bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear behavior during semi‐quantitative analysis of thin organic layers by laser desorption mass spectrometry
Authors: Mavrinskaya Natalia , Räder Hans Joachim , Müllen Klaus 
Published: June 2011

Characterization of the surface coverage and thickness of an organic thin film is particularly important in organic electronics and optoelectronics. For surface coverage down to the submonolayer level there is still a need for characterization methods which are easily applicable. In the present work we report on the evaluation of laser desorption mass spectrometry (LD‐MS) for its use in thickness determination of organic thin films. Whereas LD‐MS is well established as a soft ionization method for small molecules, its capability for use in quantitative analysis is nearly unexplored.We carried out experiments with two different molecules, 7,7,8,8‐tetracyanoquinodimethane and hexabenzocoronene, in a series of experiments with increasing surface coverage. The obtained data were analyzed by plotting the LD signal intensities versus the relative layer thickness and they reveal a nonlinear behavior, which can be classified into regions of different desorption/ionization efficiencies. Visualization by atomic force microscopy reveals that the first efficiency change corresponds to the transition between incomplete and complete coverage of the metal surface by analyte molecules. A second transition is observed at high layer thickness where the signal intensity stays constant, independent of further thickness increments, and this is attributed to the limited penetration depth of the laser beam. The intermediate region between the two transitions shows a linear behavior and can thus be used for semi‐quantitative thickness measurements. The efficiency change observed at the point of complete surface coverage is particularly useful for thin layer preparation of organic field effect transistors, where complete surface coverage is a minimum requirement. Copyright © 2011 John Wiley & Sons, Ltd.
Columbus—a program system for advanced multireference theory calculations
Authors: Lischka Hans , Müller Thomas , Szalay Péter G. , Shavitt Isaiah , Pitzer Russell M. , Shepard Ron 
Published: June 2011

AbstractThe COLUMBUS Program System allows high‐level quantum chemical calculations based on the multiconfiguration self‐consistent field, multireference configuration interaction with singles and doubles, and the multireference averaged quadratic coupled cluster methods. The latter method includes size‐consistency corrections at the multireference level. Nonrelativistic (NR) and spin–orbit calculations are available within multireference configuration interaction (MRCI). A prominent feature of COLUMBUS is the availability of analytic energy gradients and nonadiabatic coupling vectors for NR MRCI. This feature allows efficient optimization of stationary points and surface crossings (minima on the crossing seam). Typical applications are systematic surveys of energy surfaces in ground and excited states including bond breaking. Wave functions of practically any sophistication can be constructed limited primarily by the size of the CI expansion rather than by its complexity. A massively parallel CI step allows state‐of‐the art calculations with up to several billion configurations. Electrostatic embedding of point charges into the molecular Hamiltonian gives access to quantum mechanical/molecular mechanics calculations for all wave functions available in COLUMBUS. The analytic gradient modules allow on‐the‐fly nonadiabatic photodynamical simulations of interesting chemical and biological problems. Thus, COLUMBUS provides a wide range of highly sophisticated tools with which a large variety of interesting quantum chemical problems can be studied. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 191‐199 DOI: 10.1002/wcms.25This article is categorized under:

Software > Quantum Chemistry
Metadynamics
Authors: Barducci Alessandro , Bonomi Massimiliano , Parrinello Michele 
Published: June 2011

AbstractMetadynamics is a powerful technique for enhancing sampling in molecular dynamics simulations and reconstructing the free‐energy surface as a function of few selected degrees of freedom, often referred to as collective variables (CVs). In metadynamics, sampling is accelerated by a history‐dependent bias potential, which is adaptively constructed in the space of the CVs. Since its first appearance, significant improvements have been made to the original algorithm, leading to an efficient, flexible, and accurate method that has found many successful applications in several domains of science. Here, we discuss first the theory underlying metadynamics and its recent developments. In particular, we focus on the crucial issue of choosing an appropriate set of CVs and on the possible strategies to alleviate this difficulty. Later in the second part, we present a few recent representative applications, which we have classified into three main classes: solid‐state physics, chemical reactions, and biomolecules. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 826‐843 DOI: 10.1002/wcms.31This article is categorized under:

Molecular and Statistical Mechanics > Free Energy Methods
Polarization effects in molecular interactions
Authors: Luque F. Javier , Dehez François , Chipot Christophe , Orozco Modesto 
Published: June 2011

