyclopropyl units rigidly fixed in ans‐trans(ap) conformation (Θ = 180°). Their PE spectra reveal that the interaction parameter βww= −1.73 eV for this arrangement is the same as that for Θ = 0°.
Can Electron Transmission from Aza‐Crown Ethers Contribute to Diels‐Alder π‐Facial Selectivity?
Authors: Gugelchuk Melinda , Paquette Leo A.
Published: November 2013

A pair of isodicyclopentafulvenes that carries an exocyclic phenyl group para‐substituted with an aza‐15‐crown‐5 or aza‐18‐crown‐6 ring has been prepared. These molecules (5a and 5b) and their respective NaClO4 (11) and KSCN (12) complexes were examined for the extent of π‐facial stereoselectivity operational during their Diels‐Alder cycloaddition to (Z)‐1,2‐bis(phenylsulfonyl)ethylene (2) under conditions of high pressure. Whereas 5a and 5b engage in [4 + 2] condensation with a 2.5–3.1 preference for dienophile capture from the above‐plane direction, their complexes show a substantially reduced tendency for doing so (14/13 = 1.2–1.4). However, this response goes contrary to those para‐substituent effects previously observed. The linear correlation noted earlier conformed to an increased preference for above‐plane cycloaddition to 2 as the para‐substituent became progressively more electron‐withdrawing. Probable reasons for this seemingly divergent behavior are presented.
Azo Bridges from Azine 9. [2 + 2 + 1] Cycloadditions of Parallel C=C and N=N Bonds with Dihalocarbenes
Authors: Hünig Siegfried , Schmitt Michael
Published: November 2013

Schemes 1 and 2 are examples of type A compounds in which the groups ‐N=N‐ and ‐CH=CH‐ are held in a close parallel position. They react with dichloro‐ and fluorochlorocarbene to form a unique pyrazolidine moiety (3–5) in a formal [2 + 2 + 1] cycloaddition which, despite the substitution pattern, is stable to ionization and hydrolysis according to Bredt's rule. The reaction is considered to start with the addition of the carbenes to the azo group. The azomethine imine thus formed subsequently undergoes a rapid [3 + 2] dipolar cycloaddition with the bridging C=C bond. The different isomers from 3–5 are identified from their NMR spectra.
Benzyl Ethers as Chromophores in the Exciton Chirality Method for Absolute Configurational Studies of Compounds with Hindered Hydroxyls
Authors: Takeda Reiji , Park Myung Hwan , Nakanishi Koji
Published: November 2013

p‐Phenylbenzyl ethers and, in general, other benzyl ethers, can be substituted for benzoates in the exciton chirality method for determining absolute configurations of polyols. This is useful when dealing with hydroxyl groups that resist acylation. If necessary, the phenylbenzylates can be oxidized to the corresponding phenylbenzoates with concomitant enhancement in sensitivity.
Normal Mode Solution for Frequency‐Dependent Damping of a Free Particle
Authors: Pollak Eli
Published: November 2013

The normal mode transformation of the Hamiltonian equivalent of the Generalized Langevin Equation for the free particle is used to provide explicit solutions for the classical and quantum‐mechanical diffusion of a free particle.
Hyperthermal Surface Ionization
Authors: Danon Albert , Amirav Aviv
Published: November 2013

Surface ionization of molecules with hyperthermal kinetic energy (1–20 eV) was found to be very efficient, demonstrating several unique features. We have used the technique of aerodynamic acceleration in supersonic seeded beams in order to obtain molecular kinetic energies in the range 1–20 eV. Three types of hyperthermal surface ionization (HSI) processes were observed: (a) surface‐molecule electron transfer was demonstrated in the I2/diamond system where negative molecular iodine (I−2) ions were produced; (b) molecule‐surface electron transfer was found for the anthracene molecule where positive molecular anthracene ions were generated; (c) hyperthermal surface‐induced dissociative ionization (HSIDI) was observed in 1‐iodopropane, 1‐chloro‐3‐iodopropane, benzyl bromide, and many other molecules. In these processes, we have observed a large current of negative halogen ions and positive molecular residue ions (ion‐pair formation). The mechanism of HSI is described in terms of electron transfer processes. It occurs due to a curve crossing between the neutral scattering interaction potential surface and the ionic interaction potential surface and nonunity reneutralization second curve crossing of the scattered molecules or fragment ions.
Excitation Transfer in Porous Silicas — A Fractal Approach
Authors: Pines Dina , Huppert Dan
Published: November 2013

