bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the importance of orbital localization in QC‐DMRG calculations
Authors: Mitrushchenkov Alexander O. , Fano Guido , Linguerri Roberto , Palmieri Paolo 
Published: December 2011

AbstractWe investigate the importance of orbital localization in the application of the Density Matrix Renormalization Group (DMRG) technique to ab initio studies of molecular electronic structure. Our previous implementation of DMRG has been generalized to allow for the use of localized nonorthogonal orbitals. Simple cycles of equidistant hydrogen atoms, which are good examples of one dimensional metal‐like lattices with fully delocalized electronic structures, have been taken as test models. In this study, the efficiency of the DMRG method and the importance of orbital localization for the generation of the DMRG building blocks are confirmed. However, it is found that the convergence of the procedure based on nonorthogonal orbitals is slower and requires more DMRG components than the standard orthogonal formulation. Symmetrically orthonormalized atomic orbitals are shown to be a good compromise solution: they satisfy the requirement of orbital localization for the generation of the DMRG blocks and improve the convergence, reducing the number of components of the DMRG expansion. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Theoretical investigation on identical anionic halide‐exchange SN2 reaction processes on N‐haloammonium cation NH3X+ (X = F, Cl, Br, and I)
Authors: Xiong Yan , Zhang Shuting , Ling Xuege , Zhang Xu , Wang Jinyue 
Published: December 2011

AbstractCCSD(T) calculations have been used for identically nucleophilic substitution reactions on N‐haloammonium cation, X− + NH3X+ (X = F, Cl, Br, and I), with comparison of classic anionic SN2 reactions, X− + CH3X. The described SN2 reactions are characterized to a double curve potential, and separated charged reactants proceed to form transition state through a stronger complexation and a charge neutralization process. For title reactions X− + NH3X+, charge distributions, geometries, energy barriers, and their correlations have been investigated. Central barriers ΔE for X− + NH3X+ are found to be lower and lie within a relatively narrow range, decreasing in the following order: Cl (21.1 kJ/mol) > F (19.7 kJ/mol) > Br (10.9 kJ/mol) > I (9.1 kJ/mol). The overall barriers ΔE relative to the reactants are negative for all halogens: −626.0 kJ/mol (F), −494.1 kJ/mol (Cl), −484.9 kJ/mol (Br), and −458.5 kJ/mol (I). Stability energies of the ion–ion complexes ΔEcomp decrease in the order F (645.6 kJ/mol) > Cl (515.2 kJ/mol) > Br (495.8 kJ/mol) > I (467.6 kJ/mol), and are found to correlate well with halogen Mulliken electronegativities (R2 = 0.972) and proton affinity of halogen anions X− (R2 = 0.996). Based on polarizable continuum model, solvent effects have investigated, which indicates solvents, especially polar and protic solvents lower the complexation energy dramatically, due to dually solvated reactant ions, and even character of double well potential in reactions X− + CH3X has disappeared. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The influence of hydrophobic amino acid side groups on the acidity of the aromatic imidazole ring of histidine: A theoretical study
Authors: Najafabadi Reza Izadi , Housaindokht Mohammad Reza , Sadeghi Googheri Mohammad Sadegh , Sargolzaei Mohsen , Izadyar Mohammad 
Published: December 2011

AbstractIn this study we have calculated the acidity constant (pKa) of imidazole ring in Histidine‐Hydrophobic amino acid dipeptides using the quantum chemistry and continuum solvation methods. Density functional theory calculations with the large basis sets are used to determine the Gibbs free energy of deprotonate in the gas and liquid phases. Based on our results ΔGS values are located between −69.38 and −18.82 kcal mol−1 which are related to His+–Gly and His forms, respectively. pKa of the dipeptides in the aqueous phase was obtained from the calculated gas‐phase and solvation free energies through a thermodynamic cycle and the solvation model chemistry of Martin Karplus et al. Solvation effects are treated using a self‐consistent reaction field formalism involving polarized continuum models. According to our calculations pKa values are between 5.50 and 8.19 that are belong to His+–ILe and His+–Ala forms, respectively. Natural bond orbital analysis of dipeptides reveals that the electron delocalization in imidazole ring is the most effective factor in determination of acidity order for these compounds. Structural analysis confirmed that the orientation of carbonyl group with respect to imidazole ring is an effective factor in imidazole ring stability. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Local angular momentum as ring strain descriptor
Authors: Azami S. M. , Kheirmand M. , Rezaei G. 
Published: December 2011

