bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical studies on high‐valent manganese porphyrins: Toward a deeper understanding of the energetics, electron distributions, and structural features of the reactive intermediates of enzymatic and synthetic manganese‐catalyzed oxidative processes
Authors: Ghosh Abhik , Gonzalez Emmanuel 
Published: April 2004

AbstractWe present here a relatively comprehensive theoretical study, based on nonlocal density functional theory calculations, of the energetics, electron distributions, and structural features of the low‐lying electronic states of various high‐valent intermediates of manganese porphyrins. Two classes of molecules have been examined: (a) compounds with the general formula [(P)MnX2]0 (P = porphyrin; X = F, Cl, PF6) and (b) high‐valent manganese‐oxo species. For [(P)Mn(PF6)2]0, the calculations reveal a number of nearly equienergetic quartet and sextet states as the lowest states, consistent with experimental results on a comparable species, [(TMP)Mn(ClO4)2]0 (TMP = tetramesitylporphyrin). In contrast, [(P)MnCl2]0 and [(P)MnF2]0 have a single well‐defined S = 3/2 Mn(IV) ground state, again in agreement with experiment, with the three unpaired spins largely concentrated (>90%) on the manganese atom. Manganese(IV)‐oxo porphyrins have an S = 3/2 ground state, with the three unpaired spins distributed approximately 2.3:0.7 between the manganese and oxygen atoms. The metal‐to‐oxygen spin delocalization, as measured by the oxygen spin population, for MnIV = O porphyrins is less than, but still qualitatively similar to, that in analogous iron(IV)‐oxo intermediates, indicating that the MnIV = O bond is significantly weaker than the FeIV = O bond in an analogous molecule. Thus, the optimized metal—oxygen bond distances are 1.654 and 1.674 Å for (P)FeIV(O)(Py) and (P)MnIV(O)(Py), respectively (Py = pyridine). This is consistent with the experimental observation that MnIV = O stretching frequencies are over 10% lower than FeIV = O stretching frequencies for analogous compounds. For [(P)Mn(O)(PF6)]0, [(P)Mn(O)(Py)]+, and [(P)Mn(O)(F)]0, the ground states clearly correspond to a (dxy)2 Mn(V) configuration and the short Mn–O distances of 1.541, 1.546, and 1.561 Å for the three compounds, respectively, reflect the formal triple bond character of the Mn–O interaction. Interestingly, the corresponding Mn(IV)‐oxo porphyrin cation radical states are calculated to be a few tenths of an electrovolt higher than the Mn(V) ground states, suggesting that the Mn(IV)‐oxo porphyrin cation radicals are not likely to exist as ground‐state species.
Deviation of Fiber Tracts in the Vicinity of Brain Lesions: Evaluation by Diffusion Tensor Imaging
Authors: Assaf Yaniv , Pianka Pazit , Rotshtein Pia , Sigal Michal , Hendler Talma 
Published: April 2004

AbstractDiffusion Tensor Imaging (DTI) is used to characterize the diffusion properties of deviated white matter caused by brain tumors. DTI was recently shown to be very helpful in delineating white matter both within brain lesions and surrounding them. Displacement of white matter fibers may be one of the consequences of tumor growth adjacent to white matter. The combination of white matter mapping with DTI and gray matter mapping using functional MRI, in some cases, facilitated assessment of the relation between the shifted cortical areas and the corresponding white matter tracts. We found that the fractional anisotropy extracted from DTI is increased by 38% in areas of non‐edematous shifted white matter fibers. By contrast, trace apparent diffusion coefficient (ADC) values in those areas were found to be similar to contralateral side and normal control values. Analysis of the three diffusion tensor eigenvalues revealed that the increase in the fractional anisotropy is a result of two processes. The first is the increase in the diffusion parallel to the fibers—λ1 (by 18%), and the second is the decrease in the diffusion perpendicular to fibers—λ3 (by 34%) as compared with the contralateral side. These opposing changes cause an increase in the diffusion anisotropy but no change in the trace ADC. It is suggested that the pressure caused by the tumor may lead to an increase in white matter fiber tension, thus causing an increase in λ1. On the other hand, the same pressure causes increased fiber density per unit area, leading to a higher degree of restricted diffusion in the extracellular space and, hence, a reduction in λ3.
Ab initio molecular dynamics: Propagating the density matrix with gaussian orbitals. IV. Formal analysis of the deviations from born‐oppenheimer dynamics
Authors: Iyengar Srinivasan S. , Schlegel H. Bernhard , Voth Gregory A. , Millam John M. , Scuseria Gustavo E. , Frisch Michael J. 
Published: April 2004

