bluuebunny/crossref_metadata_2025_split huggingface dataset:
A non‐uniqueness problem of the Dirac theory in a curved spacetime
Authors: Arminjon M. , Reifler F. 
Published: June 2011

AbstractThe Dirac equation in a curved spacetime depends on a field of coefficients (essentially the Dirac matrices), for which a continuum of different choices are possible. We study the conditions under which a change of the coefficient fields leads to an equivalent Hamiltonian operator H, or to an equivalent energy operator E. We do that for the standard version of the gravitational Dirac equation, and for two alternative equations based on the tensor representation of the Dirac fields. The latter equations may be defined when the spacetime is four‐dimensional, noncompact, and admits a spinor structure. We find that, for each among the three versions of the equation, the vast majority of the possible coefficient changes do not lead to an equivalent operator H, nor to an equivalent operator E, whence a lack of uniqueness. In particular, we prove that the Dirac energy spectrum is not unique. This non‐uniqueness of the energy spectrum comes from an effect of the choice of coefficients, and applies in any given coordinates.
Pore Network Model and Simulation of Transport Process for Grain Drying
Authors: Chang J. , Yuan Y.‐J. , Yang D.‐Y. , Liu X.‐D. 
Published: June 2011

AbstractA nonequilibrium model was developed and simulated by adopting a dual‐scale pore network approach. The distributions of temperature, moisture, and pressure in drying air, as well as the temperature and moisture content profiles in grain kernels were obtained from the pore scale model and the kernel scale model, respectively. A small test bin was built to conduct in‐bin drying experiments and to validate the model. The results from the experiments and the simulations indicate that the dual‐scale pore network approach could explain the drying process of the deep‐bed grain drying process well. The influences of grain bulk porosity and cereal particle size distribution were also investigated by numerical simulations.
A New Control‐Volume Finite‐Element Scheme for Heterogeneous Porous Media: Application to the Drying of Softwood
Authors: Carr E. J. , Turner I. W. , Perré P. 
Published: June 2011

AbstractAn improved mesoscopic model is presented for simulating the drying of porous media. The aim of this model is to account for two scales simultaneously: the scale of the whole product and the scale of the heterogeneities of the porous medium. The innovation of this method is the utilization of a new mass‐conservative scheme based on the Control‐Volume Finite‐Element (CV‐FE) method that partitions the moisture content field over the individual sub‐control volumes surrounding each node within the mesh. Although the new formulation has potential for application across a wide range of transport processes in heterogeneous porous media, the focus here is on applying the model to the drying of small sections of softwood consisting of several growth rings. The results conclude that, when compared to a previously published scheme, only the new mass‐conservative formulation correctly captures the true moisture content evolution in the earlywood and latewood components of the growth rings during drying.
Cytoarchitecture and ultrastructure of neural stem cell niches and neurogenic complexes maintaining adult neurogenesis in the olfactory midbrain of spiny lobsters, Panulirus argus
Authors: Schmidt Manfred , Derby Charles D. 
Published: June 2011