AbstractA new method is demonstrated to quantify local ring strain, which is based on the expectation value of orbital angular momentum along the internuclear axis. In contrast to energy based methods which provide overall ring strain, this method is able to identify the local strain in every part of the ring. The formalism is benchmarked on several cycloalkanes in which the presence of ring strain is well understood. The ring strain plays a decisive role in carbon nanotubes (CNTs) properties; for instance, the hydrogen storage capability of CNTs is related to their diameter, which in turn has a close relation to the ring strain in their CC bonds. On this basis, the ring strain in five CNTs with different diameters is analyzed and the results reflected meaningful correlation between the CNTs diameter and ring strain. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Diffusion monte carlo study of the hydrogen molecules adsorbed on C4H3Li
Authors: Jiang Xiaoxu , Cheng Xinlu , Chen Guanyu , Zhang Hong 
Published: December 2011

AbstractDiffusion Monte Carlo (DMC) simulations were used to calculate the binding energies for hydrogen molecules adsorbed on the lithium metal–organic complex C4H3Li. The calculations use all‐electron DMC techniques where every electron is explicitly included in the simulation. Also we have systematically studied it using density functional theory (DFT) methods, revealing that each C4H3Li can hold up to four H2 molecules and the adsorption distance is about 2.2 Å. The DMC binding energies are in the range of 0.055–0.143 eV and are compared with those obtained with DFT using various exchange‐correlation functionals, with values ranging from 0.029 to 0.504 eV. These results indicate that caution is required applying DFT methods to weakly bound systems such as hydrogen storage materials based on lithium‐doped metal–organic frameworks. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The rotation‐vibration spectrum of diatomic molecules with the tietz‐hua rotating oscillator
Authors: Hamzavi M. , Rajabi A. A. , Thylwe K.‐E. 
Published: December 2011

AbstractThe Tietz‐Hua (TH) potential is one of the very best analytical model potentials for the vibrational energy of diatomic molecules. By using the Nikiforov‐Uvarov method, we have obtained the exact analytical s‐wave solutions of the radial Schrödinger equation for the TH potential. The energy eigenvalues and the corresponding eigenfunctions are calculated in closed forms. Some numerical results for diatomic molecules are also presented. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The IR spectrum of supercritical water: Combined molecular dynamics/quantum mechanics strategy and force field for cluster sampling
Authors: Bordat P. , Bégué D. , Brown R. , Marbeuf A. , Cardy H. , Baraille I. 
Published: December 2011

AbstractSupercritical water was analyzed recently as a gas of small clusters of waters linked to each other by intermolecular hydrogen‐bonds, but unexpected “linear” conformations of clusters are required to reproduce the infra‐red (IR) spectra of the supercritical state. Aiming at a better understanding of clusters in supercritical water, this work presents a strategy combining classical molecular dynamics to explore the potential energy landscape of water clusters with quantum mechanical calculation of their IR spectra. For this purpose, we have developed an accurate and flexible force field of water based on the TIP5P 5‐site model. Water dimers and trimers obtained with this improved force field compare well with the quantum mechanically optimized clusters. Exploration by simulated annealing of the potential energy surface of the classical force field reveals a new trimer conformation whose IR response determined from quantum calculations could play a role in the IR spectra of supercritical water. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The investigation of nonadiabatic effects for the N + ND → N2 + D reaction
Authors: Zhang Ai‐Jie , He Guo‐Zhong 
Published: December 2011

AbstractNonadiabatic quantum dynamical calculations have been carried out on the two coupled potential energy surfaces (12A′ and 22A′) (Mota et al., J Theor Comput Chem 2009, 8, 849) for the title reaction. Initial state‐resolved reaction probabilities and cross sections for ground and excited states for collision energies of 0.005–1.0 eV are determined, respectively. Nonadiabatic transition is enhanced about four times by isotopic substitution of N + NH by N + ND reaction. It turns out that the nonadiabatic effects exert no significant contribution in the N + ND → N2 + D reaction. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Rayleigh light scattering from hydrogen‐bonded dimers of small astrophysical molecules
Authors: da Silva Arnaldo Machado , Chakraborty Sumana , Chaudhuri Puspitapallab 
Published: December 2011

