bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protonation of phenylboronic acid: Comparison of G3B3 and G2MP2 methods
Authors: De Senjuti , Drew Michael G. B. , Price David W. , Nag Samik , Datta Dipankar 
Published: August 2006

AbstractG3B3 and G2MP2 calculations using Gaussian 03 have been carried out to investigate the protonation preferences for phenylboronic acid. All nine heavy atoms have been protonated in turn. With both methodologies, the two lowest protonation energies are obtained with the proton located either at the ipso carbon atom or at a hydroxyl oxygen atom. Within the G3B3 formalism, the lowest‐energy configuration by 4.3 kcal · mol−1 is found when the proton is located at the ipso carbon, rather than at the electronegative oxygen atom. In the resulting structure, the phenyl ring has lost a significant amount of aromaticity. By contrast, calculations with G2MP2 show that protonation at the hydroxyl oxygen atom is favored by 7.7 kcal · mol−1. Calculations using the polarizable continuum model (PCM) solvent method also give preference to protonation at the oxygen atom when water is used as the solvent. The preference for protonation at the ipso carbon found by the more accurate G3B3 method is unexpected and its implications in Suzuki coupling are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Common generating function for two‐dimensional hydrogen atom complete wave functions
Authors: Chaos‐Cador L. , Ley‐Koo E. 
Published: August 2006

AbstractThe Schrödinger equation for the two‐dimensional hydrogen atom is known to be separable and integrable in circular, parabolic, and elliptical coordinates. This makes it possible to construct a common generating function for the complete wave functions of the atom in the respective coordinates. The connections with the corresponding generating function and wave functions for the harmonic oscillator are recognized and applied in this work. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Structure and stability of Be6, Be, and Be clusters
Authors: Zhao Yi , Li Nan , Xu Wen Guo , Li Qian Shu 
Published: August 2006

AbstractThe structure and stability of Be6, Be, and Be clusters have been investigated at the B3LYP, B3PW91, and second‐order Møller–Plesset (MP2) levels of theory, along with the 6‐311G* basis set for neutral and cationic clusters and the 6‐311+G* basis set for anion clusters. CCSD(T)/6‐311+G* has also been used to calculate some neutral structure to find the most stable structure. Twelve Be6, six Be, and eight Be isomers are identified. The distortion octahedron structure, pentagonal pyramids structure, and trapezoidal bipyramid structure are found to be the most stable structure on the neutral, cationic, and anionic surface, respectively. They are in agreement with the results reported previously. Natural bond orbital (NBO) analysis, molecular orbital (MO) pictures, and the nucleus independent chemical shift (NICS) values suggest aromatic of the neutral and cationic clusters and antiaromatic of the anionic cluster. The multi‐center σ bonds and delocalized π bonds play important role in the bonding of the beryllium clusters. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Optimization of nonlinear wave function parameters
Authors: Shepard Ron , Minkoff Michael 
Published: August 2006

AbstractAn energy‐based optimization method is presented for our recently developed nonlinear wave function expansion form for electronic wave functions. This expansion form is based on spin eigenfunctions, using the graphical unitary group approach (GUGA). The wave function is expanded in a basis of product functions, allowing application to closed‐shell and open‐shell systems and to ground and excited electronic states. Each product basis function is itself a multiconfigurational function that depends on a relatively small number of nonlinear parameters called arc factors. The energy‐based optimization is formulated in terms of analytic arc factor gradients and orbital‐level Hamiltonian matrices that correspond to a specific kind of uncontraction of each of the product basis functions. These orbital‐level Hamiltonian matrices give an intuitive representation of the energy in terms of disjoint subsets of the arc factors, they provide for an efficient computation of gradients of the energy with respect to the arc factors, and they allow optimal arc factors to be determined in closed form for subspaces of the full variation problem. Timings for energy and arc factor gradient computations involving expansion spaces of >1024 configuration state functions are reported. Preliminary convergence studies and molecular dissociation curves are presented for some small molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Quantal density functional theory: Wave function arbitrariness of the noninteracting fermion model
Authors: Sahni Viraht , Slamet Marlina 
Published: August 2006

AbstractIn quantal density functional theory (Q‐DFT), the mapping from either a ground or excited state of the interacting system to one of noninteracting fermions with equivalent density is such that the state of the latter model S system is arbitrary. Thus, in principle, there are an infinite number of local (multiplicative) effective potential energy functions that can reproduce the density of the interacting system. In the present work, we note that there is also an arbitrariness in the wave function of the model fermions when the S system is constructed in an excited state. Different wave functions lead to the same density. As the principal requirement of the model system is met, viz. to reproduce the interacting system density, these wave functions are all equally valid representations, irrespective of whether they are eigenfunctions of various symmetry operators. However, the corresponding nonlocal properties such as the Fermi and Coulomb hole charge distributions, and the resulting Pauli and Coulomb energies, will differ. This wave function arbitrariness within Q‐DFT is demonstrated via the exactly solvable Hooke's atom. Finally, Q‐DFT and Kohn–Sham DFT are contrasted with regard to the state and wave function arbitrariness of the model S system. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Application of electronic structure and transition state theory: Reaction of hydrogen with silicon radicals
Authors: Crosby Lonnie D. , Kurtz Henry A. 
Published: August 2006

AbstractThe reaction of molecular hydrogen with silicon radicals is investigated through direct dynamics calculations. Previous studies of this reaction with E′ centers vary in their description of the reaction thermodynamics and kinetics. A survey of methods is conducted to illuminate the best method for describing these properties. This is achieved via a similar reaction with a silyl radical, in which both the forward and reverse directions are considered, discussed in terms of theory, basis, and the importance of tunneling corrections. The methods studied include Hartree–Fock (SCF), two density functionals (B3LYP and MPW1K), Møller–Plesset second‐order perturbation (MP2), and coupled‐cluster singles and doubles (CCSD) with a variety of all electron basis sets ranging from 6‐31G to aug‐cc‐pVTZ. Two methods are identified as good candidates: a density functional theory (DFT) method (MPW1K) and a dual‐level method including MP2, and CCSD theories. These methods yield rate constants that agree within one order of magnitude of experiment and activation energies within 1 kcal/mol over the 293–683 K temperature range. The B3LYP and SCF methods do not perform as well and are discounted early. Basis sets that perform well are found to include diffuse and polarizing functions on all atoms, including hydrogen. These include the 6‐31++G** and aug‐cc‐pVDZ basis sets. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Density functional theory studies of quantum transport in molecular systems
Authors: Meunier Vincent , Lu Wenchang , Sumpter Bobby G. , Bernholc Jerry 
Published: August 2006

AbstractConventional semiconducting devices are rapidly approaching their physical limits, encouraging an increasing number of researchers across multiple disciplines to attempt to devise innovative ways to decrease the size and increase the performance of critical features in microelectronic circuits. One possible route is based on the idea of using molecules and molecular structures as functional electronic devices. While impressive experimental progress toward the realization of molecular electronics has been achieved, full insight into the potential for molecular‐based electronics requires accurate theoretical investigations of the processes governing their functioning. In the present study, we show that large‐scale quantum electronic structure calculations coupled with nonequilibrium Green function theory can be employed to determine quantum conductance on practical length scales. The combination of state‐of‐the‐art quantum mechanical methods, efficient numerical algorithms, and high‐performance computing allows for realistic evaluation of properties at length scales that are routinely reached experimentally. Two illustrations of the method are presented. First, we investigate the electron transport properties of a Si/organic‐molecule/Si junction, using a numerically optimized basis. Second, quantum chemical calculations using up to 104 basis functions are carried out to investigate amphoteric doping of carbon nanotubes by encapsulation of organic molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Portal hypertension in a patient with Hunter disease
Authors: Kato Tomomi , Isogai Koji , Orii Koji , Kuratsubo Izumi , Kondo Naomi , Orii Tadao , Suzuki Yasuyuki 
Published: August 2006

SummaryHepatosplenomegaly is one of the cardinal signs of Hunter disease; however, portal hypertension has not been described. We report portal hypertension in an adult Hunter patient with the attenuated phenotype.
Lipoprotein lipase gene analyses in one Turkish family and three different Chinese families with severe hypertriglyceridaemia: One novel and several established mutations
Authors: Nierman Melchior C. , Peter Jorge , Khoo Kah‐Lin , Defesche Joep C. 
Published: August 2006

SummaryLipoprotein lipase (LPL, triacylglycerol acylhydrolase; EC 3.1.1.3) deficiency (OMIM 238600) is an autosomal recessive inherited condition caused by mutations in the LPL gene, either in a homozygous or in a compound heterozygous state, leading to loss of lipolytic activity and resulting in severe hypertriglyceridaemia and subsequent risk for developing pancreatitis. Numerous LPL gene mutations leading to loss of catalytic function have been described. In this present study, we describe full clinical, biochemical and molecular analyses of severe hypertriglyceridaemic individuals in one Turkish and three Chinese families. We established one novel mutation (delCT1312–1313), a new combination of mutations (S193R and I194T) and four previously reported mutations (L252R, L252V, S193R and I194T) of the LPL gene and report phenotypes for these and four previously described mutations. Finally, we show that two patients homozygous for the LPL gene delCT1312–1313 mutations are characterized by absence of LPL activity that coincides with absence of LPL protein.
Fumaric aciduria: Mild phenotype in a 8‐year‐old girl with novel mutations
Authors: Maradin M. , Fumić K. , Hansikova H. , Tesarova M. , Wenchich L. , Dorner S. , Sarnavka V. , Zeman J. , Barić I. 
Published: August 2006

SummaryFumaric aciduria is a rare, autosomal recessive disorder caused by deficient acitivity of fumarate hydratase (FH). Common clinical features are hypotonia, failure to thrive, severe psychomotor retardation and seizures. Facial dysmorphism and brain malformations are frequent. Recently, some FH gene mutations have been associated with inherited cutaneous and uterine leiomyomas and papillary renal cell cancer. Our patient had a relatively mild phenotype, a previously not reported genotype and familial tumour predisposition. The mother and grandmother had uterine myomas. The paternal grandfather and his two brothers died from lung and laryngeal cancers. The pregnancy was complicated by bleeding and intrauterine growth retardation. Delivery was after 35 weeks, with normal Apgar score. The girl was hypotonic since birth. At age 2 months the parents noticed short apnoeic crises. She could sit at age 1.5 years, and walk with assistance at 4 years. At age 8 years highly increased excretion of fumaric acid was found twice (217 and 445 mmol/mol creatinine). Shortly before that the girl started to have leg and arm spasms. Grand mal seizures occurred twice. Facial dysmorphism included depressed nasal bridge, anteverted ears, hypertelorism and microcephaly. Speech was limited to few disyllables. She was atactic with spastic paraparesis. Brain MRI showed slight ventriculomegaly, white‐matter atrophy and hypoplasia of corpus callosum. Activity of FH in fibroblasts was 1.9 nmol/min/mg protein (controls 40–80). Analysis of the FH gene revealed the maternally derived c.1029_1031delAGT mutation, resulting in Val deletion and substitution of Gln by His, and paternally derived c.976C > T mutation, resulting in substitution of Pro by Ser.
Prolonged moderate‐intensity exercise without and with L‐carnitine supplementation in patients with MCAD deficiency
Authors: Huidekoper H. H. , Schneider J. , Westphal T. , Vaz F. M. , Duran M. , Wijburg F. A. 
Published: August 2006

SummaryMedium‐chain acyl‐CoA dehydrogenase deficiency (MCADD) is probably the most common inborn error of fatty acid oxidation (FAO). Routine L‐carnitine supplementation in the treatment of MCADD is controversial. To establish the effects of L‐carnitine supplementation during prolonged moderate‐intensity exercise in MCADD, five patients and three control subjects were studied during 2 hours of moderate‐intensity exercise after a 12‐hour fast. Patients were studied twice, once with and once without L‐carnitine supplementation (50 mg/kg per day). Blood samples were collected before, during and after exercise, and analysed for routine parameters, acylcarnitines and carnitine biosynthesis intermediates. Urine was collected before and after exercise, and analysed for acylcarnitines. All patients were able to complete the exercise test without any apparent clinical or biochemical adverse effects, even without L‐carnitine supplementation. A significant rise in plasma free fatty acids and octanoylcarnitine levels during exercise was seen in all patients, indicating a substantial increase in FAO during exercise. Octanoylcarnitine levels in plasma were significantly higher in patients with L‐carnitine supplementation, suggesting increased clearance of accumulating acylcarnitines. A statistically significant increase of plasma and urinary free carnitine levels, as well as of plasma γ‐butyrobetaine was seen in MCADD patients without L‐carnitine supplementation. These data suggest an increase in carnitine biosynthesis. In conclusion, although L‐carnitine supplementation may promote clearance of accumulating acylcarnitines during moderate‐intensity exercise, no apparent beneficial effect of this supplementation on clinical and biochemical parameters was observed in MCADD patients. Our results suggest that MCADD patients are able to increase carnitine biosynthesis during exercise to compensate for carnitine losses.
Needs assessment and review of services for people with inherited metabolic disease in the United Kingdom
Authors: Burton Hilary , Sanderson Simon , Shortland Graham , Lee Philip 
Published: August 2006

SummaryPatients with inherited metabolic diseases need to be viewed as a specialist care group because of the range of expertise required for their diagnosis and management. In the UK, professional concerns have been expressed that existing services would struggle to meet needs resulting from new diagnostic and screening techniques, new treatments and increased survival. This needs assessment and service review was therefore undertaken at the request of the Joint Committee on Medical Genetics, guided by a national multidisciplinary stakeholder group. All 24 specialist centres identified in the UK provided evidence for the review. Approximately 10 000 patients are known to services and their annual number of referrals is increasing. Possible shortfalls in the number of patients attending specialist services were estimated for the UK as a whole by extrapolating the results from the region with the most comprehensive service and comparing this with known patient numbers. This analysis suggests that a further 5600 children and 3300 adults are not looked after by specialist services or have been lost to follow‐up. The comprehensiveness of services was assessed using a new scoring system for clinical and organizational criteria. There are major regional disparities in the comprehensiveness of service provision across the country, with some regions having little or no specialist service. Unmet need will increase as a result of new diagnostic technologies, more effective treatments and new neonatal screening programmes; specialist services need to be developed and expanded to provide a comprehensive and more equitable service to the UK population.
Receptor Signal Output Mediated by the ETR1 N Terminus Is Primarily Subfamily I Receptor Dependent
Authors: Xie Fang , Liu Qian , Wen Chi-Kuang 
Published: August 2006

Abstract
etr1-1 is a dominant ethylene receptor gene in Arabidopsis (Arabidopsis thaliana) and confers ethylene insensitivity. The truncated etr1-1(1-349) protein is capable of repressing ethylene responses, whereas etr1(1-349) is not, lending support to a hypothesis that the dominant etr1-1(1-349) could convert wild-type receptors to an ethylene-insensitive state. Assuming that etr1-1(1-349) and etr1(1-349) would share the same signaling mechanism, we hypothesize that the etr1(1-349) protein is capable of repressing ethylene responses when not bound with ethylene. In this study, we show that both etr1(1-349) and etr1-1(1-349) are capable of receptor signal output, which is primarily dependent on subfamily I receptors. The etr1(1-349) and etr1-1(1-349) clones were individually transformed to mutants and the resulting phenotypes were scored. Each of those transgenes restored the rosette growth and flower fertility of etr1-7 ers1-2 to a similar extent. In contrast, neither etr1(1-349) nor etr1-1(1-349) was capable of signal output in etr1-7 ers1-3. The ERS1 transcript was detectable in ers1-2 but not in ers1-3, implying that ETR1 N-terminal signaling is subfamily I dependent. Loss of the subfamily II receptor genes did not perturb etr1-1(1-349)-mediated ethylene insensitivity. Possible roles of subfamily I receptors and disulfide linkages in ETR1 receptor signal output mediated through the N terminus are discussed.
The Frequency and Efficiency of Endogene Suppression by Transitive Silencing Signals Is Influenced by the Length of Sequence Homology
Authors: Bleys Annick , Vermeersch Leen , Van Houdt Helena , Depicker Anna 
Published: August 2006

Abstract
Transitivity, the spread of RNA silencing along primary target sequences, leads to the degradation of secondary targets that have no sequence homology to the initial silencing trigger. We demonstrate that increasing the distance between direct and adjacent target sequences in a transgenic primary target delays the onset of silencing of a secondary target gene. Silencing can spread in a 3′ to 5′ direction over a distance of at least 500 nucleotides (nt), but this requires consistently more time compared to a distance of 98 nt or 250 nt. The efficiency and frequency of transitive silencing of an endogene depends on the length of its sequence homology with the primary target. With a length of 500 nt, efficient silencing can eventually be established in all plants, whereas lengths of 250 nt and 98 nt homology result in less efficient and less frequent suppression. These results suggest that amplification of secondary small interfering RNAs (siRNAs) is a time-requiring process that gradually expands the population of siRNAs until a steady-state level is reached. Moreover, the length of the sequence homology in the primary target providing secondary siRNAs determines whether this steady-state level readily exceeds the threshold necessary for efficient silencing.
Chimeric Proteins Suggest That the Catalytic and/or C-Terminal Domains Give CesA1 and CesA3 Access to Their Specific Sites in the Cellulose Synthase of Primary Walls
Authors: Wang Jian , Howles Paul A. , Cork Ann H. , Birch Rosemary J. , Williamson Richard E. 
Published: August 2006

Abstract
CesA1 and CesA3 are thought to occupy noninterchangeable sites in the cellulose synthase making primary wall cellulose in Arabidopsis (Arabidopsis thaliana L. Heynh). With domain swaps and deletions, we show that sites C terminal to transmembrane domain 2 give CesAs access to their individual sites and, from dominance and recessive behavior, deduce that certain CesA alleles exclude others from accessing each site. Constructs that swapped or deleted N-terminal domains were stably transformed into the wild type and into the temperature-sensitive mutants rsw1 (Ala-549Val in CesA1) and rsw5 (Pro-1056Ser in CesA3). Dominant-positive behavior was assayed as root elongation at the restrictive temperature and dominant-negative effects were observed at the permissive temperature. A protein with the catalytic and C-terminal domains of CesA1 and the N-terminal domain of CesA3 promoted growth only in rsw1 consistent with it accessing the CesA1 site even though it contained the CesA3 N-terminal domain. A protein having the CesA3 catalytic and C-terminal domains linked to the CesA1 N-terminal domain dramatically affected growth, but only in the CesA3 mutant. This is consistent with the operation of the same access rule taking this chimeric protein to the CesA3 site. In this case, however, the transgene behaved as a genotype-specific dominant negative, causing a 60% death rate in rsw5, but giving no visible phenotype in wild type or rsw1. We therefore hypothesize that possession of CesA3WT protects Columbia and rsw1 from the lethal effects of this chimeric protein, whereas the mutant protein (CesA3rsw5) does not.
Adenosine Kinase Modulates Root Gravitropism and Cap Morphogenesis in Arabidopsis
Authors: Young Li-Sen , Harrison Benjamin R. , U.M. Narayana Murthy , Moffatt Barbara A. , Gilroy Simon , Masson Patrick H. 
Published: August 2006

Abstract
Adenosine kinase (ADK) is a key enzyme that regulates intra- and extracellular levels of adenosine, thereby modulating methyltransferase reactions, production of polyamines and secondary compounds, and cell signaling in animals. Unfortunately, little is known about ADK's contribution to the regulation of plant growth and development. Here, we show that ADK is a modulator of root cap morphogenesis and gravitropism. Upon gravistimulation, soluble ADK levels and activity increase in the root tip. Mutation in one of two Arabidopsis (Arabidopsis thaliana) ADK genes, ADK1, results in cap morphogenesis defects, along with alterations in root sensitivity to gravistimulation and slower kinetics of root gravitropic curvature. The kinetics defect can be partially rescued by adding spermine to the growth medium, whereas the defects in cap morphogenesis and gravitropic sensitivity cannot. The root morphogenesis and gravitropism defects of adk1-1 are accompanied by altered expression of the PIN3 auxin efflux facilitator in the cap and decreased expression of the auxin-responsive DR5-GUS reporter. Furthermore, PIN3 fails to relocalize to the bottom membrane of statocytes upon gravistimulation. Consequently, adk1-1 roots cannot develop a lateral auxin gradient across the cap, necessary for the curvature response. Interestingly, adk1-1 does not affect gravity-induced cytoplasmic alkalinization of the root statocytes, suggesting either that ADK1 functions between cytoplasmic alkalinization and PIN3 relocalization in a linear pathway or that the pH and PIN3-relocalization responses to gravistimulation belong to distinct branches of the pathway. Our data are consistent with a role for ADK and the S-adenosyl-l-methionine pathway in the control of root gravitropism and cap morphogenesis.