bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculation of the free energy of solvation from molecular dynamics simulations
Authors: Gonçalves P. F. B. , Stassen H. 
Published: October 2007

Abstract
Molecular dynamics simulation has been employed in the computation of the free energy of solvation for a large number of solute molecules with different chemical functionalities in the solvents water, acetonitril, dimethyl sulfoxide, tetrahydrofuran, and carbon disulfide. The free solvation energy has been separated into three contributions: the work necessary to create a cavity around the solute in the solvent, the electrostatic contribution, and the free energy containing the short-range interactions between solute and solvent molecules. The cavitational contribution was computed from the Claverie-Pierotti model applied to excluded volumes obtained from nearest-neighbor solute-solvent configurations treating the solvent molecules as spherical. The electrostatic term was calculated from a dielectric continuum approach with explicitly incorporating the solvent's partial charges. The short-range contribution to the free solvation energy was obtained from the force field employed in the simulations. For solutions with available experimental data for the free energy of solvation, we found a satisfactory agreement of the computed free solvation energies and the experimental data set.
Vibration-rotation spectra of hydrogen halides in rare-gas liquids: Q-branch absorption
Authors: Medina A. , Roco J. M. M. , Hernández A. C. , Velasco S. 
Published: October 2007

Abstract
Near-infrared spectra of HCl highly diluted in liquid Ar show intense absorption in the P-R interbranch region, so-called Q-branch absorption. In spite of its relevance for the shape of the bands, its physical origin has been elusive to date. We employ molecular dynamics simulations to study the influence of some physical effects that could contribute to Q-branch absorption. We check that multipole-induced dipole induction mechanisms are not quantitatively relevant in this spectral region. We show that the particular characteristics of accurate HCl-Ar anisotropic potentials and the peculiar hindered rotational motion they provoke on the diatomic probe are essential to understand Q-branch absorption.
Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol revisited
Authors: Torii H. 
Published: October 2007

Abstract
Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol is examined with the combination of molecular dynamics (MD) simulations and the intermolecular resonant vibrational interactions determined by the transition dipole coupling (TDC) mechanism (MD/TDC method). It is shown that the observed decrease of the Raman noncoincidence νNCE of the CO stretching band with increasing density reported in the literature is quantitatively reproduced by the present calculation. As the density increases, the hydrogen bonds get slightly shorter, but molecules belonging to different hydrogen-bond chains get closer to each other to a greater extent. This anisotropic change in the liquid structure is the reason for the behavior of νNCE. It is also shown that the concentration dependence of νNCE in the methanol/CCl4 binary mixtures reported in a previous study, and the pressure dependence of νNCE in methanol may be described in a consistent way as a function of the number density of methanol in the liquid systems.
Molecular structure, reorientational dynamics, and intermolecular interactions in the neat ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate
Authors: Antony J. H. , Mertens D. , Breitenstein Tobias , Dölle Andreas , Wasserscheid P. , Carper W. R. 
Published: October 2007

Abstract
Results on the molecular and liquid structure and the reorientational dynamics are reported for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]). In quantum-chemical calculations for [BMIM][PF6] in the gas phase, hydrogen bonding between the proton at carbon 2 in the aromatic ring and the fluorine atoms of the hexafluorophosphate anion was found. From the analysis of 13C relaxation data, the reorientational motions were evaluated, and the Vogel-Fulcher-Tammann and Arrhenius activation energies for the overall and internal reorientational motions, respectively, of the different 13C-1H vectors are given as well as correlation times at 300 K. By performing molecular dynamics (MD) simulations, pair distribution functions between moieties in the cation and the phosphorous atom in the anion were determined. The pair distribution function for the proton at carbon 2 exhibits a particular sharp and strong maximum indicating a strong interaction with the anion. The quantum-chemical calculations, the motional parameters, and the results from the MD simulations support the existence of hydrogen bonding and the formation of ion pairs in the ionic liquid.
Photodegradation and photosensitization in pharmaceutical products: Assessing drug phototoxicity
Authors: Cosa Gonzalo 
Published: October 2007