AbstractHigh level ab initio calculations of the Rayleigh scattering activities of the hydrogen‐bonded dimers of formic acid (HCOOH), nitrosyl hydride (HNO), and hydrogen cyanide (HCN) molecules have been performed. All these molecules have already been detected in interstellar space and are of great importance from the astrochemical point of view. The geometries of the homo‐ and hetero‐dimers have been optimized using Hartree–Fock and second‐order Møller‐Plesset perturbation theory. Dipole moment, mean dipole polarizability, and polarizability anisotropy have been calculated utilizing Pople‐type 6‐311++G(d,p) and Dunning's aug‐cc‐pVDZ basis sets for all the complexes. The polarizabilities are then used to calculate and analyze the Rayleigh scattering parameters. The results for the dimers, HCN···HCN, HCOOH···HCOOH, HNO···HNO, HCN···HCOOH, HCN···HNO, and HNO···HCOOH are compared with those of the isolated molecules, HCN, HCOOH, and HNO to see the effect of hydrogen bond formation on the molecular interaction with radiation. © 2011 Wiley Periodicals, Inc.
Density functional study on electronic structures and reactivity in carbazol‐oxadiazole dyads used in organic light emitting diodes
Authors: Mejia‐Urueta Rafael , Nuñez‐Zarur Francisco , Vivas‐Reyes Ricardo 
Published: December 2011

AbstractIn this contribution, a complete study of Triarylamine—Oxadiazole derivatives for organic light emitting diodes (OLED) applications is presented. Our purpose in this article is the establishment of correlations between the computational calculations based on density functional theory (DFT) and the experimental results with some electronic and reactivity properties. The geometries of the Triarylamine—Oxadiazole molecules are discussed in terms of the substituents groups (CF3, t‐Bu‐, CN, and CH3) and the electronics structures are described in detail in terms of the distribution of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). We also calculate the ionization potential and electron affinity with to gain insights into the nature of nucleophilic and electrophilic interactions in the studied molecules. To study the global and local reactivities use make use suitable reactivity descriptors defined on the framework of DFT. The descriptors involved in the model are global and local electrophilicity index (ω), chemical hardness (η) and softness (S), Fukui functions (f(r)), local softness (s). Correlation between the values of these quantities and the electron‐withdrawing and electron‐donor effects of triarylamine—Oxadiazole derivatives is addressed. © 2011 Wiley Periodicals, Inc.
Rapid screening of drug compounds in urine using a combination of microextraction by packed sorbent and rotating micropillar array electrospray ionization mass spectrometry
Authors: Nielsen Katrine , Lauritsen Frants R. , Nissilä Teemu , Ketola Raimo A. 
Published: December 2011

RATIONALEScreening of drugs from urine samples can be non‐selective or laborous, using either immunological, gas chromatography/mass spectrometry (GC/MS) or liquid chromatography (LC)/MS methods. Therefore, a rapid screening method for selected drugs in urine sample was developed in a proof‐of‐principle manner, utilizing simple and fast techniques for both sample treatment and sample analysis.METHODSSample treament of spiked urine samples was performed with microextraction by packed sorbent (MEPS). Five different sorbent materials (C2, C8, C18, M1 (cation exchanger), and Sil (pure silica)) were tested for the MEPS. The sample analysis was performed using a circular microchip with 60 micropillar electrospray ionization (μPESI) tips combined with a mass spectrometer (either a triple‐quadrupole or ion‐trap mass spectrometer) without any chromatographic step.RESULTSThe sample treatment/analysis setup was tested using three drug compounds at a concentration of 1 μM. We found that the C2, C8 and C18 sorbents in combination with 96% alkaline methanol as an eluent worked the best. All compounds were easily detected and identified by MS/MS in spiked urine samples. The whole qualitative analytical procedure was rapid as the sample treatment together with the MS analysis took about 5 min per sample.CONCLUSIONSA rapid screening method for selected drugs from urine samples was developed, providing adequate selectivity and sensitivity, as well as a short total analysis cycle time. This new method can provide a new alternative for screening purposes, as both the extraction and analysis steps could be totally automatized. Copyright © 2011 John Wiley & Sons, Ltd.
A system consisting of cation‐exchange chromatography, combined surface‐activated chemical and electrospray ionization, and ion‐trap analysis for the analysis of 8‐oxo‐7,8‐dihydro‐2'‐deoxyguanosine in urine
Authors: Cristoni Simone , Zingaro Lorenzo , Rota Cristina , Cariani Elisabetta , Trenti Tommaso 
Published: December 2011

