bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathway‐Dependent Self‐Assembly of Perylene Diimide/Peptide Conjugates in Aqueous Medium
Authors: Tidhar Yaron , Weissman Haim , Wolf Sharon G. , Gulino Antonino , Rybtchinski Boris
Published: May 2011

Most molecular self‐assembly strategies involve equilibrium systems, leading to a single thermodynamic product as a result of weak, reversible non‐covalent interactions. Yet, strong non‐covalent interactions may result in non‐equilibrium self‐assembly, in which structural diversity is achieved by forming several kinetic products based on a single covalent building block. We demonstrate that well‐defined amphiphilic molecular systems based on perylene diimide/peptide conjugates exhibit kinetically controlled self‐assembly in aqueous medium, enabling pathway‐dependent assembly sequences, in which different organic nanostructures are evolved in a stepwise manner. The self‐assembly process was characterized using UV/Vis circular dichroism (CD) spectroscopy, and cryogenic transmission electron microscopy (cryo‐TEM). Our findings show that pathway‐controlled self‐assembly may significantly broaden the methodology of non‐covalent synthesis.
Mechanistic Insights into Photochromic Behavior of a Ruthenium(II)–Pterin Complex
Authors: Ishizuka Tomoya , Sawaki Takuya , Miyazaki Soushi , Kawano Masaki , Shiota Yoshihito , Yoshizawa Kazunari , Fukuzumi Shunichi , Kojima Takahiko
Published: May 2011

The pterin‐coordinated ruthenium complex, [RuII(dmdmp)(tpa)]+ (1) (Hdmdmp=N,N‐dimethyl‐6,7‐dimethylpterin, tpa=tris(2‐pyridylmethyl)amine), undergoes photochromic isomerization efficiently. The isomeric complex (2) was fully characterized to reveal an apparent 180° pseudorotation of the pterin ligand. Photoirradiation to the solution of 1 in acetone with incident light at 460 nm resulted in dissociation of one pyridylmethyl arm of the tpa ligand from the RuII center to give an intermediate complex, [Ru(dmdmp)(tpa)(acetone)]2+ (I), accompanied by structural change and the coordination of a solvent molecule to occupy the vacant site. The quantum yield (ϕ) of this photoreaction was determined to be 0.87 %. The subsequent thermal process from intermediate I affords an isomeric complex 2, as a result of the rotation of the dmdmp2− ligand and the recoordination of the pyridyl group through structural change. The thermal process obeyed first‐order kinetics, and the rate constant at 298 K was determined to be 5.83×10−5 s−1. The activation parameters were determined to be ΔH≠=81.8 kJ mol−1 and ΔS≠=−49.8 J mol−1 K−1. The negative ΔS≠ value indicates that this reaction involves a seven‐coordinate complex in the transition state (i.e., an interchange associative mechanism). The most unique point of this reaction is that the recoordination of the photodissociated pyridylmethyl group occurs only from the direction to give isomer 2, without going back to starting complex 1, and thus the reaction proceeds with 100 % conversion efficiency. Upon heating a solution of 2 in acetonitrile, isomer 2 turned back into starting complex 1. The backward reaction is highly dependent on the solvent: isomer 2 is quite stable and hard to return to 1 in acetone; however, 2 was converted to 1 smoothly by heating in acetonitrile. The activation parameters for the first‐order process in acetonitrile were determined to be ΔH≠=59.2 kJ mol−1 and ΔS≠=−147.4 kJ mol−1 K−1. The largely negative ΔS≠ value suggests the involvement of a seven‐coordinate species with the strongly coordinated acetonitrile molecule in the transition state. Thus, the strength of the coordination of the solvent molecule to the RuII center is a determinant factor in the photoisomerization of the RuII–pterin complex.
Silica Nanocapsules of Fluorescent Conjugated Polymers and Superparamagnetic Nanocrystals for Dual‐Mode Cellular Imaging
Authors: Tan Happy , Wang Miao , Yang Chang‐Tong , Pant Shilpa , Bhakoo Kishore Kumar , Wong Siew Yee , Chen Zhi‐Kuan , Li Xu , Wang John
Published: May 2011

We describe here a facile and benign synthetic strategy to integrate the fluorescent behavior of conjugated polymers and superparamagnetic properties of iron oxide nanocrystals into silica nanocapsules, forming a new type of bifunctional magnetic fluorescent silica nanocapsule (BMFSN). The resultant BMFSNs are uniform, colloidally stable in aqueous medium, and exhibit the desired dual functionality of fluorescence and superparamagnetism in a single entity. Four conjugated polymers with different emissions were used to demonstrate the versatility of employing this class of fluorescent materials for the preparation of BMFSNs. The applicability of BMFSNs in cellular imaging was studied by incubating them with human liver cancer cells, the result of which demonstrated that the cells could be visualized by dual‐mode fluorescence and magnetic resonance imaging. Furthermore, the superparamagnetic behavior of the BMFSNs was exploited for in vitro magnetic‐guided delivery of the nanocapsules into the cancer cells, thereby highlighting their potential for targeting biomedical applications.
Proton‐Fueled DNA‐Duplex‐Based Stimuli‐Responsive Reversible Assembly of Single‐Walled Carbon Nanotubes
Authors: Zhao Chao , Qu Konggang , Ren Jinsong , Qu Xiaogang
Published: May 2011