AbstractNew interneurons are continuously generated in small proliferation zones within neuronal somata clusters in the olfactory deutocerebrum of adult decapod crustaceans. Each proliferation zone is connected to a clump of cells containing one neural stem cell (i.e., adult neuroblast), thus forming a “neurogenic complex.” Here we provide a detailed analysis of the cytoarchitecture of neurogenic complexes in adult spiny lobsters, Panulirus argus, based on transmission electron microscopy and labeling with cell‐type‐selective markers. The clump of cells is composed of unique bipolar clump‐forming cells that collectively completely envelop the adult neuroblast and are themselves ensheathed by a layer of processes of multipolar cell body glia. An arteriole is attached to the clump of cells, but dye perfusion experiments show that hemolymph has no access to the interior of the clump of cells. Thus, the clump of cells fulfills morphological criteria of a protective stem cell niche, with clump‐forming cells constituting the adult neuroblast's microenvironment together with the cell body glia processes separating it from other tissue components. Bromodeoxyuridine pulse‐chase experiments with short survival times suggest that adult neuroblasts are not quiescent but rather cycle actively during daytime. We propose a cell lineage model in which an asymmetrically dividing adult neuroblast repopulates the pool of neuronal progenitor cells in the associated proliferation zone. In conclusion, as in mammalian brains, adult neurogenesis in crustacean brains is fueled by neural stem cells that are maintained by stem cell niches that preserve elements of the embryonic microenvironment and contain glial and vascular elements. J. Comp. Neurol. , 2011. © 2011 Wiley‐Liss, Inc.
Mass spectrometric characterization of urinary metabolites of the selective androgen receptor modulator S‐22 to identify potential targets for routine doping controls
Authors: Thevis Mario , Thomas Andreas , Möller Ines , Geyer Hans , Dalton James T. , Schänzer Wilhelm 
Published: June 2011

Drugs that promote anabolic processes with limited undesirable effects are of considerable therapeutic interest; some notable examples include those for the treatment of cancer cachexia and muscle‐wasting diseases. Anabolic properties are not only therapeutically beneficial to critically ill and debilitated patients, but are also desirable to athletes seeking artificial enhancements in endurance, strength and accelerated recovery. The use of anabolic agents in the clinical setting is being reconsidered with the emergence of a new class of drugs referred to as SARMs (selective androgen receptor modulators). SARMs have the potential to complement or even replace anabolic androgenic steroidal use with the benefit of a reduction of the undesirable side effects associated with steroid administration alone. Arylpropionamide‐based SARMs such as andarine (S‐4) and S‐22 have shown promising therapeutic properties and have attracted the interest of elite and amateur athletes despite the absence of clinical approval, and evidence for trafficking and misuse in sport has been obtained by doping control authorities.In this communication, the elucidation of urinary metabolites of the SARM drug candidate S‐22 is compared with earlier in vitro metabolism studies. Following oral administration of illicit S‐22, urine samples were collected after 62 and 135 h and analyzed for the active drug and its major metabolic products. Liquid chromatography interfaced with high‐resolution/high‐accuracy (tandem) mass spectrometry was used to identify and/or confirm the predicted target analytes for sports drug testing purposes. S‐22 was detected in both specimens accompanied by its glucuronic acid conjugate. This was the B‐ring hydroxylated derivative of S‐22 plus the corresponding glucuronide (with the phase‐II metabolites being the more abundant analytes). In addition, the samples collected 62 h post‐administration also contained the phase‐I metabolite hydroxylated at the methyl residue (C‐20) and the B‐ring depleted degradation product ('dephenylated' S‐22) together with the corresponding carboxy analog that was previously reported for canine metabolism. The obtained data supports future efforts to effectively screen for and confirm the misuse of the non‐approved S‐22 drug candidate in doping controls. Copyright © 2011 John Wiley & Sons, Ltd.
Carbocations
Authors: Aue Donald H. 
Published: June 2011

AbstractThe role of quantum calculations in the field of carbocations is reviewed mainly over the past 10 years. The importance of structure and energy is emphasized. New nuclear magnetic resonance results in solution and infrared spectra in the gas phase give structural insights when coupled with theory. A critical review of applications of popular theoretical methods to the prediction of hydrocarbon and carbocation energies is presented, showing where problems can be anticipated, particularly for density functional theory methods. Gas‐phase stabilities of carbocations are discussed along with the interpretation of their hydride ion affinities in terms of the fundamental factors that determine stability: polarization, inductive, ring‐strain, hybridization, hyperconjugation, conjugation, and aromaticity/antiaromaticity effects. Interesting new carbocation structures and new bifurcation mechanisms are featured, along with examples of the role of carbocations in petroleum chemistry and zeolite catalysis, environmental chemistry and carcinogenic polynuclear aromatic hydrocarbons, and the biosynthesis of terpenes. In all of these areas, theoretical calculations often lead the way, filling experimental gaps that can lead to proper interpretation of experiments, providing insights that lead to a fundamental understanding of experimental results, and making new predictions of unexpected structures, properties, and reaction mechanisms for carbocations. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 487–508 DOI: 10.1002/wcms.12This article is categorized under:

Structure and Mechanism > Molecular Structures
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Electronic Structure Theory > Density Functional Theory
Cross‐conjugation
Authors: Limacher Peter A. , Lüthi Hans P. 
Published: June 2011

AbstractCross‐conjugation, even though very common in chemistry, has only sparsely been visited by experiment or by theory. Until very recently, this form of conjugation, in which two separate conjugated branches are linked to the same carbon atom which is part of a (shared) double bond, was considered to be much less able to promote electron delocalization than through‐conjugation. Therefore, exploiting cross‐conjugation to design new materials was considered difficult and not very promising. In this article, we show that this view, at least for neutral molecules in their electronic ground state, is essentially correct. For cross‐conjugated radical ions, the situation is different: There is appreciable charge delocalization across the bifurcation point, i.e., the point where the two conjugated branches meet. Simple Hückel molecular orbital considerations show that the connectivity pattern encountered in cross‐conjugation will lead to enhanced electron delocalization effects. This observation, confirmed by density functional calculations, also applies for electronically excited species. Therefore, cross‐conjugation may be exploited to build molecular switches or may be used to design devices such as molecular transistors. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 477‐486 DOI: 10.1002/wcms.16This article is categorized under:

Structure and Mechanism > Molecular Structures
Structure and Mechanism > Computational Materials Science
Excited‐state dynamics
Authors: Lasorne Benjamin , Worth Graham A. , Robb Michael A. 
Published: June 2011

AbstractExcited‐state dynamics is the field of theoretical and physical chemistry devoted to simulating molecular processes induced upon UV‐visible light absorption. This involves nuclear dynamics methods to determine the time evolution of the molecular geometry used in concert with electronic structure methods capable of computing electronic excited‐state potential energy surfaces. Applications concern photochemistry (see Chapter CMS‐030: Computational photochemistry) and electronic spectroscopy. Most of the work in this field looks at unsaturated organic molecules as these provide widely used chromophores with a straightforward photochemistry that can be described by a small number (usually two) of electronic states. The electronic ground state of closed‐shell organic molecules is a singlet (electronic spin zero) termed S0. Molecules are promoted to their electronic excited states through absorption of UV‐visible light (200–700 nm), usually to the first or second singlet, S1 or S2. Typical examples are well represented as a one‐electron transition from the π or n highest occupied molecular orbital to a π* or σ* low‐lying unoccupied molecular orbital. The photo‐excited system will deactivate and return to the electronic ground state over a timescale that can be as short as about 100 fs for ultrafast mechanisms. For example, the initial event of vision is a photo‐isomerization of the retinal chromophore in the rhodopsine protein that occurs in ca. 200 fs.1,2 The goal of a computational approach to the simulation of photo‐induced processes is the complete description of what happens at the molecular level from the promotion to the excited electronic state to the formation of products or regeneration of reactants back in the electronic ground state. © John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 460‐475 DOI: 10.1002/wcms.26This article is categorized under:

Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics
Pseudopotentials and modelpotentials
Authors: Cao Xiaoyan , Dolg Michael 
Published: June 2011

AbstractThe basic assumptions of quantum chemical ab initio valence‐only (VO) schemes, i.e., pseudopotential and modelpotential approaches, are briefly discussed. Both effective core potential schemes lead to a reduction of the computational effort for wavefunction‐based as well as density functional theory electronic structure calculations in comparison to corresponding all‐electron treatments and allow to include the most important relativistic contributions implicitly into formally nonrelativistic calculations by means of a suitable parameterization of the VO model Hamiltonian. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 200‐210 DOI: 10.1002/wcms.28This article is categorized under:

Structure and Mechanism > Molecular Structures
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Receptor flexibility in small‐molecule docking calculations
Authors: Kokh Daria B. , Wade Rebecca C. , Wenzel Wolfgang 
Published: June 2011

AbstractProtein structural flexibility plays a critical role in receptor–ligand binding processes and should be considered in computational drug design. However, the treatment of protein conformational changes is still a major challenge because it is associated with a large increase in the conformational space that needs to be sampled and requires highly accurate scoring functions that incorporate the receptor reorganization energy. A number of different approaches have been proposed recently to address this problem. Most of them have been shown to be successful in reproducing the correct docking pose of known ligands, but their benefit regarding enrichment, affinity prediction, and screening of large molecular libraries is less clear. Here, we review current methodologies to treat receptor conformational changes in structure‐based docking procedures, and show their impact on the accuracy of docking and scoring. We also discuss pitfalls and limitations of state‐of‐the‐art flexible‐receptor docking strategies and perspectives for their improvement. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 298‐314 DOI: 10.1002/wcms.29This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Proline‐derived organocatalysis and synergism between theory and experiments
Authors: Sunoj Raghavan B. 
Published: June 2011

AbstractThe ability of proline and its derivatives toward catalyzing asymmetric organic reactions is highlighted. Illustration of the impact of interdisciplinary efforts between computational and experimental research is provided through a number of interesting examples. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 920–931 DOI: 10.1002/wcms.37This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Chemical patent information systems
Authors: Downs Geoffrey M. , Barnard John M. 
Published: June 2011

AbstractThe chemical structure information in patents remains difficult to access, partly because it is frequently expressed in the form of Markush structures, which can encompass enormous numbers of individual compounds. Early search systems were based on chemical ‘fragment codes’ that have still not been entirely superseded by the ‘topological’ systems developed during the 1980s.There are a number of databases of specific patented structures, which can be searched using standard substructure search software, and the more recently developed ones use automated data mining techniques to extract chemical nomenclature from patent text and translate it into searchable representations. Although some work has been done on automatic reconstruction of searchable Markush structures from patent text, this has proved to be considerably more refractory.A number of alternative approaches to chemical patent searching are being explored, some involving similarity and nearest‐neighbor searching concepts, and some based on both existing curated databases and direct utilization of full‐text patents. In‐house systems, which facilitate integration with other cheminformatics systems, are also under development. These new systems may allow improvements in retrieval performance, especially with regard to search precision. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 727‐741 DOI: 10.1002/wcms.41This article is categorized under:

Computer and Information Science > Chemoinformatics
Algorithms for chemoinformatics
Authors: Brown Nathan 
Published: June 2011

AbstractThe field of chemoinformatics makes use of a great number of different computational algorithms from mathematics and computer science as well as algorithms that are defined explicitly for challenges specific to chemoinformatics. This article provides an overview of algorithms and algorithmic complexity together with a review of common algorithmic design paradigms. These approaches are then given context with a set of relevant examples from chemoinformatics with definitions of the algorithms and, where relevant, graphical explanations. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 716‐726 DOI: 10.1002/wcms.42This article is categorized under:

Computer and Information Science > Chemoinformatics
Prediction of protein binding sites and hot spots
Authors: Fernández‐Recio Juan 
Published: June 2011