In this paper, we present both experimental data and a theoretical study of the excited state energy transfer in irregular systems. Picosecond time‐resolved luminescence techniques were employed to resolve the fluorescence curves of both donor and acceptor molecules. By analyzing the kinetics of direct electronic energy transfer, the effective dimensions describing the distributions of adsorbed dye molecules on the surfaces of silica gels and controlled‐pore glasses were obtained. The same dimensions for silica gels were obtained in fluorescence depolarization experiments in one‐component (only donors) systems and in migration‐accelerated trapping (indirect energy transfer) measurements.
The Isolated Binary Collision Picture of Vibrational Energy Transfer Processes in Condensed Phases
Authors: Krueger Herman , Weitz Eric
Published: November 2013

A selective review of experimental studies of vibrational energy transfer in cryogenic solutions is presented, with a focus on work carried out within the last five years. The applicability of isolated binary collision (IBC) models to a number of experimentally studied systems is considered. Also discussed are possible circumstances under which current IBC treatments may break down and possible experimental studies that might test the range of applicability of this model.
Two‐Color Charge Transfer Transitions as a Probe of Electronic Relaxation and Photodissociation Dynamics at High Densities: Molecular Halogens in Xenon
Authors: Lawrence William G. , Apkarian V. Ara
Published: November 2013

Two‐color charge transfer transitions are developed as a probe of intermolecular potentials, electronic relaxation, and photodissociation dynamics of halogens in condensed rare gases. Two illustrative examples are given: electronic relaxation of Br2 in liquid Xe and recombination dynamics of Cl atoms in high pressures of Xe. The Br2 A(3π1+u) and A'(3π2+u) states, which are in fast equilibrium, are not quenched by the solvent in liquid Xe. In dilute solutions, they relax radiatively via the A' state with a lifetime of ∼ 100 μs. In concentrated solutions, diffusion‐controlled self‐quenching of Br2(A/A') proceeds with a probability of 0.07 per encounter. An encounter is found to be equivalent to four gas kinetic collisions. The photodissociation of Cl2 and recombination of Cl atoms in gaseous Xe, 1–55 atm, are studied. The recombination kinetics is well reproduced by incorporation of diffusion‐controlled encounter frequencies in the rate constants. An equilibrium constant for formation of XeCl(X) of 2.3 × 10−22 cm3 is derived from the kinetic analysis.
Selective Chemistry
Authors: Jortner Joshua , Levine Raphael D.
Published: November 2013

The possibility for nonstatistical reaction dynamics is explored with special reference to many‐atom systems. Starting with the early example of photoselective processes in van der Waals molecules, we consider other examples where the same physical mechanism may apply due to similar or other chemical reasons.
On the Mechanism of Palladium(0)‐Catalyzed Reactions of Allylic Substrates with Nucleophiles. Origin of the Loss of Stereospecificity
Authors: Bäckvall Jan‐E. , Granberg Kenneth L. , Heumann Andreas
Published: November 2013

The mechanism of the loss of stereospecificity in palladium‐catalyzed nucleophilic substitution of allylic substrates has been investigated. Eight substrates (cis and trans isomers of 1a‐d) and two nucleophiles (Et2NH and NaCH(SO2Ph)2) were studied. In the animation reactions two pathways are responsible for the formation of anomalous inversion product, viz., isomerization of the starting material (path B, Scheme 2) and isomerization of the π‐allyl intermediate via displacement of palladium by Pd(0) (path C, Scheme 2), the latter of which predominates. In the alkylation the results indicate that loss of stereospecificity is caused only by path C. The use of a more reactive substrate increased the stereospecificity of the reaction and suppressed the isomerization pathway. An analysis of the kinetics is consistent with the hypothesis that path C is the major pathway for the stereochemical loss.
Structure and Dynamics in the Interfacial Zone Between Partly Compatible Polymers
Authors: Klein Jacob
Published: November 2013

The interface between two partly miscible polymers is characterized by a finite interfacial region of width w comparable to the polymer size. The composition variation and in particular the time development of this restricted zone have recently been studied experimentally using a new depth‐profiling approach based on nuclear reaction analysis. The results show w to vary quantitatively in a way consistent with mean‐field models, while its time development appears to follow a power law w ∝ tα, with the mean value of the exponent α = 0.34 ± 0.06 being significantly lower than its free interdiffusion value of 0.5.
Synthesis of Cembranolides by SE′ Cyclization of Enantioenriched α‐Alkoxy Allylstannanes
Authors: Marshall James A. , Gung Benjamin W.
Published: November 2013