RATIONALE8‐Hydroxy‐2'‐deoxyguanosine has served as a biomarker for oxidative damage to DNA from different types of biological samples, and various techniques have been used to analyze it. In particular, liquid chromatography coupled to mass spectrometry has been used to identify 8‐hydroxy‐2'‐deoxyguanosine in urine samples. Usually, a triple quadrupole analyzer and multiple reaction monitoring have been employed for its detection. Only a few studies have used a less expensive ion‐trap analyzer instead.METHODSWe have developed a new liquid chromatography/mass spectrometry procedure that incorporates cation‐exchange chromatography in conjunction with surface‐activated and electrospray ionization with an ion trap analyzer for the mass spectral step.RESULTSThe combination of two ionization sources reduced the matrix effect arising from in‐source reactions, thus increasing the sensitivity to levels comparable with those obtained by triple quadrupole analyzers.CONCLUSIONSThis new method for 8‐hydroxy‐2'‐deoxyguanosine detection provided increased sensitivity and reduced chemical noise, using a less expensive, stable and accurate mass spectrometric technology. Copyright © 2011 John Wiley & Sons, Ltd.
Quantized stabilization for stochastic discrete‐time systems with multiplicative noises
Authors: Wei Li , Zhang Huanshui , Fu Minyue 
Published: December 2011

SUMMARYThis paper considers the problem of quadratic mean‐square stabilization of a class of stochastic linear systems using quantized state feedback. Different from the previous works where the system is restricted to be deterministic, we focus on stochastic systems with multiplicative noises in both the system matrix and the control input. A static quantizer is used in the feedback channel. It is shown that the coarsest quantization density that permits stabilization of a stochastic system with multiplicative noises in the sense of quadratic mean‐square stability is achieved with the use of a logarithmic quantizer, and the coarsest quantization density is determined by an algebraic Riccati equation, which is also the solution to a special stochastic linear control problem. Our work is then extended to exponential quadratic mean‐square stabilization of the same class of stochastic systems. Copyright © 2011 John Wiley & Sons, Ltd.
Model‐driven rapid prototyping with Umple
Authors: Forward Andrew , Badreddin Omar , Lethbridge Timothy C. , Solano Julian 
Published: December 2011

SUMMARYThe emergence of model‐driven software development brings new opportunities and challenges for rapid prototyping. On the one hand, the modeling process is inherently abstract, removing the prototyper from details, and letting him or her focus on exploring design alternatives for various aspects of the system. On the other hand, the most popular modeling languages and tools entirely omit the modeling and generating of user interfaces. As a result, the benefit of user interface prototypes as a medium for interaction with the user and customer is lost. This paper presents a model‐oriented technology called Umple that can be used for prototyping and also supporting model driven engineering. Umple allows end users to quickly create class and state machine models and to incrementally embed implementation artifacts. At any point in the modeling process, users can quickly generate a fully functional prototype that exposes modeling implications on the user interface, and allows stakeholders to get a feel of how the full system will behave. Copyright © 2011 John Wiley & Sons, Ltd.
Thermal Stability of Fibroblast Growth Factor Protein Is a Determinant Factor in Regulating Self-Renewal, Differentiation, and Reprogramming in Human Pluripotent Stem Cells
Authors: Chen Guokai , Gulbranson Daniel R. , Yu Pengzhi , Hou Zhonggang , Thomson James A. 
Published: December 2011