AbstractProtein–protein interactions are involved in the majority of cell processes, and their detailed structural and functional characterization has become one of the most important challenges in current structural biology. The first ideal goal is to determine the structure of the specific complex formed upon interaction of two or more given proteins. However, since this is not always technically possible, the practical approach is often to locate and characterize the protein residues that are involved in the interaction. This can be achieved by experimental means at expense of time and cost, so a growing number of computer tools are becoming available to complement experimental efforts. Reported methods for interface prediction are based on sequence information or on structural data, and make use of a variety of evolutionary, geometrical, and physicochemical parameters. As we show here, computer predictions can achieve a high degree of success, and they are of practical use to guide mutational experiments as well as to explain functional and mechanistic aspects of the interaction. Interestingly, it has been found that typically only a few of the interacting residues contribute significantly to the binding energy. The identification of such hot‐spot residues is important for understanding basic aspects of protein association. In addition, these residues have received recent attention as possible targets for drug design, so several computer methods have been developed to predict them. We will review here existing computer approaches for the prediction of protein binding sites and hot‐spot residues, with a discussion on their applicability and limitations. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 680–698 DOI: 10.1002/wcms.45This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
Fluctional molecules
Authors: McKee Michael L. 
Published: June 2011

AbstractFluctional molecules are defined as molecules that can interconvert rapidly with respect to a reference timescale. The most common timescale is Nuclear Magnetic Resonance (NMR), which is millisecond (10−3 s). The rate constant of interconversion is given by the Eyring equation , where kB is Boltzmann constant, T is absolute temperature, h is Planck constant, ΔG‡ is the Gibbs free energy of activation, and R is gas constant that can be reduced to ln . A variety of spectroscopic techniques are often employed to study fluctional processes. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 943‐951 DOI: 10.1002/wcms.47This article is categorized under:

Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics
Organocatalysis: acylation catalysts
Authors: Larionov Evgeny , Zipse Hendrik 
Published: June 2011

AbstractThis review shows how experimental and theoretical methods can help chemists to clarify the mechanism of acylation reactions and subsequently use this insight to develop improved acylation catalysts. Theoretical methods can be used in this context in a variety of ways, starting from the structural optimization of reactants, products, and reaction intermediates up to the full characterization of potential energy surfaces. Whether, in the end, all of this is necessary for the theory‐guided development of acylation catalysts is discussed in the last section of this review. The most challenging area in acylation catalyst development remains that of stereoselective catalysis, in which major advances have recently been made, but where theoretical prediction of catalyst selectivity is still exceedingly rare. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 601–619 DOI: 10.1002/wcms.48This article is categorized under:

Structure and Mechanism > Molecular Structures
Enabling future drug discovery by de novo design
Authors: Hartenfeller Markus , Schneider Gisbert 
Published: June 2011

AbstractComputer‐assisted drug design is evolving as a source of innovation for drug discovery. In particular, de novo design approaches are being increasingly applied to find novel drug‐like compounds, molecular scaffolds, and bioisosteric replacements for established or unwanted fragments. Although some of the early software tools had a certain tendency to generate compounds of limited chemical attraction, modern de novo design algorithms put a strong emphasis on the synthesizability and drug‐likeness of machine‐generated compounds. We give an overview of the various methodologies for virtual compound construction, evaluation, and optimization in machina, and how they can support medicinal chemistry projects in the early phase of drug discovery. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 742–759 DOI: 10.1002/wcms.49This article is categorized under:

Computer and Information Science > Chemoinformatics
Carbodicarbenes—divalent carbon(0) compounds exhibiting carbon–carbon donor–acceptor bonds
Authors: Frenking Gernot , Tonner Ralf 
Published: June 2011

AbstractTheoretical and experimental studies of the recently introduced class of divalent carbon(0) compounds CL2, wherein L is a carbene ligand, are described. Carbodicarbenes posses two donor–acceptor bonds between carbene ligands and a bare carbon atom that retains its four valence electrons as two lone pairs. Carbodicarbenes R2C → C ← CR2are very strong Lewis bases. They are σ‐ and π‐donors and thus may bind to two Lewis bases. © 2011 John Wiley & Sons, Ltd.WIREs Comput Mol Sci2011 1 869–878 DOI: 10.1002/wcms.53This article is categorized under:Structure and Mechanism > Molecular Structures