AbstractIn the context of the recently developed Atom‐centered Density Matrix Propagation (ADMP) approach to ab initio molecular dynamics, a formal analysis of the deviations from the Born—Oppenheimer surface is conducted. These deviations depend on the fictitious mass and on the magnitude of the commutator of the Fock and density matrices. These quantities are found to be closely interrelated and the choice of the fictitious mass provides a lower bound on the deviations from the Born—Oppenheimer surface. The relations are illustrated with an example calculation for the Cl−(H2O)25 cluster. We also show that there exists a direct one‐to‐one correspondence between approximate Born—Oppenheimer dynamics, where SCF convergence is restricted by a chosen threshold value for the commutator of the Fock and density matrices, and extended Lagrangian dynamics performed using a finite value for the fictitious mass. The analysis is extended to the nuclear forces used in the ADMP approximation. The forces are shown to be more general than those standardly used in Born—Oppenheimer dynamics, with the addition terms in the nuclear forces depending on the commutator mentioned above.
Quantum quadratic brownian oscillator model for absorption lineshapes
Authors: Barsegov Valeri , Chernyak Vladimir , Mukamel Shaul 
Published: April 2004

AbstractThe absorption lineshape of a two‐level chromophore coupled quadratically to a collective Gaussian solvation coordinate with an arbitrary Brownian oscillator spectral density is calculated exactly using a path‐integral representation of the dipole correlation function in Liouville space.
Current–voltage–temperature characteristics for 2D arrays of metallic quantum dots
Authors: Remacle F. , Levine R. D. 
Published: April 2004

AbstractComputational results for the temperature‐dependent conductivity of compressed arrays of size‐selected Ag nanodots are discussed. Special attention is given to the role of phase transitions of the array as a function of external control variables: the applied voltage, the temperature, and the compression of the array. The computations are based on a scattering formalism that is presented in detail so that all the assumptions are explicitly spelled out. The results demonstrate the ability of low‐lying excited electronic states of 2D lattices to probe by temperature‐dependent conductivity measurements.
Structural models for the alkaline conformers of yeast iso‐1‐ferricytochrome c
Authors: Ness Steven R. , Lo Terence P. , Mauk A. Grant 
Published: April 2004

AbstractStructural models for three alkaline conformers of yeast iso‐1‐ferricytochrome c have been calculated from the atomic coordinates of the native protein through the use of molecular dynamics simulation. In the three models produced by this work, the Met80 axial ligand to the heme iron has been replaced by either Lys72, Lys73, or Lys79, and the related changes in structure of the cyto‐chrome are described. The principal changes in cytochrome structure predicted to result from this pH‐linked change in axial ligation involve location of residues 70–80, a region of the protein sequence that is phylogenetically conserved. The remainder of the protein fold in each model is essentially unchanged from the structure of the native protein, which is consistent with available spectroscopic information. The observation that this highly conserved region is apparently integrally involved in this conformational change may be interpreted as indicating a possible physiological role for the pH‐linkage of ferricytochrome c structure.
Quantum monte carlo methods for electronic structure of nanosystems
Authors: Mitas Lubos 
Published: April 2004

AbstractWe provide a brief review of recent applications of quantum Monte Carlo (QMC) methods to the electronic structure of nanosystems. We report on calculations of carbon rings with second‐order Jahn‐Teller effect, energy ordering of silicon clusters, dissociation enthalpies of protonated hydrogen clusters, and other interesting challenges. We point out the QMC accuracy and outline a few ideas that characterize the current position of QMC among the electronic structure methods and its future development.
Atmospheric trace gas analysis with cavity ring‐down spectroscopy
Authors: Kleine Daniel , Mürtz Manfred , Lauterbach Jörg , Dahnke Hannes , Urban Wolfgang , Hering Peter , Kleinermanns Karl 
Published: April 2004