Abstract
Fibroblast growth factor (FGF), transforming growth factor (TGF)/Nodal, and Insulin/insulin-like growth factor (IGF) signaling pathways are sufficient to maintain human embryonic stem cells (ESCs) and induced pluripotent stem cells in a proliferative, undifferentiated state. Here, we show that only a few FGF family members (FGF2, FGF4, FGF6, and FGF9) are able to sustain strong extracellular-signal-regulated kinase (ERK) phosphorylation and NANOG expression levels in human ESCs. Surprisingly, FGF1, which is reported to target the same set of receptors as FGF2, fails to sustain ERK phosphorylation and NANOG expression under standard culture conditions. We find that the failure of FGF1 to sustain ES is due to thermal instability of the wild-type protein, not receptor specificity, and that a mutated thermal-stable FGF1 sustains human ESCs and supports both differentiation and reprogramming protocols.
Disclosure of potential conflicts of interest is found at the end of this article.
Reliable information rate of signal‐time coding for half‐duplex additive white Gaussian noise relay networks
Authors: Xiong Ke , Fan Pingyi , Qiu Zhengding , Letaief Khaled Ben 
Published: December 2011

ABSTRACTSignal‐time coding (STC) is a newly proposed transmission scheme for half‐duplex relay networks, which is able to achieve higher information flow rate by combining the traditional encoding/modulation mode in the signal domain with the signal pulse phase modulation in the time domain. However, most of the results for STC are only obtained under the ideal assumptions that the signal detections at physical layer are perfect and there are still a lot of fundamental problems to be explored. This paper considers the implementing issues of STC at physical layer in additive white Gaussian noise relay networks. Firstly, a performance evaluation criterion, the reliable information per symbol (RIPS), is proposed to characterize the performance of STC in noisy wireless networks. Secondly, a new construction scheme based on route ID for the codeword of STC is presented, and some structural properties of the codeword of STC are investigated. Thirdly, the error probabilities of STC in both the signal domain and the time domain are discussed. Furthermore, two implementing schemes, that is, the energy detection based STC (ED‐STC) and the symbol detection based STC (SD‐STC), are proposed, and their performance bounds in terms of RIPS are discussed. Numerical analyses show that both ED‐STC and SD‐STC outperform traditional transmission methods in terms of effective information rate even under some practical conditions. Copyright © 2011 John Wiley & Sons, Ltd.
Breast Radiation Correlates with Side of Parathyroid Adenoma
Authors: Woll Monica L. , Mazeh Haggi , Anderson Bethany M. , Chen Herbert , Sippel Rebecca S. 
Published: December 2011

AbstractBackgroundPrior head and neck irradiation is a known risk factor for hyperparathyroidism. It is not clear whether irradiation for breast cancer, which may expose the neck to radiation, is also a risk factor for hyperparathyroidism. The present study analyzes the association between the side of radiation to the chest following breast surgery and the side of subsequent parathyroid adenoma development.MethodsWe analyzed a prospective database of 1,428 consecutive patients who underwent parathyroidectomy at our institution between November 2000 and August 2010. Patients who had previously undergone breast surgery were identified. Patients with multigland disease were excluded. Patients with bilateral breast surgery were counted as having had two separate procedures; one on each side. Patients who had radiation therapy following breast surgery (RadRx) were compared to those who had breast surgery without radiation treatment (No RadRx).ResultsA total of 146 breast procedures were performed in 121 patients. Forty procedures were in the RadRx group versus 106 cases in the No RadRx group. Patients with radiation therapy were older (68 ± 1.8 years versus 63 ± 1.2 years; P = 0.02) and had higher preoperative calcium levels (11.3 ± 0.1 mg/dl versus 10.9 ± 0.1 mg/dl; P = 0.001). However, there was no significant difference in either parathyroid hormone (PTH) level or gland weight. The latency period between breast irradiation and parathyroid surgery was 8 ± 0.9 years. Interestingly, the side of radiation therapy was associated with the side of the parathyroid adenoma in 76% of cases, compared to only 44% in those who had breast surgery without radiation exposure (P = 0.0004).ConclusionsThe present study demonstrates that, similar to prior head and neck radiation, prior breast irradiation correlates with the development of parathyroid disease. Specifically, there is a strong correlation between the side of the radiation therapy and the side of a subsequent parathyroid adenoma. Breast irradiation should therefore be considered a risk factor for the development of parathyroid adenomas.