Single‐walled carbon nanotubes (SWNTs) have received much attention in nanotechnology because of their potential applications in molecular electronics, field‐emission devices, biomedical engineering, and biosensors. Carbon nanotubes as gene and drug delivery vectors or as “building blocks” in nano‐/microelectronic devices has been successfully explored. However, since SWNTs lack chemical recognition, SWNT‐based electronic devices and sensors are strictly related to the development of a bottom‐up self‐assembly technique. Here we present an example of using DNA duplex‐based protons (H+) as a fuel to control reversible assembly of SWNTs without generation of waste duplex products that poison DNA‐based systems.
A data‐operation model based on partial vector space for batch processing in workflow
Authors: Liu Jianxun , Wen Yiping , Li Ting , Zhang Xuyun
Published: May 2011

Batch processing in workflow schedules activity instances in multiple workflow cases of the same workflow type to run as a group. It can optimize business processes execution dynamically. To achieve this goal, it is necessary to define a dataflow operation language to group and ungroup the data in multiple cases of a workflow. Though our previous work has preliminarily investigated the model and its implementation, there is still lack of a formally defined model. In this paper, we first propose a method that is based on a partial vector space to model the dataflow in multiple workflow cases. Based on this model, the data operation primitives for batch processing are specified and defined formally. Since most WfMSs (Workflow Management Systems) use RDBMS (relational database management system) to store their data currently, an SQL (Structured Query Language)‐like implementation language, namely DBOL (Data Batch Operation Language), is proposed. Evaluation experiments have also been done to show its performance. Copyright © 2011 John Wiley & Sons, Ltd.
Flexible and efficient profiling with aspect‐oriented programming
Authors: Binder Walter , Ansaloni Danilo , Villazón Alex , Moret Philippe
Published: May 2011

Many profilers for virtual execution environments, such as the Java virtual machine (JVM), are implemented with low‐level bytecode instrumentation techniques, which is tedious, error‐prone, and complicates maintenance and extension of the tools. In order to reduce the development time and cost, we promote building profilers for the JVM using high‐level aspect‐oriented programming (AOP). We show that the use of aspects yields concise profilers that are easy to develop, extend, and maintain, because low‐level instrumentation details are hidden from the tool developer. In order to build efficient profilers, we introduce inter‐advice communication, an extension to common AOP languages that enables efficient data passing between advices that are woven into the same method using local variables. We illustrate our approach with two case studies. First, we show that an existing, instrumentation‐based tool for listener latency profiling can be easily recast as an aspect. Second, we present an aspect for comprehensive calling context profiling. In order to reduce profiling overhead, our aspect parallelizes application execution and profile creation, resulting in a speedup of 110% on a machine with more than two cores, compared with
a primitive, non‐parallel approach. Copyright © 2011 John Wiley & Sons, Ltd.
Corporate Social Reporting in European Banks: The Effects on a Firm's Market Value
Authors: Carnevale Concetta , Mazzuca Maria , Venturini Sergio
Published: May 2011

Despite the increasing level of interest in CSR issues, it is not yet clear what real value the market assigns to social reporting. By applying the value relevance analysis to a sample of 130 European‐listed banks, the present work proposes a key to understanding the relationship between social reporting and the value that the market attributes to banks that publicize their commitment to CSR through social reporting. The analysis for the entire sample does not provide evidence that investors attribute value relevance to social reporting (i.e. there is not a significant correlation between the publication of a social report and the stock price). Cross‐country analysis shows that in some countries the social report is value‐relevant, and positively affects the stock price; in others it remains value‐relevant but negatively affects the stock price. Our findings could have several implications for banks, investors, and policymakers. Copyright © 2011 John Wiley & Sons, Ltd and ERP Environment.
Expression and rapid experience‐dependent regulation of type‐A GABAergic receptors in the songbird auditory forebrain
Authors: Jeong Jin Kwon , Terleph Thomas A. , Burrows Kaiping , Tremere Liisa A. , Pinaud Raphael
Published: May 2011

GABAergic transmission influences sensory processing and experience‐dependent plasticity in the adult brain. Little is known about the functional organization of inhibitory circuits in the auditory forebrain of songbirds, a robust model extensively used in the study of central auditory processing of behaviorally relevant communication signals. In particular, no information is currently available on the expression and organization of GABAA receptor‐expressing neurons. Here, we studied the distribution and regulation of GABAA receptors in the songbird auditory forebrain, with a specific focus on α5, a subunit implicated in tonic inhibition and sensory learning. We obtained a zebra finch cDNA that encodes the α5‐subunit (GABRA5) and carried out a detailed analysis of its expression via in situ hybridization. GABRA5 was highly expressed in the caudomedial nidopallium (NCM), caudomedial mesopallium, and field L2. Using double fluorescence in situ hybridization, we demonstrate that a large fraction of GABRA5‐expressing neurons is engaged by auditory experience, as revealed by the song‐induced expression of the activity‐dependent gene zenk. Remarkably, we also found that α5 expression is rapidly regulated by sensory stimulation: 30 min of conspecific song playbacks significantly increase the number of GABRA5‐expressing neurons in NCM, but not in other auditory areas. This effect is selective for α5, but not γ2 transcripts. Our results suggest that α5‐containing GABAA receptors likely play a key role in central auditory processing and may contribute to the experience‐dependent plasticity underlying auditory learning. © 2011 Wiley Periodicals, Inc. Develop Neurobiol 71: 803–817, 2011
Amphetamine induced dopamine release increases anxiety in individuals recovered from anorexia nervosa
Authors: Bailer Ursula F. , Narendran Rajesh , Frankle W. Gordon , Himes Michael L. , Duvvuri Vikas , Mathis Chester A. , Kaye Walter H.
Published: May 2011