Abstract
Toxic reactants are a common result of the interaction of sunlight with pharmaceutical agents transported in the blood system or applied topically. Over the past decade there has been a considerable amount of research toward understanding both the unimolecular deactivation pathway of photoexcited pharmaceutical products and their photosensitizing capability in the presence of biological substrates. This work summarizes recent developments in the study of the photodegradation mechanism of ketoprofen, fenofibric acid, and tiaprofenic acid. An analysis of excited-state electronic energy levels, the type of intermediates formed following excitation, and transient intermediate lifetimes is presented. The analysis involves both parent drugs and their major photoproducts. Phototoxicity, usually the result of adverse photochemical reactions following direct photoexcitation of the drugs, is shown to be strongly related to the photoexcitation of photoproducts when high radiation dose conditions prevail. The photoproducts are the species directly involved in photosensitizing reactions.
Recent developments in the coordination chemistry of stable free radicals
Authors: Lemaire M. T. 
Published: October 2007

Abstract
Several advances in the coordination chemistry of stable free-radical species over the past six years are documented in this review article. Specifically, a number of recent reports focused on the coordination chemistry of chelating nitroxide ligands are highlighted, with an emphasis on enhanced magnetic or optical properties in these complexes. Furthermore, very intriguing recent magnetic and optical studies with one-dimensional nitroxide chain complexes (new "Glauber" chains and chiral magnets) are also discussed. The verdazyls are another family of stable radicals whose coordination chemistry was literally unexplored prior to 1997. A summary of recent reports discussing metal-verdazyl coordination complexes is also presented, followed by an eye to the future of stable radical design and the coordination chemistry of these interesting molecules.
Simulations on many scales: The synapse as an example
Authors: Tai K. 
Published: October 2007

Abstract
Computer simulation methods spanning several temporal and spatial scales are reviewed, focusing on their applications on the neuromuscular synapse. Quantum mechanics treats the enzymatic catalysis of neurotransmitters on the picometer scale. Molecular dynamics reveals conformational changes of the enzyme acetylcholinesterase for nanoseconds. Brownian dynamics follow the substrate molecule in its diffusion on the microsecond level. Methods such as finite elements describe the diffusion of neurotransmitters as a changing concentration continuum in the synapse. Promising directions for future research include integration of methods on several scales, and applying these methods to the acetylcholine receptor.
Understanding the reaction that powers this world: Biomimetic studies of respiratory O2 reduction by cytochrome oxidase
Authors: Boulatov Roman 
Published: October 2007

Abstract
Cytochrome c oxidase (CcO) is an enzyme that catalyzes efficient, selective, and fast reduction of molecular oxygen to water as a means of respiratory energy generation. The biomimetic approach provides a valuable alternative to traditional biochemical methods to unravel the structural and electronic properties of the CcO's catalytic (heme/CuB) site that endow the enzyme with its unique reactivity. However, the contribution of biomimetic studies of CcO to our understanding of CcO's biochemistry has been complicated by the lack of convincing evidence that the reactivity of the biomimetic analogs is relevant to that of CcO. Recently reported porphyrin-based compounds are the first analogs that reproduce key aspects of the reactivity of CcO toward O2. Extensive data collected with these biomimetic analogs demonstrate that the bimetallic nature of the CcO's catalytic site may be an adaptation to reduction of O2 under turnover-limiting electron flux; a monometallic heme-only site appears sufficient for rapid O2 reduction under physiologically relevant conditions of pH and electrochemical potential, provided that electron flow to the heme is not kinetically limited. These biomimetic data suggest that in CcO the distal Cu ion (CuB) may serve as an electron-preloading site to allow the enzyme to accumulate a sufficient number of external reducing equivalents before it even binds O2. This mechanism minimizes the population of enzymatic species containing partially reduced oxygen species.
Copper(II) proteins are amenable for NMR investigations
Authors: Bertini Ivano , Pierattelli R. 
Published: October 2007

Abstract
The possibility of investigating copper proteins by nuclear magnetic resonance is here treated. It is shown that the solution structure and dynamic information can be obtained on Type I Cu(II) proteins, which have a relatively short electron relaxation time (τ
S = 10-10 s). The experimental approach, in this case, is routine, although tailored for fast-relaxing nuclei.
In the case of Type II Cu(II) proteins, when the electron relaxation times are larger (τ
S = 10-8 - 10-9 s) and proton linewidths are broadened beyond detectable limits, heteronuclear 13C spectra with direct detection can be used and the solution structure can again be obtained.
In this review, it is shown that Cu(II) proteins are now amenable for NMR investigation, the size being the only limit as in diamagnetic proteins.
Probing fundamental mechanisms of nitric oxide reactions with metal centers
Authors: Ford P. C. 
Published: October 2007