A total synthesis of the unnamed cembranolide 35 is described starting from enal XV, an intermediate derived from geraniol. Key transformations include asymmetric reduction of stannyl ketone 1 with (R)‐(+)‐BINAL‐H to give the hydroxy stannane 2 of high ee, and cyclization of the derived MOM ether 6 to the cis‐(Z) hydroxy enol ether 7 in high yield. Further elaboration of 7 to the natural product was achieved by OH‐directed hydroalanation‐iodination of the derived diol 17, methylation of iodide 17 with methyl cuprate and selective protection, oxidation, lactonization, and α‐methylenation. The resulting product was identified by comparison of 1H NMR, 13C NMR, IR, and optical rotation with an authentic sample. The synthesis defines the absolute configuration of the natural cembranolide.
A Discriminating Protecting Group Strategy for Alcohols and Amines
Authors: Liotta Louis J. , Ganem Bruce
Published: November 2013

The protection of alcohols and amines as O‐ and N‐benzyl derivatives has long played a central role in organic synthesis. For cases where the conventional method of benzylation under strongly basic conditions is not applicable, we now describe an alternate method using phenyldiazomethane that proceeds under near‐neutral conditions with HBF4 as a catalyst. O‐Benzylation occurs at −40 °C and works well on primary, secondary, and tertiary alcohols. The technique is compatible with ester, acetal, and reactive halide functionalities. Under the same conditions PhCHN2 also N‐benzylates primary and secondary amines, albeit more slowly. However S‐benzylation is only marginally successful. As a consequence aminoalcohols like 2‐hydroxymethylpiperidine can be O‐benzylated cleanly and in good yield. Thus HBF4‐mediated benzylations using PhCHN2 achieve a kinetic selectivity not customarily possible in the standard Williamson ether synthesis. Preliminary experiments with other, substituted phenyldiazomethanes indicate the method can be extended to the production of substituted benzyl ethers and amines.
MyristoylCoA:protein N‐Myristoyltransferase: Probing Host‐Guest Interactions Using Synthetic Substrates
Authors: Gokel George W. , Lu Tianbao , Rudnick David A. , Jackson‐Machelski Emily , Gordon Jeffrey I.
Published: November 2013

MyristoylCoA:protein N‐myristoyl transferase (NMT) catalyzes the cotranslational covalent attachment of myristate (C14:0) to the ammo‐terminal glycine residues of a variety of biologically important proteins. An extensive survey of myristic acid analogs has previously allowed us to infer the conformational constraints imposed upon the fatty acid when bound to the enzyme's acylCoA binding site. A series of myristic acid analogs has now been synthesized and studied in an in vitro assay to probe further the conformation of NMT's bound ligand and to assess the importance of the distance between the carboxyl and the proposed bend in the fatty acid.
Topological Editing of Cross‐Relaxation Networks
Authors: Macura Slobodan , Fejzo Jasna , Hoogstraten Charles G. , Westler William M. , Markley John L.
Published: November 2013

We have used the elements of graph theory to describe NMR cross‐relaxation networks in macromolecules and to analyze different experiments used for topological editing. We propose a new experiment, block decoupled NOESY (B.D. NOESY), that splits the cross‐relaxation network of a macromolecular system into two noninteracting subdomains. Splitting is achieved by arranging for the effective z‐components of the magnetization in one subdomain, as viewed from the other subdomain, to be zero. The B.D. NOESY experiment, in favorable cases, can usefully simplify the analysis of cross‐relaxation spectra by removing certain ambiguities. We demonstrate the method by separating the aromatic resonances from the rest of the cross‐relaxation network of a small globular protein: turkey ovomucoid third domain, Mr 6000. The resulting spectrum provides a clearer picture of cross‐relaxation pathways that involve only aromatic or only aliphatic spins. By comparing the B.D. NOESY spectrum with the normal NOESY spectrum, we were able to identify cross peaks that contain contributions from indirect magnetization transfer (spin diffusion) mediated by the aromatic side chains. In the terminology of graph theory, these experiments decompose topological networks of cross‐relaxation into two subgraphs, the join of which generates the original graph.
Orientation Dependence of Electron Spin Phase Memory Relaxation Times in Copper(II) and Vanadyl Complexes in Frozen Solution
Authors: Du Jing‐Long , More Kundalika M. , Eaton Sandra S. , Eaton Gareth R.
Published: November 2013