Objective:

Genetic, pharmacologic, and physiological data suggest that individuals with anorexia nervosa (AN) have altered striatal dopamine (DA) function.

Method:

We used an amphetamine challenge and positron emission tomography [11C]raclopride paradigm to explore DA striatal transmission in 10 recovered (REC) AN compared with 9 control women (CW).

Results:

REC AN and CW were similar for baseline, postamphetamine [11C]raclopride binding potential (BPND) and change (Δ) in BPND for all regions. In CW, ventral striatum Δ BPND was associated with euphoria (r = −0.76; p = 0.03), which was not found for REC AN. Instead, REC AN showed a significant relationship between anxiety and Δ BPND in the precommissural dorsal caudate (r = −0.62, p = 0.05).

Discussion:

REC AN have a positive association between endogenous DA release and anxiety in the dorsal caudate. This finding could explain why food‐related DA release produces anxiety in AN, whereas feeding is pleasurable in healthy participants. © 2011 by Wiley Periodicals, Inc. (Int J Eat Disord 2012)
Zinc Halide and Alkylzinc Complexes of a Neutral Doubly Base‐Stabilized Diborane(4)
Authors: Schulenberg Nikola , Litters Sebastian , Kaifer Elisabeth , Himmel Hans‐Jörg
Published: May 2011

The doubly base‐stabilized diborane(4) [HB(μ‐hpp)]2 (hpp = 1,3,4,6,7,8‐hexahydro‐2H‐pyrimido[1,2‐a]pyrimidinate) was used as a ligand in the first authenticated example of a dialkylzinc complex and the second example of a zinc halide complex featuring a neutral boron hydride as ligand. The three complexes [ZnCl2{HB(μ‐hpp)}2] (2), [ZnBr2{HB(μ‐hpp)}2] (3), and [ZnMe2{HB(μ‐hpp)}2] (4) were fully characterized. The bonding properties were analysed in detail. This analysis indicated a complex bonding situation involving not only the two hydrogen atoms, but also the two boron atoms of the [HB(μ‐hpp)]2 ligand.
Synthesis of α‐N‐Linked Glycopeptides
Authors: Colombo Cinzia , Bernardi Anna
Published: May 2011

A practical synthesis of Nα‐fluorenylmethoxycarbonyl‐Nγ‐(2,3,4,6‐tetra‐O‐acetyl‐α‐D‐glycopyranosyl)‐L‐asparagine in the gluco and galacto series has been achieved by using the methodology developed by DeShong and co‐workers. The resulting α‐N‐linked glycosyl amino acids were used in a linear approach to the synthesis of glycopeptides featuring the unnatural α‐N‐glycosyl linkage. Activation conditions for both C‐ and N‐terminus elongation in solution have been defined. The main side‐reaction encountered was the formation of cyclization by‐products (aspartimide) from the activated amino acid during C‐terminus elongation. Appropriate condensing agents were identified, which allowed a high yield of dipeptide formation and no epimierization of the glycosyl amino acids. Conditions for sugar deacetylation have also been optimized. Solid‐phase synthesis (Fmoc protocol) conditions were explored and PyBROP was found to be the reagent of choice for the activaton of glycosyl amino acids. The synthesis of more complex α‐N‐linked glycopeptides has thus become feasible, which will allow the properties of these neo‐glycoconjugates to be studied.
Implementation intentions as goal primes: Boosting self‐control in tempting environments
Authors: van Koningsbruggen Guido M. , Stroebe Wolfgang , Papies Esther K. , Aarts Henk
Published: May 2011

People often forget their long‐term strivings because their environment confronts them with attractive temptations. Previous research suggests that self‐control failures can be prevented by reminding people of their higher‐order goal. Therefore, we hypothesized that using implementation intentions as a tool to directly re‐activate people's higher‐order goal in tempting situations would effectively enhance self‐control. We tested this in the domain of dieting behavior. Results demonstrated that this specific planning strategy activated the dieting goal for unsuccessful dieters when exposed to tempting food cues (Study 1) and reduced their consumption of calorically dense food across 2 weeks (Study 2) compared to those in control conditions. This suggests that preparing people to think of their higher‐order goal when tempted can be used to protect ongoing goal striving. Appealing to higher‐order goals potentially makes implementation intentions flexible instruments of self‐regulation as this should trigger motivated behavior to reach goals and initiate various goal‐instrumental actions. Copyright © 2011 John Wiley & Sons, Ltd.
Theoretical Treatment of a Cathodic Stripping Mechanism of an Insoluble Salt Coupled with a Chemical Reaction in Conditions of Square Wave Voltammetry. Application to 6‐Mercaptopurine‐9‐D‐Riboside in the Presence of Ni(II)
Authors: Mirčeski Valentin , Guziejewski Dariusz , Ciesielski Witold
Published: May 2011