AbstractCavity ring‐down spectroscopy (CRDS) is a highly sensitive laser absorption method. It can be used for quantitative analysis of molecular species at the sub‐ppb level. The absorption cell (cavity) is sealed by two high‐reflective mirrors on each side, which results in an effective absorption path‐length of some kilometers. Our experiments for atmospheric gas analysis have been carried out so far with an Excimer pumped dye laser in the UV‐VIS and a CO overtone sideband laser in the wavelength region around 3 μm. Experiments with an all solid‐state difference frequency laser system will follow. In the UV‐VIS region, we measured trace gas molecules like SO2, NO2, and CH2O. In the mid‐infrared, around 3 μm, we measured hydrocarbons like CH4, C2H6, and C2H4 with a detection limit of less than 1 ppb. The noise equivalent absorption coefficients in the MIR are in the order of 1.7·10−9 cm−1. Due to the high data acquisition rate and the high sensitivity, CRDS enables real‐time detection of trace gases in ambient air.
Second‐order nonlinear optical response of thin films containing organic chromophores. Theoretical aspects
Authors: Di Bella Santo , Fragalà Ignazio , Marks Tobin J. 
Published: April 2004

AbstractThis paper discusses some theoretical aspects associated with the unusual second‐order nonlinear optical response of chromophoric self‐assembled stilbalzolium superlattices, and of (N,N‐dimethylamino)‐4‐nitrostilbene (DANS)‐doped glass polymers poled in an “in‐plane” configuration. It is found that the bulk nonlinearity of such materials strongly depends upon specific chromophore interactions. While for the stilbalzolium superlattices the supramolecular hyperpola‐rizability is strongly affected by the ion‐pair configuration, the formation of (formally) centrosymmetric charged chromophore aggregates is likely responsible for the observed anomalous strong nonlinearity in DANS‐doped in‐plane poled polymers. The simple “chromophore gas” model is thus inadequate to describe the non‐linearity of such materials.
Electron transfer in the ruthenated heme domain of cytochrome P450BM‐3
Authors: Sevrioukova Irina F. , Immoos Chad E. , Poulos Thomas L. , Farmer Patric 
Published: April 2004

AbstractTwo mutants of the heme domain of Bacillus megaterium cytochrome P450BM‐3 (BMP) have been modified by covalent attachment of a photoactive Ru(bpy)3 complex at the surface‐exposed cysteine residues, 62 and 387. The laser‐flash/quench technique was used to study Ru1+ → Fe3+ electron transfer (ET) within the Ru‐BMP complexes. There was no reduction of the ferric heme by Ru1+ in Ru‐62‐BMP. In Ru‐387‐BMP, ET from Ru1+ to Fe3+ occurred with the rate constant of 4.6 × 105 s−1 and 2.5 × 106 s−1 in the absence and presence of substrate, respectively. The study demonstrates the importance of through‐bond pathways for electron flow to the heme iron of P450 and that the Gln387–Cys400 peptide is a potential ET root in P450BM‐3.
Classical description of the level density and the relaxation behavior of multidimensional molecular curve‐crossing systems
Authors: Dilthey Stefan , Stock Gerhard 
Published: April 2004

AbstractBased on the mapping formulation of nonadiabatic dynamics (Phys. Rev. Lett. 1997, 78, 578), explicit classical expressions for the total level density N(E) of a vibronically coupled molecular system as well as quantum corrections to it are derived. The analytical results for N(E) reveal the relative importance of the various molecular parameters of a curve‐crossing system, such as the electronic bias, the reorganization energy, and the topology of the potential‐energy surfaces. To study the accuracy of the approximate description, numerical studies employing various spin‐boson models as well as a two‐state, three‐mode model of the ultrafast S2 → S1 electronic relaxation in pyrazine are presented. Comparing exact quantum and approximate classical data, the connection between the level density of a vibronically coupled molecular system and its nonadiabatic relaxation behavior is discussed in some detail.
[4 + 3] Cycloaddition Reactions
Authors: Rigby* James H. , Pigge F. Christopher 
Published: April 2004

Abstract
Cycloaddition in its many manifestations represents one of the most powerful methods in organic chemistry for making cyclic structures. The high levels of convergency and stereoselectivity that frequently characterize these processes are particularly attractive from a preparative point of view. Five‐ and six‐membered rings are typically made by the well‐known 1, 3‐dipolar and Diels–Alder cycloaddition reactions, respectively, and so‐called higher‐order cycloaddition processes have emerged recently as useful methodology for the construction of medium‐sized carbocycles.