The orientation dependence of the electron spin phase memory relaxation time (T) was measured for vanadyl 5‐(4‐carboxyphenyl)‐10, 15, 20‐tritolylporphyrin at 22, 50, and 100 K, copper(II) bis(diethyldithiocarbamate) at 50 and 100 K, and copper(II) 5, 10, 15, 20‐tetratolylporphyrin at 50, 70, and 100 K in frozen solution. Tm was determined by fitting a single exponential to two‐pulse electron spin echo data. The values of Tm were strongly dependent on the orientation of the molecule in the magnetic field. Longer values were obtained when the magnetic field was along a principal axis or along a non‐canonical turning point in the spectrum. Shorter values of Tm were observed at intermediate orientations. The orientation dependence of Tm is attributed to molecular motion. The EPR spectra for the three systems examined are approximately axial, so the relevant motion is motion of the molecular z axis with respect to the external magnetic field. Longer values of Tm (slower relaxation) occur for orientations at which the resonant condition is less sensitive to a change in orientation of the molecular z axis. Shorter values of Tm (faster relaxation) occur at orientations for which the resonant condition is more sensitive to a change in orientation of the molecular z axis.
GaAs Quantum Dots
Authors: Nozik A.J. , Uchida H. , Kamat P.V. , Curtis C.
Published: November 2013

GaAs quantum dots have been prepared by reacting gallium acetylacetonate with trimethylsilylarsine in triethylene glycol ether at 216 K. The colloidal dispersion of GaAs nanocrystals has been characterized by transmission electron microscopy, electron diffraction, ultrafiltration, optical absorption and photoluminescence spectroscopy, and transient pump‐probe spectroscopy; the spectral data were also fitted to a model that accounts for the size‐dependent optical properties of a Gaussian distribution of particle sizes. Our results indicate that the spectral region above 470 nm can be assigned solely to GaAs nanocrystals having a mean diameter of 40.0 Å with a standard deviation of 9.7 Å. The origin of spectral features below 470 nm has not yet been determined conclusively.
Femtosecond Chemical Dynamics in Solution: Photodissociation of I3‐
Authors: Banin Uri , Kosloff Ronnie , Ruhman Sanford
Published: November 2013

We report a study of the UV photolysis of I3− in alcohol solutions, using femtosecond time‐resolved transient transmission experiments. We interpret our results to indicate that photoexcitation leads to direct formation, within 300 fs, of diiodide ions which are vibrating coherently. The time scales for vibrational dephasing, vibrational relaxation, and reorientation of the fragment ions are 400 fs, 4 ps, and 5 ps, respectively. UV transient transmission experiments were conducted in order to characterize the time scales for recombination. Recombination takes place on several time scales. A fast component is assigned to primary recombination, followed by vibrational relaxation on the ground state of I3−. The prominence of this recombination route is found to be strongly dependent on the solvent. Finally, time domain quantum simulation techniques are employed in order to gain insight into the nature of the nascent diiodide vibrational distribution, and to introduce a semiquantitative model for the stage of bond fission for isolated ions.
Femtosecond‐Picosecond Laser Photolysis Studies on Proton Transfer Process of Excited 1‐Pyrenol‐Triethylamine Hydrogen Bonding Complex in Solutions
Authors: Miyasaka Hiroshi , Wada Keisuke , Ojima Seishi , Mataga Noboru
Published: November 2013

The proton transfer (PT) process in the excited hydrogen bonding (HB) complex of 1‐pyrenol and triethylamine, leading to the formation of a hydrogen‐bonded ion pair (HBIP*) of excited pyrenolate anion and triethylammonium cation, PyO−* ··· H‐N+(C2H5)3, and subsequent reaction processes of HBIP* in various solvents were investigated by picosecond and femtosecond laser photolysis, as well as by steady‐state absorption and fluorescence measurements. Time constants for the PT process taking place in the time region of a few picoseconds were almost independent of the polarity of the solvent and it was suggested that the intermolecular slow motion in the HB complex, such as the intermolecular vibration and/or the torsional motion of the two moieties, might regulate the PT process. Moreover, the ionic dissociation process following the photoinduced PT process in polar solvent was directly measured. The dynamic behaviors of the excited intermolecular HB complex and underlying mechanisms are discussed by comparing these results with those on the intramolecular photoinduced PT process and with results of investigations of electron transfer systems.
Isomerization Dynamics of Dicyanine A in n‐Alcoholic Solution
Authors: Pines Dina , Goldberg Sinay Y. , Huppert Dan
Published: November 2013