Cathodic stripping mechanism of an insoluble salt coupled with a homogenous chemical reaction is considered both theoretically and experimentally under conditions of square‐wave voltammetry. For the mercury electrode in aqueous solution, the electrode reaction is described as L(aq)+Hg(l)=HgL(s)+2e−, where L(aq) is the reactive ligand that forms a sparingly soluble compound HgL(s). The electrode reaction is coupled with a homogenous, first‐order chemical reaction, A(aq)=L(aq). Theoretical predictions are confirmed by experiments with 6‐mercaptopurine‐9‐D‐riboside in the presence of nickel(II) ions.
N‐(3,4‐Dihydroxyphenethyl)‐3,5‐dinitrobenzamide‐Modified Multiwall Carbon Nanotubes Paste Electrode as a Novel Sensor for Simultaneous Determination of Penicillamine, Uric acid, and Tryptophan
Authors: Ensafi Ali A. , Karimi‐Maleh Hassan , Mallakpour Shadpour
Published: May 2011

N‐(3,4‐dihydroxyphenethyl)‐3,5‐dinitrobenzamide modified multiwall carbon nanotubes paste electrode was used as a voltammetric sensor for oxidation of penicillamine (PA), uric acid (UA) and tryptophan (TP). In a mixture of PA, UA and TP, those voltammograms were well separated from each other with potential differences of 300, 610, and 310 mV, respectively. The peak currents were linearly dependent on PA, UA and TP concentrations in the range of 0.05–300, 5–420, and 1.0–400 µmol L−1, with detection limits of 0.021, 2.0, and 0.82 µmol L−1, respectively. The modified electrode was used for the determination of those compounds in real samples.
Solid‐State Electrochemistry and Electrochemiluminescence of Porous Thin Film of [(2,2′‐Bipyridyl)(4‐(2‐pyrrol‐1‐ylethyl)‐4′‐methyl‐2,2′‐bipyridyl)2]ruthenium(II) Monomer Precipitation
Authors: Ding Shou‐Nian , Zhu Wei , Shan Dan , Wan Neng , Sun Yue‐Ming , Cosnier Serge
Published: May 2011

A novel fluorescent porous thin film based on the precipitation of the [(2,2′‐bipyridyl)(4‐(2‐pyrrol‐1‐ylethyl)‐4′‐methyl‐2,2′‐bipyridyl)2]ruthenium(II) (BF4)2 complex (pyr‐Ru) was fabricated by easily spreading 2 µL of pyr‐Ru (1 mM in acetonitrile solution) onto the surface of a platinum electrode and drying it in ambient conditions. The morphology of the resulting pyr‐Ru thin film was characterized by scanning electron microscopy (SEM) and fluorescence microscopy. The coating exhibits fluorescent properties of the ruthenium complex and a porous structure with pore diameters of micrometers. The solid‐state electrochemistry and electrochemiluminescence behaviors of the porous pyr‐Ru thin film were investigated in aqueous solution by cyclic voltammetry and step potential.
Electrochemical Sensor Based on Oxidation of 2,8‐Dihydroxyadenine to Monitor DNA Damage in Calf Thymus DNA
Authors: Goyal Rajendra N. , Chatterjee Sanghamitra , Rana Anoop Raj Singh
Published: May 2011

A novel and reliable direct electrochemical method has been established to monitor DNA damage in acid hydrolyzed calf thymus DNA, based on the determination of 2,8‐dihydroxyadenine (2,8‐DHA). A single‐wall carbon nanotubes (SWCNT) modified edge plane pyrolytic graphite electrode (EPPGE) has been used as a sensor to monitor the DNA damage. 2,8‐DHA the main in vivo adenine oxidation product undergoes oxidation at ∼395 mV at SWCNT modified EPPGE using square wave voltammetry (SWV). The sensor exhibits potent and persistent electron‐mediating behavior. A well‐defined oxidation peak for the oxidation of 2,8‐DHA was observed at modified electrode with lowering of peak potential and increase in peak current as compared to bare EPPGE. At optimal experimental conditions, the catalytic oxidative peak current was responsive with the 2,8‐DHA concentrations ranging from 0.05 nM to 100 nM. The detection limit was 3.8×10−11 M and limit of quantification was 1.27×10−10 M. The modified electrode exhibited high stability and reproducibility.
Electrokinetic transport through nanochannels
Authors: Movahed Saeid , Li Dongqing
Published: May 2011