Abstract
Studies in this laboratory have been concerned with mapping the chemical properties and mechanisms of NO interactions with hemes and other metal centers. These are models relevant to the mammalian biology of nitric oxide, an important bioregulatory molecule. Presented here will be an overview of flash photolysis kinetics investigations of ferri- and ferro-heme nitrosyl formation in model complexes and several heme proteins. Also described will be ongoing studies of reductive nitrosylation mechanisms involving the reactions of NO with water-soluble Fe(III) porphyrins and ferri-heme proteins and of several Cu(II) model complexes.
Cooperation of metals with electroactive ligands of biochemical relevance: Beyond metalloporphyrins
Authors: Kaim Wolfgang , Schwederski B. 
Published: October 2007

Abstract
In addition to the widely studied biometal complexes of tetrapyrrole ligands such as hemes (Fe), cobalamins (Co), and factor F430 (Ni), there are other, more recently established systems in which transition metals and redox-active cofactors such as pterins, flavins, quinones, or phenoxyl radicals cooperate in electron transfer and substrate activation. The cases of the molybdenum or tungsten containing oxotransferases involving pyranopterin as essential ligand and the copper-dependent quinoproteins such as amine oxidases will be discussed. The structural and functional description of these systems will be complemented by results from model studies.
Synthesis of texaphyrin conjugates
Authors: Magda D. J. , Wang Z. , Gerasimchuk Nikolay , Wei W.-H. , Anzenbacher P. , Sessler J. L. 
Published: October 2007

Abstract
This paper summarizes recent synthetic efforts devoted to the generation of new, second-generation texaphyrin-type drugs, specifically species that involve known or potential anticancer agents covalently attached to a tumor-localizing texaphyrin core. Particular emphasis will be placed on the strategies needed to prepare such systems, as well as on the choice of active group being subject to attachment.
Adenosine 5'-triphosphate (ATP4-): Aspects of the coordination chemistry of a multitalented biological substrate
Authors: Sigel H. 
Published: October 2007

Abstract
Firstly, the self-stacking properties of ATP4- and the effects of metal ions and protons on these properties are described. Some examples involving macrochelate formation between phosphate-coordinated metal ions (M2+) and N7 of the adenine residue in MATP2- are discussed, and this is followed by considerations on mixed ligand complexes consisting of ATP4-, M2+, and amino acid anions with side chains that allow either aromatic-ring stacking or hydrophobic interactions with the adenine moiety; this gives rise to selectivity. Next, the properties of diphosphorylated 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2-; Adefovir), i.e., of PMEApp4-, are compared with those of (2'-deoxy)ATP4- with regard to their metal ion-binding qualities, and in this way it can be explained why PMEApp2- is initially an excellent substrate for nucleic acid polymerases. Of course, after incorporation of the PMEA residue into the growing nucleic acid chain, this is terminated and this is how PMEA exerts its antiviral properties [its bis(pivaloyloxymethyl)ester, Adefovir dipivoxil, was recently approved for use in hepatitis B therapy]. Finally, the change in free energy connected with (macro)chelate formation or intramolecular stacking interactions and the effect of a reduced dielectric constant of the solvent on the stability of complexes and their structures in solution is considered.
Rheological and mechanical properties of poly(α-methylstyrene-co-acrylonitrile)/ poly[(methyl acrylate-co-methyl methacrylate)] blends in miscible and phase separated regimes of various morphologies. Part IV: Influence of the morphology on the mechanical properties (IUPAC Technical Report)
Authors: Altstädt V. , de Freitas L. Lucca , Schubert D. W. 
Published: October 2007