The radiationless relaxation of dicyanine A molecules in n‐alcohols methanol to butanol has been studied by picosecond fluorescence spectroscopy and time‐resolved nonlinear spectroscopy. The fluorescence decay rates have been measured as a function of viscosity, temperature, and fluorescence wavelength. It is shown that the wavelength dependence can be explained by coexistence of two ground‐state conformers. The intrinsic activation barrier for the nonradiative decay from the excited surface is very small, much less than 1 kcal/mol. In a particular solvent the time constants of the nonradiative relaxation show a linear dependence on the variation of viscosity. The experimental data are discussed in relation to the BFO theory (Bagchi, B.; Fleming, G.R.; Oxtoby, D.W. J. Chem. Phys. 1983, 78: 7375).
Polyatomic Molecules without Electron‐Pair Bonds: High‐Spin Trigonal, Tetrahedral, and Octahedral Lithium Clusters
Authors: Glukhovtsev Mikhail N. , Schleyer Paul Von Ragué
Published: November 2013

Bound polyatomic molecules without any spin‐paired valence electrons are exemplified by lithium clusters in high‐spin states. Three unpaired valence electrons are able to bind the (4A1) quartet states of Li3and of Li4+in trigonal (D3h) geometries. The tetrahedral Li4and Li5+(5A1) quintet state structures illustrate bound molecules with four unpaired valence electrons. Five, six, and seven spin‐uncoupled valence electrons bind the square pyramidal Li5(6B1) structure, the Li6(7A2u) distorted octahedral structure, and the Li6−(8A1g) octahedral (Oh) octuplet, respectively. However, these high‐multiplicity structures are only local minima; forms with lower spin states are more favorable energetically. Other high symmetry, high multiplicity clusters, e.g., triangular Be3+(6A1′), also have positive atomization energies. The results demonstrate that chemical bonding in multiatom species does not require spin‐coupling.
Overtone State‐Selective Isomerization by a Series of Picosecond Infrared Laser Pulses: Model Simulations for Be2H3D‐(C2v) → C3v)
Authors: Manz J. , Paramonov G.K. , Polášek M. , Schütte C.
Published: November 2013

The vibrational state‐selective isomerization of Be2H3D− in the electronic ground state by a series of picosecond infrared laser pulses is simulated, using a one‐dimensional model in the framework of the Born‐Oppenheimer and semiclassical dipole approximations. Three pulses pumping the sequential overtone transitions serve to excite the anion from its vibrational ground state, representing the stable C2v configuration, to a delocalized vibrational state with energy close to the potential energy barrier. These three pump‐pulses are followed by a dump‐pulse which induces the overtone transition from the delocalized state to a vibrationally‐excited state of the slightly less stable isomer of Be2H3D− with C2v symmetry. The overall reaction probability for optimal laser pulses with sin2‐shapes is about 95%.

The model is based on ab initio calculations of the potential energy surface and the dipole function for the electronic ground state of Be2H3D− at the MP4/6–31 ++G* level, with corresponding vibrational energies and dipole transition matrix elements. The laser‐stimulated dynamics of the ultrafast state‐selective isomerization is described by a representative, time‐dependent wave packet which is driven by the laser pulses, according to the time‐dependent Schrödinger equation, equivalent to a set of linear differential equations for the time‐dependent amplitudes of vibrational eigenstates which constitute the wave packet. This set ofdifferential equations is solved by using both standard numerical techniques and an efficient quasiresonant smoothing algorithm.
Acetylcholinesterase: Effects of Ionic Strength and Dimerization on the Rate Constants
Authors: Antosiewicz Jan , Gilson Michael K. , Mccammon J. Andrew
Published: November 2013