This article presents a numerical study of the electrokinetic transport phenomena (electroosmosis and electrophoresis) in a three‐dimensional nanochannel with a circular cross‐section. Due to the nanometer dimensions, the Boltzmann distribution of the ions is not valid in the nanochannels. Therefore, the conventional theories of electrokinetic flow through the microchannels such as Poisson–Boltzmann equation and Helmholtz–Smoluchowski slip velocity approach are no longer applicable. In the current study, a set of coupled partial differential equations including Poisson–Nernst–Plank equation, Navier–Stokes, and continuity equations is solved to find the electric potential field, ionic concentration field, and the velocity field in the three‐dimensional nanochannel. The effects of surface electric charge and the radius of nanochannel on the electric potential, liquid flow, and ionic transport are investigated. Unlike the microchannels, the electric potential field, ionic concentration field, and velocity field are strongly size‐dependent in nanochannels. The electric potential gradient along the nanochannel also depends on the surface electric charge of the nanochannel. More counter ions than the coions are transported through the nanochannel. The ionic concentration enrichment at the entrance and the exit of the nanochannel is completely evident from the simulation results. The study also shows that the flow velocity in the nanochannel is higher when the surface electric charge is stronger or the radius of the nanochannel is larger.
Semi‐automatic porting of a large‐scale Fortran CFD code to GPUs
Authors: Corrigan Andrew , Camelli Fernando , Löhner Rainald , Mut Fernando
Published: May 2011

The development of automatic techniques to port a substantial portion of FEFLO, a general‐purpose legacy CFD code operating on unstructured grids, to run on GPUs is described. FEFLO is a typical adaptive, edge‐based finite element code for the solution of compressible and incompressible flows, which is primarily written in Fortran 77 and has previously been ported to vector, shared memory parallel and distributed memory parallel machines. Owing to the large size of FEFLO and the likelihood of human error in porting, as well as the desire for continued development within a single codebase, a specialized Python script, based on FParser (Int. J. Comput. Sci. Eng. 2009; 4:296–305), was written to perform automated translation from the OpenMP‐parallelized edge and point loops to GPU kernels implemented in CUDA, along with GPU memory management. The results of verification benchmarks and performance indicate that performances achieved by such a translator can rival those of codes rewritten by specialists. The approach should be of general interest, as how best to run on GPUs is being presently considered for many so‐called legacy codes. Copyright © 2011 John Wiley & Sons, Ltd.
Stereomutation of a diastereomeric pair of 10‐P‐5 hydroxyphosphoranes
Authors: Kojima Satoshi , Nakamoto Masaaki , Matsukawa Shiro , Akiba Kin‐ya
Published: May 2011

The stereomutation rates between a pair of stable diastereomeric hydroxyphosphoranes (2c‐exo and 2c‐endo) were measured by monitoring the change in the relative diastereomeric ratios and by 19F NMR magnetization transfer. Analysis of the data gave averaged kinetic parameters of ΔH≠ = 15.7 kcal mol−1; ΔS ≠ = −19.3 eu; ΔG≠298 = 21.4 kcal mol−1 for interconversion in toluene‐d8 and ΔH≠ = 18.9 kcal mol−1; ΔS≠ = 4.8 eu; ΔG≠298 = 20.4 kcal mol−1 for that in pyridine. These results suggested that the ring‐opening of 2c to yield a phosphinate occurred and that the process involving the attack of the hydroxy group of this phosphinate to the phosphorus atom from the side opposite of a carbon atom was the rate‐determining step. X‐ray crystallographic analysis of their symmetric analog 2b was also carried out. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:491–499, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/hc.20712
Synthesis and structure of peri‐substituted boron/pnictogen naphthalene derivatives
Authors: Wade Casey R. , Saber Mohamed R. , Gabbaï François P.
Published: May 2011

The reaction of tetrakis(thf)lithium dimesityl‐1,8‐naphthalenediylborate with either Ph2 SbCl or Ph2BiCl afforded 1‐(diphenylantimony)‐8‐(dimesitylboron)naphthalenediyl (1) and 1‐(diphenylbismuth)‐8‐(dimesitylboron) naphthalenediyl (2). These unprecedented boron/antimony and boron/bismuth derivatives have been characterized by multinuclear NMR spectroscopy, elemental analysis, and X‐ray single‐crystal analysis. The latter reveals that the 1,8‐naphthalenediyl backbone enforces short E→B (E = Sb, Bi) distances of 3.216 Å for 1 and 3.330 Å for 2. Natural bond order studies indicate that these short contacts are associated to lp(E)→p(B) interactions, which contribute to the stability of the compounds by 8.65 kcal/mol−1 in the case of 1 and 6.32 kcal/mol−1 in the case of 2. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:500–505, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/hc.20713
Radical addition reaction of bis(naphth‐1,8‐diyl‐8‐oxy)hydrophosphorane to olefins
Authors: Kajiyama Kazumasa , Itou Daisuke , Hazama Yuki , Yamamoto Yusuke , Miyamoto Takeshi K.
Published: May 2011