Abstract
Influences of the morphology on the thermal and mechanical properties of poly(α-methylstyrene-co-acrylonitrile)/poly[(methyl acrylate-co-methyl methacrylate)] (PαMSAN/PMMA) blends have been investigated. DSC measurements confirm that all blends were phase-separated due to the temperature at which they have been extruded and squeeze-molded. Based on the cloudpoints of 17 blends and TEM micrographs, the interaction parameters as a function of temperature and composition were calculated for the lower critical solution temperature (LCST) system. Varying the morphology by annealing without changing the composition of the system resulted in a finer morphology for the 85/15 blends, while the 40/60 blend showed an increase in the domain size with annealing time. Tensile strength and fracture toughness indicate that the PαMSAN domains in the tougher PMMA matrix cause a deterioration in the mechanical properties of the blends, while the PMMA domains in the PαMSAN matrix improve the mechanical properties. No clear conclusions on the influence of morphology on fracture toughness could be drawn because in one case (40/60 blend) the fracture toughness decreases slightly by annealing and in the other case (85/15 blend) fracture toughness values increase slightly with decreasing phase separation by annealing. In situ strained thin sections in the TEM indicated no effect of annealing on the micromechanical behavior. Shear deformation was observed as the prevailing deformation mechanism in the PαMSAN and fibrillized crazing in the PMMA-rich blends. From fatigue crack growth experiments it was concluded that the fatigue crack propagation threshold is higher for PMMA than for PαMSAN. Tests on the annealed samples of PαMSAN/PMMA 85/15 and 40/60 showed that the differences in morphology did not affect the fatigue crack growth resistance significantly. From the features of the fracture surface investigated by SEM, the conclusion can be drawn that the fatigue crack propagates faster in the more brittle PαMSAN phase, but the overall advance of the crack front is controlled at the interphases, resulting in a crack propagation gradient along the interphase.
Determination of trace elements bound to soil and sediment fractions (IUPAC Technical Report)
Authors: Hlavay József , Prohaska T. , Weisz M. , Wenzel W. W. , Stingeder G. J. 
Published: October 2007

Abstract
This paper presents an overview of methods for chemical speciation analysis of elements in samples of sediments and soils. The sequential leaching procedure is thoroughly discussed, and examples of different applications are shown. Despite some drawbacks, the sequential extraction method can provide a valuable tool to distinguish among trace element fractions of different solubility related to mineralogical phases. The understanding of the speciation of trace elements in solid samples is still rather unsatisfactory because the appropriate techniques are only operationally defined. The essential importance of proper sampling protocols is highlighted, since the sampling error cannot be estimated and corrected by standards. The Community Bureau of Reference (BCR) protocols for sediment and soil give a good basis for most of the solid samples, and the results can be compared among different laboratories.
Terminology for analytical capillary electromigration techniques (IUPAC Recommendations 2003)
Authors: Riekkola M.-L. , Jönsson J. Å. , Smith R. M. 
Published: October 2007

Abstract
This paper presents terms and definitions for capillary electromigration techniques for separation, qualitative and quantitative analysis and physico-chemical characterization. Names and descriptions for such techniques (e.g., capillary electrophoresis and capillary electrochromatography) as well as terms for the phenomenon of electroosmotic flow are included.
Metal cyclopropyl carbenes in the reactions of alkynes with alkenes and furans
Authors: Echavarren Antonio M. , Méndez María , Muñoz M. P. , Nevado C. , Martín-Matute Belén , Nieto-Oberhuber C. , Cárdenas D. J. 
Published: October 2007

Abstract
Electrophilic transition-metal complexes catalyze the reaction of enynes in the presence of water or alcohols to give hydroxy- or alkoxycyclization derivatives. The reaction proceeds by the anti addition of the alkene and the metal to the alkyne. The key intermediates in this reaction are cyclopropyl metal carbenes, which are also probably involved in the metathesis-type rearrangement of enynes. A general scheme is proposed for the cyclization of enynes initiated by the coordination of the metal to the enyne by transition metals, which included 5-exo -dig and 6-endo -dig pathways. The intramolecular reaction of furans with alkynes also proceeds via cyclopropyl metal carbenes.
Rhodium-catalyzed asymmetric addition of aryl- and alkenylboron reagents to electron-deficient olefins
Authors: Hayashi T. 
Published: October 2007