Brownian dynamics simulations are used to calculate diffusion‐controlled rate constants for the binding of a positively‐charged ligand to acetylcholinesterase (AChE) at 300 K, pH 7, and several ionic strengths. Models of the enzyme were constructed on the basis of the crystal structure of Torpedo californica AChE, and the ligand was modeled as a 5‐Å sphere. Assignment of the charge distribution of the enzyme is based on calculation of the fractional charges of its ionizable groups as a function of pH and ionic strength, by the finite difference Poisson‐Boltzmann method. We find that the mean charge of the enzyme increases significantly with increasing ionic strength, with most of the increase occurring between 0 and 200 mM ionic strength. The charge distribution results in a very high dipole moment for the monomeric subunit of the protein: 1500 D relative to the Center of Diffusion. The magnitude and orientation of the dipole moment are relatively insensitive to the ionic strength. At physiological ionic strength, electrostatic steering of the ligand increases the rate constant of the enzyme‐ligand encounter by more than one order of magnitude. The increase in protein charge with rising ionic strength weakens the ionic strength dependence of the rate somewhat. The calculations reproduce the experimentally observed decrease of the rate constants with increasing ionic strength. We observe no intrinsic rate difference for dimeric AChE as compared to the monomer: the rate constant of the dimer is twice that of the monomer.
Thermal Motion and Conformational Disorder in Protein Crystal Structures: Comparison of Multi‐Conformer and Time‐Averaging Models
Authors: Burling F. Temple , Brünger Axel T.
Published: November 2013

Models describing thermal motion and conformational variability in protein crystal structures were applied to the refinement of a 1.8 Å crystal structure of penicillopepsin. Three methods were tested: conventional refinement using restrained B factors, multiple‐conformer refinement, and time‐averaging refinement using molecular dynamics. The information content of the models was assessed by cross‐validation and by estimating the phase accuracy of the model using phases obtained by multiple isomorphous replacement. The R value always decreased when using multi‐conformer and time‐averaging methods, as compared to conventional refinement. In contrast, the cross‐validated (“free”) R value and the phase accuracy worsened for time‐averaging in vacuum. Inclusion of solvent produced a slight improvement of both measures compared to conventional refinement. Multi‐conformer refinements always improved both measures. An optimum was reached for simultaneous refinement of between four and eight conformers. At the resolution limit of the penicillopepsin data, multi‐conformer refinement is an efficient method to describe conformational variability and thermal motion.
Modeling the Combining Site of the Human Asialoglycoprotein Receptor
Authors: Khier Sharona , Tolchinsky Sandra , Lederkremer Gerardo Z. , Shaanan Boaz
Published: November 2013

A model for the carbohydrate recognition domain (CRD) and combining site of the human asialoglycoprotein (ASGP) receptor has been computed on the basis of the close sequence homology with the mannose‐binding lectin (MBP), whose three‐dimensional structure in complex with a ligand has been determined by crystallographic methods (Weis, W.I.; Drickamer, K.; Hendrickson, W.A. Nature 1992, 360: 127). Within the limitations of modeling methods, the model is compatible with data on ligand binding of the family C‐type lectins, of which the MBP and the ASGP receptor are members. The model derived can serve as a guide for designing site‐directed mutagenesis experiments in order to further elucidate the origins of specificity of the ASGP receptor toward galactose. In particular, the model focuses attention on the possible role of position 207 (MBP sequence numbering) in promoting galactose binding.
Aspects of Modeling the Tropospheric Hydroxyl Radical Concentration
Authors: Thompson Anne M.
Published: November 2013

The global abundance of the hydroxyl radical, OH, is a principal determinant of the amount of acid deposition and the lifetime of literally hundreds of atmospheric trace gases. Local (“in situ” or point) measurements of OH have been made in a number of environments, and technical challenges in this area are being met over time. Typical concentrations near the surface range from (0.5 to 10) × 106 molecules cm−3. These measurements test photochemical theory. Discrepancies between models and measurements are sometimes larger than the apparent uncertainty in either one. There is no way to measure tropospheric OH directly on a global scale. Instead, measurement of species that react with OH are used with models to derive an estimate for the global burden. Through this route it appears that global OH has not significantly increased or decreased over the past decade. The complexities of OH interaction with O3, carbon monoxide, methane, nitrogen oxides, and nonmethane hydrocarbons and uncertainties in models make it difficult to interpret or predict global OH behavior.
The Conversion of SO2 to Sulfate in the Atmosphere
Authors: Eatough D.J. , Caka F.M. , Farber R.J.
Published: November 2013