Seven‐membered ring systems, owing primarily to their broad occurrence as substructures in many classes of natural products, are particularly important targets for synthesis, but there are relatively few ways currently available for
de novo
synthesis of these ring systems. As a general solution to this problem, [4 + 3] cycloaddition between a 1, 3‐diene and an allyl, or more frequently an oxyallyl, cation offers rapid access to functionalized seven‐membered carbocycles with many of the attendant virtues of other cycloaddition processes. Considerable effort has been expended recently to exploit the synthetic utility of these reactions, and several informative reviews of the subject are currently available. Electronically, the process is quite similar to the Diels–Alder reaction and can be viewed as a [4π(4C) + 2π(3C)] combination in which the allyl cation participates as the reactive 2π component. Much of the developmental work associated with [4 + 3] cycloaddition has focused on approaches to the generation of the allyl or oxyallyl cation reaction partner, and a number of useful methods have emerged.

While a wide range of 1, 3‐diene partners have been employed in these reactions, π‐excessive heterocycles such as furan and pyrrole have been shown to be particularly useful participants and, recently, intramolecular versions of the [4 + 3] process have been effectively applied to natural product synthesis.
This chapter reviews the literature of [4 + 3] cycloadditions that involve allyl and oxyallyl cations and closely related 2π(3C) reactants to mid‐1996. Those [4 + 3] cycloadditions previously compiled by Noyori and Hayakawa in their 1983 review of reductive dehalogenations of polyhaloketones are also included in the current review so that all relevant examples are located in one document. Other 4 + 3 annulation processes that afford seven‐membered carbocycles but that employ other types of reactive intermediates are not covered in this survey.
The Retro–Diels–Alder Reaction PartI.CCDienophiles
Authors: Rickborn Bruce 
Published: April 2004

AbstractThe Diels–Alder (“DA”) reaction is so familiar to organic chemists that the retro‐Diels–Alder or retro‐diene reaction (hereafter “rDA”) requires no conceptual introduction. However, a working definition is needed to indicate the coverage of this review. The intent is to include all reported examples of the general skeletal process excluded in this chapter.Any of the atoms in the starting material (cycloadduct) may be carbon or heteroatom, and substituents on all positions are allowed. In addition, any bond order available to the element in any oxidation state is included, as well as bonding to non‐nearest neighbor atoms (bicyclics, etc.).The volume of literature required separation of this review into two parts. Part I covers all expelled C–C dienophiles, i.e. those reactions that generate a new carbon‐carbon double or triple bond in the dienophile that is formed. Part II, to appear later, covers those expelled dienophiles in which one or both atoms is a heteroatom.Certain specific topics are intentionally omitted. These are: rDA reactions invoked under mass spectral conditions; rDA reactions of polymeric substrates; Electrocyclic processes, some of which are arguably very similar to rDA reactions (these are not addressed unless needed for clarification of an rDA sequence); and a thorough discussion of homo‐rDA reactions.CAS‐Online searches resulted in ca. 1,300 references, of which ca. 900 proved pertinent to the rDA topic as defined and delimited above. Active literature searching was halted in April 1995, but occasional more recent articles are included.Over 2,500 pertinent references were eventually found. Most were obtained by perusal of primary literature (articles) and secondary sources (books and reviews). Computer based search success was limited mainly by the failure of authors or abstractors to key‐word this topic, an especially common occurrence when the expelled dienophile was a simple substance such as N2or CO2. Overall, approximately 3,500 books, chapters, reviews, articles, and abstracts were consulted in an effort to make this review as comprehensive as possible. This was done with the certainty that some pertinent literature would be missed, tempered by the view that these omissions are probably also lost to any future rational search method.Many secondary sources proved valuable not only for in‐depth discussion of certain rDA reaction types, but also for providing comparisons with related topics. To assist the reader, these secondary sources are referenced (alphabetically by first author within broad subject areas) with a title or brief note on the topic(s) addressed. The first group lists earlier reviews with primary focus on rDA reactions, followed by items of Historical/General Interest, reviews that deal with Experimental Methods, DA reactions (general and specific), reviews of Related Topics (these impinge in more or less significant ways on rDA reactions), and general treatments of Theory and Mechanism.
Aromatic Substitution by the SRN1 Reaction
Authors: Rossi Roberto A. , Pierini Adriana B. , Santiago Ana N. 
Published: April 2004