Abstract
Asymmetric 1,4-arylation and -alkenylation was achieved by use of organoboronic acids or their derivatives in the presence of a rhodium catalyst coordinated with binap or its related ligands. The scope of this asymmetric addition is very broad, α, β-unsaturated ketones, esters, amides, 1-alkenylphosphonates, and 1-nitroalkenes being efficiently converted into the corresponding 1,4-addition products with over 95% enantioselectivity. The catalytic cycle in water is proposed to involve three intermediates [aryl-or alkenyl-rhodium (oxa-π-allyl) rhodium, and hydroxo-rhodium] by NMR studies on the rhodium intermediates.
Synthetic applications of planar chiral cationic η3-allylmolybdenum complexes
Authors: Kocienski P. , Bell Richard , Bourque Elyse , Christopher J. A. , Cooksey John , Gunn Andrew , Kuhl Alexander , Li Y. , Uppal S. , Yuen Josephine 
Published: October 2007

Abstract
The synthesis of planar chiral η3-allylmolybdenum complexes is described together with some examples of the nucleophilic addition of organocopper(I) reagents.
Application of allylic substitutions in natural products synthesis
Authors: Helmchen G. , Ernst Martin , Paradies G. 
Published: October 2007

Abstract
Synthesis routes are described, allowing all known jasmonoids as well as their enantiomers to be synthesized in enantiomerically and diastereomerically pure form. The routes are based on a set of closely related lactones containing an electrophilic allylic moiety, which are accessible via asymmetric Pd-catalyzed allylic alkylation. Regio- and diastereoselective SN2'-anti-reactions of the electrophilic lactones with organocopper compounds furnished 2,3-cis-disubstituted cyclopentenones, which were further transformed into the target compounds, i.e., 12-oxophytodienoic acid (12-OPDA) in excellent overall yields. The methodology also allowed iridoids and isoprostanes to be prepared. The configuration of an Archaea membrane lipid constituent containing cyclopentane rings was determined by total synthesis of a diol that was also obtained by degradation of the natural product.
Development of catalysts for the hydroamination of olefins
Authors: Hartwig J. F. 
Published: October 2007

Abstract
Studies on the development of palladium, nickel, and rhodium catalysts for the hydroamination of dienes and vinylarenes are described. Enantioselective catalysts based on palladium have been developed for the addition of arylamines to dienes and for Markovnikov addition of arylamines to vinylarenes. In addition, nickel catalysts for the addition of aliphatic amines to dienes have been developed, and rhodium catalysts for the first transition metal-catalyzed aminations of vinylarenes that generate terminal amines as the major product are described. Mechanistic data on the hydroamination of vinylarenes with palladium and rhodium is also provided.
New regio-, stereo-, diastereo- and enantioselective one-pot reactions mediated by organometallic derivatives
Authors: Chinkov Nicka , Sklute G. , Chechik Helena , Abramovitch Adi , Amsallem Deborah , Varghese J. , Majumdar Swapan , Marek I. 
Published: October 2007

Abstract
In the first part of the lecture, we will discuss the one-pot preparation of chiral homoallylic alcohol and amine derivatives by a copper-catalyzed four-component reaction. In this process, three new carbon-carbon bonds as well as a quaternary and a tertiary chiral center are created with excellent regio- and diastereoselectivities. When the reaction was performed without adding external electrophiles, a β-elimination reaction took place to give polysubstituted allenes in good overall yields. This strategy of zinc-homologation followed by a β-elimination reaction was also synthetically used for the transformation of sp3 sulfoxides into olefins with potential application in asymmetric synthesis. Finally, in the second part of this lecture, the stereoselective preparation of metallated dienes in only two chemical steps from commercially available products will be described. This new strategy is based on a tandem allylic C-H bond activation of a remote ω-double bond followed by an elimination reaction.
Negative nonlinear effect in aquo palladium catalysis depending on tropos biphenylphosphine ligand chirality controlled by chiral diaminobinaphthyl activator
Authors: Mikami K. , Aikawa Kohsuke , Yamanaka Masahiro 
Published: October 2007

Abstract
Asymmetric activation of aquo Pd catalysts with tropos biphenylphosphine (BIPHEP) ligands by a chiral diaminobinaphtyl (DABN) activator exhibits a remarkable negative nonlinear effect, (–)-NLE, with higher catalytic efficiency than that achieved by enantiopure atropos BINAP- or tropos BIPHEP-Pd catalysts without DABN activator.