In the presence of 1,1′‐azobis(cyclohexanecarbonitrile) (ACHCN), the reaction of bis(naphth‐1,8‐diyl‐8‐oxy)hydrophosphorane with an equimolar amount of terminal and internal olefins gave the corresponding alkylphosphoranes. In the reactions with styrene and methyl acrylate, 2:1 olefin–hydrophosphorane adducts were obtained as a minor product. The reactions with terminal olefins were entirely regioselective and more efficient than those with internal olefins. In the absence of ACHCN, the radical addition reaction of the hydrophosphorane to terminal and internal olefins could also proceed slowly. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:538–544, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/hc.20719
Structure and dynamic behavior of neutral hexacoordinate antimony compounds with intramolecular coordination
Authors: Yamamichi Hideaki , Matsukawa Shiro , Kojima Satoshi , Ando Kaori , Yamamoto Yohsuke
Published: May 2011

Neutral hexacoordinate organoantimony compounds LSb(Xyl)C6H4 (o‐Y) [L = tridentate ligand; Xyl = C6H3 (3,5‐Me2); Y = CH2 OMe (4), CH2 NMe2 (5), and 2‐pyridyl (6)] with intramolecular coordination were synthesized. Single crystal X‐ray crystallography revealed that the donor atom (N or O) of 4–6 was coordinated trans to one of the two carbon atoms of the tridentate ligand. Variable temperature (VT) NMR measurements of compounds 4 and 5 indicated that the stereomutations proceeded via dissociation of the Sb‐donor (N or O) bond followed by SbC bond rotation. Compound 4 was found to have a stereomutation barrier of ca. 12 kcal mol−1. In the case of 5, dissociation of the SbN bond was found to be distinguishable from the stereomutation. Energies of SbN dissociation 5 and interconversion of enantiomers were estimated to be ca. 15 and ca. 19 kcal mol−1, respectively, from the VT‐NMR measurements. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:553–561, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/hc.20721
Hippocampal context processing is critical for interference free recall of odor memories in rats
Authors: Butterly Dan A. , Petroccione Maurice A. , Smith David M.
Published: May 2011

Interference is a critical problem for memory systems and a primary cause of retrieval failure. One strategy for minimizing interference is to associate the items to be remembered with the context in which they were learned. For example, human subjects who learn two lists of words in separate contexts experience less interference and better recall than subjects who learn both lists in the same context. The hippocampus has long been known to be involved in processing contextual information and recent studies have shown that hippocampal neurons exhibit context‐unique firing patterns that could serve as a neural representation of the context. These observations suggest that hippocampal context processing may play a critical role in overcoming interference. To test this hypothesis, we adapted the context based list learning procedure for use with rats. Control rats and rats given temporary lesions of the hippocampus were trained on two lists of eight odor pairs, either in the same context or in different contexts. To induce interference, some of the odors appeared on both lists with their predictive value reversed. As with human subjects, rats that learned the two lists in different contexts performed significantly better than rats that learned the lists in the same context. However, hippocampal lesions completely abolished this contextual learning advantage. We also trained rats on a low interference version of the task by using lists that did not contain any common items. Interestingly, rats with hippocampal lesions were entirely unimpaired when the learning situation did not involve high levels of interference. These findings are consistent with the idea that the hippocampus encodes contexts and further suggest that hippocampal context coding is beneficial because it provides a means of overcoming interference. © 2011 Wiley‐Liss, Inc.
Methylation of zebularine investigated using density functional theory calculations
Authors: Selvam Lalitha , Chen Fang Fang , Wang Feng
Published: May 2011

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Variational transition‐state theory study of the rate constant of the DMS·OH scavenging reaction by O2
Authors: RamíRez‐Anguita Juan M. , González‐Lafont àngels , Lluch José M.
Published: May 2011

The chemical tropospheric dimethyl sulfide (DMS, CH3SCH3) degradation involves several steps highly dependent on the environmental conditions. So, intensive efforts have been devoted during the last years to enhance the understanding of the DMS oxidation mechanism under different conditions. The reaction of DMS with OH is considered to be the most relevant process that initiates the whole oxidation process. The experimental observations have been explained by a two‐channel mechanism consisting of a H‐abstraction process leading to CH3S(O)CH3 and HO2 and an addition reaction leading to the DMS·OH adduct. In the presence of O2, the DMS·OH adduct is competitively scavenged increasing the contribution of the addition channel to the overall DMS oxidation. Recent experimental measurements have determined from a global fit that the rate constant of this scavenging process is independent of pressure and temperature but this rate constant cannot be directly measured. In this article, a variational transition‐state theory calculation of the low‐ and high‐pressure rate constants for the reaction between DMS·OH and O2 has been carried out as a function of temperature. Our proposal is that the slight temperature dependence of the scavenging rate constant can only be explained if the H‐abstraction bottleneck is preceded by a dynamical bottleneck corresponding to the association process between the DMS·OH adduct and the O2 molecule. The agreement between the low‐pressure and high‐pressure rate constants confirms the experimental observations. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Dipole preserving and polarization consistent charges
Authors: Zhang Peng , Bao Peng , Gao Jiali
Published: May 2011