AbstractThe SRN1 (Unimolecular Radical Nucleophilic Substitution) is a process through which nucleophilic substitution is achieved on aromatic and aliphatic compounds that do not react or react slowly through polar nucleophilic mechanisms. This transformation takes place through electron transfer steps with radicals and radical anions as intermediates.The SRN1 mechanism was proposed for the first time in 1966 for the substitution of alkyl halides with electron‐withdrawing groups and in 1970 for the substitution of unactivated aryl halides. Since then, the scope of the process has increased considerably, and it constitutes an important synthetic method for achieving the substitution of unactivated aromatic and heteroaromatic substrates, vinyl halides, perfluoroalkyl iodides, and activated and non‐activated alkyl compounds. Nucleophiles that can be used include anions derived from carbon or heteroatoms, which react to form a new carbon‐carbon or carbon‐heteroatom bond.Several reviews have been published in relation to activated and non‐activated aliphatic SRN1 reactions, to aromatic photoinitiated reactions, to SRN1 reactions at aromatic centers, to reactions performed with electrochemical techniques, and to the synthetic applications of the process. This chapter attempts to cover aromatic SRN1 reactions including all the relevant literature up to the end of 1996.
Synthesis Of Nucleosides
Authors: Vorbrüggen Helmut , Ruh‐Pohlenz Carmen 
Published: April 2004

AbstractThis chapter deals with the synthesis of nucleosides (e.g., the formation ofN‐glycosides of sugars such asD‐ribose or 2‐deoxy‐D‐ribose with heterocyclic nitrogen bases). The methods of nucleoside synthesis have been treated in a number of reviews and monographs.It is now generally accepted that nucleosides were among the first organic compounds formed at the start of evolution in the early history of our planet earth. To support this point, guanine and adenine were heated withD‐ribose in seawater, which contains the Lewis acid magnesium chloride as catalyst. One thus obtained the nucleosides guanosine and adenosine together with comparable yields of unnatural α‐nucleosides. The latter were gradually photoanomerized to the thermodynamically more stable compounds in overall yields of 5–6%. The furanose form of ribose reacts faster than the pyranose form.Corresponding syntheses of the pyrimidine nucleosides uridine and cytidine from uracil , cytosine and ribose are more problematic and remain an enigma. The recent conversion of glycolaldehyde‐O‐phosphate and formaldehyde to ribose‐2,4‐di‐O‐phosphate might give new insights into the prebiotic syntheses of uridine and cytidine. The evidence and hypotheses for these prebiotic conversions and the evolution of RNA, as well as the implications of an “RNA World,” have been reviewed.These RNA nucleosides are reduced in vivo as 5′‐O‐diphosphates by ribonucleotide reductases to the corresponding 2′‐deoxynucleosides—the building blocks of DNA such as 2′‐deoxyguanosine. The thermodynamically controlled synthesis of these four building blocks of RNA has implications for the design of efficient, high yielding, new methods for the synthesis of the naturally occurring nucleosides, nucleoside antibiotics, and modified nucleosides that may serve as antimetabolites to fight viral and parasitic diseases and cancer.The nucleoside rings in this chapter are depicted arbitrarily in theanticonformation, as occurs predominantly in the crystal and solution (based primarily on NOE‐1H‐ and13C‐NMR measurements) forms of pyrimidine nucleosides. Only a few nucleosides, such as 6‐methyluridine, occur with the heterocyclic ring predominantly in thesynconformation.The synthesis ofC‐nucleosides has been reviewed previously and is not covered in this review.