The atmospheric chemistry responsible for the conversion of SO2(g) to particulate sulfate in areas impacted by anthropogenic emission of SO2 is reviewed. The major reaction mechanism for the homogeneous conversion process in the absence of clouds or fog is the oxidation of SO2(g) by the hydroxyl radical. The rate of this conversion process increases with both increasing temperature and relative humidity. Correlations are described for the effects of these two variables on the conversion process, and equations given which correlate all of the available literature data for the homogeneous conversion process in ambient atmospheres. The conversion of S(IV) to sulfate via aqueous solution chemistry in clouds and fog is more complex and dependent on several variables, including concentrations of the principal oxidants (hydrogen peroxide and ozone), ammonia, droplet size and composition, and meteorology. The gas‐phase homogeneous conversion process can vary from less than 1% SO2(g) converted per hour to a maximum of about 10% converted per hour at high temperature and relative humidity. In contrast, the rate of conversion of S(IV) to sulfate in the aqueous‐phase homogeneous process is controlled by mixing and reactant limitations, rather than kinetic considerations. The process can involve 100% SO2 converted per hour under optimum conditions. Consequences of the various conversion processes on environmental quality are briefly illustrated with a discussion of the impact of sulfate‐containing aerosols on PM10 concentrations and visibility degradation.
Heterogeneous Reactions of Chlorine Nitrate and Dinitrogen Pentoxide on Sulfuric Acid Surfaces Representative of Global Stratospheric Aerosol Particles
Authors: Manion Jeffrey A. , Fittschen Christa M. , Golden David M. , Williams Leah R. , Tolbert Margaret A.
Published: November 2013

Increasing evidence from field measurements, modeling studies, and laboratory experiments suggests that heterogeneous reactions on stratospheric sulfate aerosol particles can change the partitioning in the nitrogen and chlorine families and thereby affect global ozone levels. In this study, a Knudsen cell flow reactor was used to measure the uptake of ClONO2 and N2O5 by sulfuric acid solutions representative of background and volcanic stratospheric aerosol particles. The uptake coefficient (γ) of chlorine nitrate on 50–75 wt% H2SO4 at 223 K was found to be markedly dependent on the acid concentration, with γ ranging from about 1 × 10−2 to 1 × 10−4. These results are in good agreement with literature reports and the data fit the expression log γ= 1.87 – 0.074 × (wt% H2SO4). This reaction will thus have its largest impact when stratospheric temperatures are low and sulfuric acid aerosols are most dilute. Uptake of N2O5 was studied on solutions with compositions in the range 58–96 wt% H2SO4 at temperatures from 193 to 303 K. N2O5 reacted readily on sulfuric acid surfaces with uptake coefficients of about 0.06. The uptake coefficient was found to be independent of the sulfuric acid concentration and the solution temperature over the ranges studied. These results suggest that the reaction of N2O5 with H2O will occur readily on sulfuric acid aerosol particles for most stratospheric conditions.
Long‐Range Interactions in Thin Smectic Films on Substrates: X‐Ray Reflectivity Studies
Authors: Davidov D. , Tarabia M. , Cohen G. , Keller P.
Published: November 2013

Long‐range forces between interfaces of thin and ultrathin smectic films are responsible for their thickness and stability. We present here X‐ray reflectivity studies of the forces in spin‐coated thin films of three different commercial liquid crystal (LC) mixtures as well as in main‐chain LC polymers based on polysiloxane. All these LC materials possess a smectic C* phase at room temperature. We demonstrate spontaneous molecular self‐assembly after spin coating into a nearly perfect smectic layer structure on various substrates. However, annealing at room temperature is essential to achieve an equilibrium state. Measurements on ultrathin annealed films of the LC mixtures show dramatic variation of the smectic layer spacing, L, as a function of the number of smectic layers, n (or film thickness, d). The functional dependence of L(n) for all three different liquid crystal mixtures suggests a long‐range interaction between the interfaces that decays algebraically as 1/nκ where κ = 2 ± 0.3. This decay is consistent with a van der Waals type of interaction, although its magnitude cannot be explained by the existing mechanisms.

X‐ray studies of thick and thin annealed polysiloxane films allow determination of the phases, the phase transition temperatures, and the temperature dependence of the tilt angle in the smectic C* phase. Thin (300 Å to 600 Å) polysiloxane films far above the bulk smectic–isotropic phase transition temperature show the formation of smectic film at the film–substrate interface due to surface freezing phenomena. Preliminary investigations of the temperature dependence of the smectic film thickness indicate that the interaction between the interfaces decays algebraically, with an exponent κ = 1.5 ± 0.5.