AbstractStandard, additive force fields used in the vast majority of molecular simulations have proven valuable for describing the essential structural and energetic features of complex chemical systems. There is, however, a growing body of evidence that such nonpolarizable force fields cannot provide a fine description in systems where induction effects are significant. Polarizable force fields are designed to account for the variations of the charge distribution in response to the local electric fields created by the environment. Over the past decade, the molecular modeling arena has witnessed the development of new nonadditive force fields at an accelerated pace, which include distinct strategies for the accurate treatment of induction effects. Unavoidably, these developments proved more challenging than anticipated, necessitating various approximations. This contribution aims to provide a concise overview of the recent advances and current status in this field. © 2011 John Wiley & Sons, Ltd.WIREs Comput Mol Sci2011 1 844‐854 DOI: 10.1002/wcms.32This article is categorized under:Structure and Mechanism > Molecular StructuresStructure and Mechanism > Computational Biochemistry and BiophysicsMolecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Geometry optimization
Authors: Schlegel H. Bernhard 
Published: June 2011

AbstractGeometry optimization is an important part of most quantum chemical calculations. This article surveys methods for optimizing equilibrium geometries, locating transition structures, and following reaction paths. The emphasis is on optimizations using quasi‐Newton methods that rely on energy gradients, and the discussion includes Hessian updating, line searches, trust radius, and rational function optimization techniques. Single‐ended and double‐ended methods are discussed for transition state searches. Single‐ended techniques include quasi‐Newton, reduced gradient following and eigenvector following methods. Double‐ended methods include nudged elastic band, string, and growing string methods. The discussions conclude with methods for validating transition states and following steepest descent reaction paths. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 790–809 DOI: 10.1002/wcms.34This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
Representation of chemical structures
Authors: Warr Wendy A. 
Published: June 2011

AbstractAt the root of applications for substructure and similarity searching, reaction retrieval, synthesis planning, drug discovery, and physicochemical property prediction is the need for a machine‐readable representation of a structure. Systematic nomenclature is unsuitable, and notations and fragment codes have been superseded, except in certain specific applications. Connection tables are widely used, but there is no formal standard. Recently the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) has started to attract interest. This review also summarizes the representation of chemical reactions and three‐dimensional structures. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 557–579 DOI: 10.1002/wcms.36This article is categorized under:

Computer and Information Science > Chemoinformatics
Green's function methods for calculating ionization potentials, electron affinities, and excitation energies
Authors: Danovich David 
Published: June 2011

AbstractGreen's function (GF; electron propagator) methods represent a very useful set of tools for direct calculation of electron detachment (ionization potentials), electron attachment (electron affinities), excitation energies, electron transition probabilities, and other properties. The main idea of GF methods is that for description of various properties of a many‐body system, one does not need to describe all the particles of the system but rather needs information about one or two particles belonging to the system. The corresponding required quantities are the one‐ and two‐particle GFs. Within one‐ or two‐particle GF methods, the energy difference between an initial state and a state with one additional or one less electron is calculated directly, thus eliminating errors due to inconsistent treatment of the initial and final states. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 377–387 DOI: 10.1002/wcms.38This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
Vibrational circular dichroism
Authors: Magyarfalvi Gábor , Tarczay György , Vass Elemér 
Published: June 2011

AbstractThis review focuses on the theoretical background of vibrational circular dichroism (VCD) spectroscopy. Besides discussing the first‐principle approaches of the theoretical evaluation of VCD spectra, practical computational considerations, such as the available electronic structure computational levels and program packages, are summarized. Illustrative examples are shown for the absolute configuration and conformation determination of mid‐sized molecules based on the comparison of calculated end experimental VCD spectra, including the comparison of the performance of different computational levels. The conformational analysis of larger biomolecules, such as carbohydrates, nucleotides, and peptides by VCD spectroscopy, and the theoretical simulation of solvent effects are also discussed. The review is concluded by a short summary of the present stage of the computation of VCD spectra and the expected future direction of theoretical developments. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 403–425 DOI: 10.1002/wcms.39This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
The atomistic simulation of DNA
Authors: Laughton Charles A. , Harris Sarah A. 
Published: June 2011

AbstractWe review the current state of the art relating to the atomistic simulation of the structure and dynamics of DNA. We begin with a brief historical overview to set the scene and introduce some of the key issues that had to be addressed to progress the field and then we divide our discussion of the current situation into two sections. First, we overview the role that simulation has played, closely intertwined with experimental studies, in increasing our understanding of the biomechanical properties of DNA, for example, the way in which its structure responds to perturbations such as stretching and over‐ and under‐twisting. Second, we discuss how atomistic simulations are contributing to our deeper understanding of nucleic acid recognition—both by proteins and by small‐molecule ligands. In both areas, we emphasize not only where simulation has been particularly successful but also where thorny problems remain to tax the ingenuity of computational scientists in close collaboration with their experimental colleagues. © 2011 John Wiley & Sons, Ltd.WIREs Comput Mol Sci2011 1 590–600 DOI: 10.1002/wcms.46This article is categorized under:Structure and Mechanism > Computational Biochemistry and Biophysics
NWChem: scalable parallel computational chemistry
Authors: van Dam H.J.J. , de Jong W.A. , Bylaska E. , Govind N. , Kowalski K. , Straatsma T.P. , Valiev M. 
Published: June 2011

AbstractNWChem is a general‐purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree–Fock theory, and density functional theory methods for both plane‐wave basis sets as well as Gaussian basis sets, tensor contraction engine‐based coupled cluster capabilities, and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message‐passing approaches could offer. In response, a global address space library, the Global Array toolkit, was developed. The programming model it offers is based on using predominantly one‐sided communication. This model underpins most of the functionality in NWChem, and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper, the core capabilities of NWChem are described as well as their implementation to achieve an efficient computational chemistry code with high parallel scalability. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 888–894 DOI: 10.1002/wcms.62This article is categorized under:

Software > Quantum Chemistry
NMR spectroscopy: quantum‐chemical calculations
Authors: Bühl Michael , van Mourik Tanja 
Published: June 2011

AbstractThe first‐principles computation of nuclear magnetic resonance parameters, in particular chemical shift and spin–spin coupling tensors, is reviewed. After a brief nontechnical introduction into the methodology behind such calculations, selected applications from chemistry and biochemistry in solution and the solid state are highlighted. Special attention is called to cases wherein theory can help in structure determination and refinement, as well as in the interpretation of the observables. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 634–647 DOI: 10.1002/wcms.63This article is categorized under:

Theoretical and Physical Chemistry > Spectroscopy
Nonadiabatic dynamics with trajectory surface hopping method
Authors: Barbatti Mario 
Published: June 2011

AbstractThe trajectory surface hopping (TSH) method is a general methodology for dynamics propagation of nonadiabatic systems. It is based on the hypothesis that the time evolution of a wave packet through a potential‐energy branching region can be approximated by an ensemble of independent semiclassical trajectories stochastically distributed among the branched surfaces. As it was proposed about 40 years ago, the TSH methodology has become one of the main tools for nonadiabatic dynamics propagation in molecular physics and chemistry. One reason for this success lies on its intuitive conceptual background allied to its high computational efficiency when compared to full quantum mechanical propagation. In this work, the TSH method is reviewed and applications from different fields are surveyed. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 620–633 DOI: 10.1002/wcms.64This article is categorized under:

Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics
Mifepristone Treatment Results in Differential Regulation of Glycerolipid Biosynthesis in Baby Hamster Kidney Cells Expressing a Mifepristone‐Inducible ABCA1
Authors: Hauff Kristin D. , Mitchell Ryan W. , Xu Fred Y. , Dembinski Thomas , Mymin David , Zha Xiaohui , Choy Patrick C. , Hatch Grant M. 
Published: June 2011

AbstractATP binding cassette A1 (ABCA1) transports cholesterol, phospholipids and lipophilic molecules to and across cellular membranes. We examined if ABCA1 expression altered cellular de novo glycerolipid biosynthesis in growing Baby hamster kidney (BHK) cells. Mock BHK cells or cells expressing a mifepristone‐inducible ABCA1 (ABCA1) were incubated plus or minus mifepristone and then with [3H]serine or [3H]inositol or [3H]ethanolamine or [methyl‐3H]choline or [3H]glycerol or [14C]oleate and radioactivity incorporated into glycerolipids determined. Mifepristone did not affect [1,3‐3H]glycerol or [14C]oleate or [3H]ethanolamine or [methyl‐3H]choline uptake in BHK cells. In contrast, [3H]glycerol and [14C]oleate incorporated into phosphatidylserine (PtdSer) were elevated 2.4‐fold (p < 0.05) and 54% (p < 0.05), respectively, upon ABCA1 induction confirming increased PtdSer biosynthesis from these precursors. However, mifepristone inhibited [3H]serine uptake and incorporation into PtdSer indicating that PtdSer synthesis from serine in BHK cells is dependent on serine uptake. Mifepristone stimulated [3H]inositol uptake in mock and ABCA1 cells but not its incorporation into phosphatidylinositol indicating that its synthesis from inositol is independent of inositol uptake in BHK cells. [3H]glycerol and [14C]oleate incorporated into triacylglycerol were reduced and into diacylglycerol elevated only in mifepristone‐induced ABCA1 expressing cells due to a decrease in diacylglycerol acyltransferase‐1 (DGAT‐1) activity. The presence of trichostatin A, a class I and II histone deacetylase inhibitor, reversed the ABCA1‐mediated reduction in DGAT‐1 activity but did not affect DGAT‐1 mRNA expression. Thus, mifepristone has diverse effects on de novo glycerolipid synthesis. We suggest that caution should be exercised when using mifepristone‐inducible systems for studies of glycerolipid metabolism in cells expressing glucocorticoid responsive receptors.
Can widespread hypersensitivity in carpal tunnel syndrome be substantiated if neck and arm pain are absent?
Authors: Schmid A.B. , Soon B.TC. , Wasner G. , Coppieters M.W. 
Published: June 2011

AbstractRecent studies demonstrated that patients with carpal tunnel syndrome (CTS) have signs of thermal and mechanical hyperalgesia in extra‐median territories suggesting an involvement of central pain mechanisms. As previous studies included patients with shoulder/arm symptoms or neck pain, a potential influence of these coexisting disorders cannot be excluded. This study therefore evaluated whether widespread sensory changes (hypoesthesia or hyperalgesia) are present in patients with unilateral CTS in the absence of coexisting disorders. Twenty‐six patients with unilateral CTS with symptoms localised to their hand and 26 healthy controls participated in the study. A comprehensive quantitative sensory testing (QST) protocol including thermal and mechanical detection and pain thresholds was performed over the hands (median, ulnar and radial innervation area), lateral elbows, neck and tibialis anterior muscle. Patients with CTS demonstrated thermal and mechanical hypoesthesia in the hand but not at distant sites. Thermal or mechanical hyperalgesia was not identified at any location with traditional QST threshold testing. However, patients with CTS rated the pain during thermal pain testing significantly higher than healthy participants. This was especially apparent for heat pain ratings which were elevated not only in the affected hand but also in the neck and tibialis anterior muscle. In conclusion, CTS alone in the absence of coexisting neck and arm pain does not account for sensory changes outside the affected hand as determined by traditional QST threshold testing. Elevated pain ratings may however be an early indication of central pain mechanisms.
Is adherence to pain self‐management strategies associated with improved pain, depression and disability in those with disabling chronic pain?
Authors: Nicholas M.K. , Asghari A. , Corbett M. , Smeets R.J.E.M. , Wood B.M. , Overton S. , Perry C. , Tonkin L.E. , Beeston L. 
Published: June 2011

AbstractThere is generally good evidence that pain management interventions that include self‐management strategies can substantially reduce disability and improve psychological well‐being in patients with chronic pain. Reductions in unhelpful responses, especially catastrophising and fear‐avoidance beliefs, have been established as key contributors to these gains. In contrast, there is surprisingly little evidence that adherence to self‐management strategies contributes to achieving these outcomes. Difficulties in defining and measuring the use of pain self‐management strategies have been obstacles for this research. Using a pragmatic way of assessing the practice of specific strategies this study investigated their ability to account for changes in pain, disability and depressive symptoms after a 3‐week cognitive‐behavioural pain management program. The post‐treatment outcomes on these dimensions were found to be statistically and, for many, clinically significant. Consistent with previous research, reductions in catastrophising and fear‐avoidance beliefs, and increased pain self‐efficacy beliefs, were also associated with these gains. But the key new finding was that there was a clear gradient between adherence to specific self‐management strategies and reductions in pain, disability and depressive symptoms. Furthermore, adherence to the self‐management strategies was predictive of better outcomes even after controlling for the moderating effects of initial catastrophising, fear‐avoidance and pain self‐efficacy beliefs.
Impaired hypoxic response in senescent mouse brain
Authors: Rabie Tamer , Kunze Reiner , Marti Hugo H. 
Published: June 2011

AbstractTissue hypoxia leads to activation of endogenous adaptive responses that involve a family of prolyl hydroxylase domain proteins (PHD1‐3) with oxygen sensing properties, hypoxia inducible transcription factors (HIFs), and cytoprotective HIF target genes such as erythropoietin (EPO) and vascular endothelial growth factor (VEGF). The hypoxic induction of these genes is regulated by oxygen‐dependent hydroxylation of HIFα subunits by PHDs, which signals their proteasomal degradation. In this study, mice of different age were exposed to hypoxia or subjected to cerebral ischemia after hypoxic pre‐conditioning. We found an impaired hypoxic response in the brain, characterized by elevated levels and impaired downregulation of PHD1. Furthermore, an attenuated hypoxic activation of VEGF and EPO, as well as of other HIF‐target genes such glucose transporter‐1 and carbonic anhydrase 9 was found in senescent brain. Finally, we observed a loss of the protective effect of hypoxic pre‐conditioning on subsequent cerebral ischemia with increasing age. Thus, the impaired hypoxic adaptation, resulting in compromised hypoxic activation of neuroprotective factors, could contribute to neurodegenerative processes with increasing age, and might have implications for treating age‐related disorders.