A method for estimating dipole preserving and polarization consistent (DPPC) charges is described, which reproduces exactly the molecular dipole moment as well as the local, atomic hybridization dipoles determined from the corresponding wave function and can yield accurate molecular polarization. The method is based on a model described by Thole and van Duijnen and a new feature is introduced to treat molecular polarization. Thus, the DPPC method offers a convenient procedure to describe molecular polarization in applications using semiempirical models and ab initio molecular orbital theory with relatively small basis functions such as 6‐31+G(d,p) or without inclusion of electron correlation; these methods tend to underestimate molecular polarizability. The trends of the DPPC partial atomic charges are found to be in good accord with those of the CM2 model, a class IV charge analysis method that has been used in a variety of applications. The DPPC method is illustrated to mimic the correct molecular polarizability in a water dimer test case and in water‐halide ion complexes using the explicit polarization (X‐Pol) potential with the Austin model 1 Hamiltonian. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Fast docking using the CHARMM force field with EADock DSS
Authors: Grosdidier Aurélien , Zoete Vincent , Michielin Olivier
Published: May 2011

The prediction of binding modes (BMs) occurring between a small molecule and a target protein of biological interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. Nowadays, the universe of docking software ranges from fast and user friendly programs to algorithmically flexible and accurate approaches. EADock2 is an example of the latter. Its multiobjective scoring function was designed around the CHARMM22 force field and the FACTS solvation model. However, the major drawback of such a software design lies in its computational cost. EADock dihedral space sampling (DSS) is built on the most efficient features of EADock2, namely its hybrid sampling engine and multiobjective scoring function. Its performance is equivalent to that of EADock2 for drug‐like ligands, while the CPU time required has been reduced by several orders of magnitude. This huge improvement was achieved through a combination of several innovative features including an automatic bias of the sampling toward putative binding sites, and a very efficient tree‐based DSS algorithm. When the top‐scoring prediction is considered, 57% of BMs of a test set of 251 complexes were reproduced within 2 Å RMSD to the crystal structure. Up to 70% were reproduced when considering the five top scoring predictions. The success rate is lower in cross‐docking assays but remains comparable with that of the latest version of AutoDock that accounts for the protein flexibility. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Role of nonlocal exchange in molecular crystals: The case of two proton‐ordered phases of ice
Authors: Labat Frédéric , Pouchan Claude , Adamo Carlo , Scuseria Gustavo E.
Published: May 2011

We present a periodic density functional theory investigation of twoproton‐ordered phases of ice. Their equilibrium lattice parameters,relative stabilities, formation energies, and densities of states havebeen evaluated. Nine exchange‐correlation functionals, representativeof the generalized gradient approximation (GGA), global hybrids,range‐separated hybrids, meta‐GGA, and hybrid meta‐GGA families havebeen taken into account, considering two oxygen basis sets. Althoughthe hydrogen‐bond network of ice is well reproduced at the B3LYP,M06‐L, or LC‐ wPBE levels, formation energies are only correctlyevaluated with the two former functionals. Band gaps on the other handare only quantitatively reproduced at the B3LYP level. These resultsindicate that this last functional, a de facto reference formolecular calculations, gives in average the most accurate results forthe considered ice properties. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Acceleration of a QM/MM‐QMC simulation using GPU
Authors: Uejima Yutaka , Terashima Tomoharu , Maezono Ryo
Published: May 2011

We accelerated an ab initio molecular QMC calculation by using GPGPU. Only the bottle‐neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a (single core CPU with double precision), getting 23.6 (11.0) times faster calculations in single (double) precision treatments on GPU. The energy deviation caused by the single precision treatment was found to be within the accuracy required in the calculation, ∼10−5 hartree. The accelerated computational nodes mounting GPU are combined to form a hybrid MPI cluster on which we confirmed the performance linearly scales to the number of nodes. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
PyADF — A scripting framework for multiscale quantum chemistry
Authors: Jacob Christoph R. , Beyhan S. Maya , Bulo Rosa E. , Gomes André Severo Pereira , Götz Andreas W. , Kiewisch Karin , Sikkema Jetze , Visscher Lucas
Published: May 2011

Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object‐oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum‐chemical multiscale simulations with a number of examples taken from recent applications. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
SwissParam: A fast force field generation tool for small organic molecules
Authors: Zoete Vincent , Cuendet Michel A. , Grosdidier Aurélien , Michielin Olivier
Published: May 2011

The drug discovery process has been deeply transformed recently by the use of computational ligand‐based or structure‐based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure‐based computational methods for drug discovery mainly involve ligand‐protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand‐protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol−1, and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer‐aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Conformational state‐specific free energy differences by one‐step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields
Authors: Lin Zhixiong , Van Gunsteren Wilfred F. , Liu Haiyan
Published: May 2011

The one‐step free energy perturbation approach can be applied to obtain conformational state‐specific free energy differences (FEDs) associated with changes in force field parameters, and thus offers the possibility to consider conformational equilibria during force field parameterization. In this work, using the alanine decapeptide in explicit water solution as a model, the α‐helical and β‐hairpin state‐specific FEDs associated with force field changes between two widely used parameter sets of the GROMOS force field, namely, 43A1 and 53A6, were determined using one‐step perturbation. The results mostly deviated by only 1 kJ mol−1 in absolute or a few percent in relative values from thermodynamic integration results, suggesting that the convergence ranges of one‐step perturbation were large enough to cover the substantial changes in nonbonded parameters between the two parameter sets. It was also found that one‐step perturbation may give larger errors when the changes from the reference state include a large decrease in van der Waals radius, as indicated by the result for the β‐hairpin state‐specific free energy change going from 53A6 to 43A1. According to the free energy results, the α‐helical state of the alanine decapeptide is destabilized by 15 kJ mol−1, i.e., 1.5 kJ mol−1 per residue, relative to the β‐hairpin state when going from 43A1 to 53A6, in agreement with previous direct simulations in which native α‐helices were often found to be unstable in simulations using 53A6, despite that the 53A6 parameters better reproduce a range of thermodynamic properties of small molecular systems. By applying one‐step perturbation to analyze the effects of perturbing individual parameters, the differential stabilization of the two secondary structure states can be traced to the changes in van der Waals parameters, especially a van der Waals parameter involved in third‐neighbor interactions. This study provides an example of the efficiency of one‐step perturbation in force field development, reducing the computational cost by orders of magnitude. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Computational study of energetic nitrogen‐rich derivatives of 1,1′‐ and 5,5′‐bridged ditetrazoles
Authors: Zhu Weihua , Zhang Chenchen , Wei Tao , Xiao Heming
Published: May 2011

Density functional theory method was used to study the heats of formation (HOFs), electronic structure, energetic properties, and thermal stability for a series of bridged ditetrazole derivatives with different linkages and substituent groups. The results show that the N3 group and azo bridge (NN) play a very important role in increasing the HOF values of the ditetrazole derivatives. The effects of the substituents on the HOMO–LUMO gap are combined with those of the bridge groups. The calculated detonation velocities and detonation pressures indicate that the NO2, NF2, NN, or N(O)N group is an effective structural unit for enhancing the detonation performance for the derivatives. An analysis of the bond dissociation energies for several relatively weak bonds suggests that the NN bond in the ring or outside the ring is the weakest one and the NN cleavage is possible to happen in thermal decomposition. Overall, the CH2CH2 or NHNH group is an effective bridge for enhancing the thermal stability of the bridged ditetrazoles. Because of their desirable detonation performance and thermal stability, five compounds may be considered as the potential candidates of high‐energy density materials (HEDMs). These results provide basic information for the molecular design of novel HEDMs. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Syntheses of dual‐radioisotope‐labeled CP‐I, a GABAA receptor partial agonist
Authors: Zhang Yinsheng , Greenfield Laura , Hong Yang
Published: May 2011

CP‐I is a potent subtype‐selective GABAA receptor partial agonist. Owing to its significant metabolic cleavage at C8 observed in preliminary biotransformation studies with non‐radiolabeled CP‐I, the syntheses of CP‐I labeled at the right or left hand side with 14C or labeled with 3H at the right hand side were required. The two compounds labeled with 14C at the left or right hand side were synthesized in 2 and 5 radio‐synthetic steps using [14C]2‐chloroacetyl chloride and [14C]NaCN as starting radiolabeled materials, respectively. CP‐I was labeled with tritium at the right hand side by a tritium de‐halogenation method. Batches of radiolabeled CP‐I were mixed to give dual‐radioisotope‐labeled CP‐I. An efficient approach to [14C]fluoropyridinyl imidazole was developed, and a short synthesis of iodo‐substituted fluoropyridinyl imidazole was also achieved. The details of these syntheses are discussed. Copyright © 2011 John Wiley & Sons, Ltd.
Functional morphology of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae), a bacterially luminous coral reef fish
Authors: Dunlap Paul V. , Nakamura Masaru
Published: May 2011

Previous studies of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae) identified a ventral light organ, reflector, lens, duct, and a ventral diffuser extending from the throat to the caudal peduncle. The control and function of luminescence in this and other species of Siphamia, however, have not been defined. Morphological examination of fresh and preserved specimens identified additional components of the luminescence system involved in control and ventral emission of luminescence, including a retractable shutter over the ventral face of the light organ, contiguity of the ventral diffuser from the caudal peduncle to near the chin, and transparency of the bones and other tissues of the lower jaw. The shutter halves retract laterally, allowing the ventral release of light, and relax medially, blocking ventral light emission; topical application of norepinephrine to the exposed light organ resulted in retraction of the shutter halves, which suggests that operation of the shutter is under neuromuscular control. The extension of the diffuser to near the chin and transparency of the lower jaw allow a uniform emission of luminescence over the entire ventrum of the fish. The live aquarium‐held fish were found to readily and consistently display ventral luminescence. At twilight, the fish left the protective association with their longspine sea urchin, Diadema setosum, and began to emit ventral luminescence and to feed on zooplankton. Ventral luminescence illuminated a zone below and around the fish, which typically swam close to the substrate. Shortly after complete darkness, the fish stopped feeding and emitting luminescence. These observations suggest that S. versicolor uses ventral luminescence to attract and feed on zooplankton from the reef benthos at twilight. Ventral luminescence may allow S. versicolor to exploit for feeding the gap at twilight in the presence of potential predators as the reef transitions from diurnally active to nocturnally active organisms. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc