bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regional self‐interaction correction of density functional theory
Authors: Tsuneda Takao , Kamiya Muneaki , Hirao Kimihiko 
Published: August 2003

AbstractWe propose a new simple scheme for self‐interaction correction (SIC) of exchange functionals in the density functional theory. In the new scheme, exchange energies are corrected by substituting exchange self‐interactions for exchange functionals in regions of self‐interaction. To classify the regions of self‐interaction, we take advantage of the property of the total kinetic energy density approaching the Weizsäcker density in the case of electrons in isolated orbitals. The scheme differs from conventional SIC methods in that it produces optimized molecular structures. Applying the scheme to the calculation of reaction energy barriers showed that it provides a clear improvement in cases where the barriers are underestimated by conventional “pure” functionals. In particular, we found that this scheme even reproduces a transition state that is not given by pure functionals. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1592–1598, 2003
A comparison of the mechanism for the reductive half‐reaction between pea seedling and other copper amine oxidases (CAOs)
Authors: Prabhakar Rajeev , Siegbahn Per E. M. 
Published: August 2003

AbstractIn a previous DFT study a mechanism for the reductive half‐reaction of pea seedling amine oxidase (PSAO) was suggested. In many of the suggested steps a lysine at the active site plays an important role. However, this lysine is not found in other amine oxidases. The primary aim of the present DFT study is therefore to investigate alternative mechanisms for those amine oxidases (CAO) where the lysine residue is not present. One of the most important roles suggested for the lysine in PSAO was to protonate the O2‐site of TPQ before the critical CH bond cleavage of the substrate. In the absence of lysine the O2‐site of TPQ is now suggested to be protonated by a water ligand on the copper metal complex, in line with experimental suggestions. In other steps the role of lysine is taken over by an asparagine. All results are compared with experimental observations and good agreement is generally found. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1599–1609, 2003
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
Authors: Taylor Richard D. , Jewsbury Philip J. , Essex Jonathan W. 
Published: August 2003

AbstractThe docking of flexible small molecule ligands to large flexible protein targets is addressed in this article using a two‐stage simulation‐based method. The methodology presented is a hybrid approach where the first component is a dock of the ligand to the protein binding site, based on deriving sets of simultaneously satisfied intermolecular hydrogen bonds using graph theory and a recursive distance geometry algorithm. The output structures are reduced in number by cluster analysis based on distance similarities. These structures are submitted to a modified Monte Carlo algorithm using the AMBER‐AA molecular mechanics force field with the Generalized Born/Surface Area (GB/SA) continuum model. This solvent model is not only less expensive than an explicit representation, but also yields increased sampling. Sampling is also increased using a rotamer library to direct some of the protein side‐chain movements along with large dihedral moves. Finally, a softening function for the nonbonded force field terms is used, enabling the potential energy function to be slowly turned on throughout the course of the simulation. The docking procedure is optimized, and the results are presented for a single complex of the arabinose binding protein. It was found that for a rigid receptor model, the X‐ray binding geometry was reproduced and uniquely identified based on the associated potential energy. However, when side‐chain flexibility was included, although the X‐ray structure was identified, it was one of three possible binding geometries that were energetically indistinguishable. These results suggest that on relaxing the constraint on receptor flexibility, the docking energy hypersurface changes from being funnel‐like to rugged. A further 14 complexes were then examined using the optimized protocol. For each complex the docking methodology was tested for a fully flexible ligand, both with and without protein side‐chain flexibility. For the rigid protein docking, 13 out of the 15 test cases were able to find the experimental binding mode; this number was reduced to 11 for the flexible protein docking. However, of these 11, in the majority of cases the experimental binding mode was not uniquely identified, but was present in a cluster of low energy structures that were energetically indistinguishable. These results not only support the presence of a rugged docking energy hypersurface, but also suggest that it may be necessary to consider the possibility of more than one binding conformation during ligand optimization. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1637–1656, 2003
A partition function algorithm for nucleic acid secondary structure including pseudoknots
Authors: Dirks Robert M. , Pierce Niles A. 
Published: August 2003

AbstractNucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N5) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1664–1677, 2003
Ab initio study of the mechanism of the atmospheric reaction: NO2 + O3 → NO3 + O2
Authors: Peiró‐García Julio , Nebot‐Gil Ignacio 
Published: August 2003

AbstractThe atmospheric reaction NO2 + O3 → NO3 + O2 (1) has been investigated theoretically by using the MP2, G2, G2Q, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. The results show that the reaction pathway can be divided in two different parts at the MP2 level of theory. At this level, the mechanism proceeds along two transition states (TS1 and TS2) separated by an intermediate, designated as A. However, when the single‐reference higher correlated QCISD methodology has been employed, the minimum A and the transition state TS2 are not found on the hypersurface of potential energy, which confirms a direct reaction mechanism. Single‐reference high correlated and multiconfigurational methods consistently predict the barrier height of reaction (1) to be within the range 2.5–6.1 kcal mol−1, in reasonable agreement with experimental data. The calculated reaction enthalpy is −24.6 kcal mol−1 and the reaction rate calculated at the highest CASPT2 level, of k = 6.9 × 10−18 cm3 molecule−1 s−1. Both results can be regarded also as accurate predictions of the methodology employed in this article. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1657–1663, 2003
Structural and dynamical properties of methane clathrate hydrates
Authors: English Niall J. , Macelroy J. M. D. 
Published: August 2003

AbstractEquilibrium molecular dynamics (MD) simulations have been performed in both the NVT and NPT ensembles to study the structural and dynamical properties of fully occupied methane clathrate hydrates at 50, 125, and 200 K. Five atomistic potential models were used for water, ranging from fully flexible to rigid polarizable and nonpolarizable. A flexible and a rigid model were utilized for methane. The phonon densities of states were evaluated and the localized rattling modes for the methane molecules were found to couple to the acoustic phonons of the host lattice. The calculated methane density of states was found to be in reasonable agreement with available experimental data. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1569–1581, 2003
Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
Authors: Wu Guosheng , Robertson Daniel H. , Brooks Charles L. , Vieth Michal 
Published: August 2003

AbstractThe influence of various factors on the accuracy of protein‐ligand docking is examined. The factors investigated include the role of a grid representation of protein‐ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper‐surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated‐annealing‐based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid‐based approximations to explicit all‐atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all‐atom representation of the protein (full force field) is used, while a lower accuracy of 66–76% is observed for grid‐based methods. All docking experiments considered a 41‐member protein‐ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid‐based docking is achieved if the explicit all‐atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower‐accuracy grid‐based energy representations can be effectively used when followed with full force field minimization. The results of these grid‐based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 13: 1549–1562, 2003
Deriving effective mesoscale potentials from atomistic simulations
Authors: Reith Dirk , Pütz Mathias , Müller‐Plathe Florian 
Published: August 2003

AbstractWe demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse‐grained an atomistic all‐atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. © 2003 Wiley Periodicals, Inc. J Comput Chem 13: 1624–1636, 2003
STO and GTO field‐induced polarization functions for H to Kr
Authors: Chong Delano P. , Grüning Myrta , Baerends Evert Jan 
Published: August 2003

AbstractField‐induced polarization (FIP) functions were proposed over two decades ago to improve the accuracy of calculated response properties, and the FIP functions in GTO form for H and C to F were tested on small molecules, with encouraging results. The concept of FIP is now extended to all atoms up to Kr. New simplifying approximations for the description of asymptotic highest occupied atomic orbitals (HOAOs) are introduced in this study. They provide the basis for STO and GTO exponents of a complete set of FIP functions from H to Kr, which are both listed for the convenience of the users. Tests on the polarizabilities of a series of atoms and molecules demonstrate that addition of the FIP basis functions to a series of standard basis sets drastically improves the performance of all these basis sets compared to converged results. Moreover, the byproduct of this study (approximate asymptotic HOAOs) provides information for the construction of accurate basis sets for long‐range ground state properties. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1582–1591, 2003
A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems
Authors: Hopkins Brian W. , Tschumper Gregory S. 
Published: August 2003

AbstractA multicentered integrated QM/QM technique has been developed. By separating high‐level calculations in distinct regions of molecules, the multicentered approach supplants a single large high‐level calculation with several smaller calculations. Due to the steep polynomial scaling of traditional ab initio quantum chemical methods, this separation significantly enhances the computational efficiency of QM/QM methods. The straightforward implementation of this multicentered approach is illustrated with several large poly‐alcohols that form hydrogen bonds with water. The largest alcohol–water complex contains 81 atoms. For properly selected model systems, this multicentered approach introduces essentially no error in the dissociation energies of these complexes relative to conventional QM/QM schemes. This multicentered technique should be easily extended to other, more general integrated methods (QM/MM, ONIOM, etc). © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1563–1568, 2003
Improved third‐order Møller–Plesset perturbation theory
Authors: Grimme Stefan 
Published: August 2003

AbstractBased on a partitioning of the total correlation energy into contributions from parallel‐ and antiparallel‐spin pairs of electrons, a modified third‐order Møller–Plesset (MP) perturbation theory is developed. The method, termed SCS–MP3 (SCS for spin‐component‐scaled) continues previous work on an improved version of MP2 (S. Grimme, J Chem Phys 2003, 118, 9095). A benchmark set of 32 isogyric reaction energies, 11 atomization energies, and 11 stretched geometries is used to assess to performance of the model in comparison to the standard quantum chemical approaches MP2, MP3, and QCISD(T). It is found, that the new method performs significantly better than usual MP2/MP3 and even outperforms the more costly QCISD method. Opposite to the usual MP series, the SCS third‐order correction uniformly improves the results. Dramatic enhancements are especially observed for the more difficult atomization energies, some of the stretched geometries, and reaction and ionization energies involving transition metal compounds where the method seems to be competitive or even superior to the widely used density functional approaches. Further tests performed for other complex systems (biradicals, C20 isomers, transition states) demonstrate that the SCS–MP3 model yields often results of QCISD(T) accuracy. The uniformity with which the new approach improves for very different correlation problems indicates significant robustness, and suggests it as a valuable quantum chemical method of general use. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1529–1537, 2003
Continuum and discrete calculation of fractional contributions to solvation free energy
Authors: Morreale Antonio , Gelpí Josep Lluis , Luque F. Javier , Orozco Modesto 
Published: August 2003

AbstractApproaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure‐activity relationships. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1610–1623, 2003
Ab initioinvestigation on the reaction path and rate for the gas‐phase reaction of HO + H2O ↔ H2O + OH
Authors: Uchimaru Tadafumi , Chandra Asit K. , Tsuzuki Seiji , Sugie Masaaki , Sekiya Akira 
Published: August 2003

AbstractThis article describes anab initioinvestigation on the potential surfaces for one of the simplest hydrogen atom abstraction reactions, that is, HO + H2O ↔ H2O + OH. In accord with the findings in the previously reported theoretical investigations, two types of the hydrogen‐bonding complexes [HOHOH] and [H2OHO] were located on the potential energy surface. The water molecule acts as a hydrogen donor in the [HOHOH] complex, while the OH radical acts as a hydrogen donor in the [H2OHO] complex. The energy evaluations at the MP2(FC) basis set limit, as well as those through the CBS‐APNO procedure, have provided estimates for enthalpies of association for these complexes at 298 K as −2.1 ≈ −2.3 and −4.1 ≈ −4.3 kcal/mol, respectively. The IRC calculations have suggested that the [H2OHO] complex should be located along the reaction coordinate for the hydrogen abstraction. Our best estimate for the classical barrier height for the hydrogen abstraction is 7.8 kcal/mol, which was obtained from the CBS‐APNO energy evaluations. After fitting the CBS‐APNO potential energy curve to a symmetrical Eckart function, the rate constants were calculated by using the transition state theory including the tunneling correction. Our estimates for the Arrhenius parameters in the temperature region from 300 to 420 K show quite reasonable agreement with the experimentally derived values. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1538–1548, 2003
Coronary heart disease, hypertension, and angiotensinogen gene variants in indian opulation
Authors: Nair K.G. , Shalia K.K. , Ashavaid T.F. , Dalal J.J. 
Published: August 2003

AbstractGene encoding components of the renin angiotensin system (RAS) have been implicated with the increased risk of cardiovascular disease (CVD). Two variants of the angiotensinogen (AGT) gene, M235T and T174M, have been shown to be associated with increased risk of hypertension. In the present study, we examined the association of these two polymorphisms and their synergistic interaction with the angiotensin I‐converting enzyme (ACE) deletion homozygote genotype (D/D) on subjects with coronary heart disease (CHD) and hypertension. We studied 131 healthy individuals, 141 angiographically verified CHD patients, and 159 hypertensive subjects. The identification of the ACE and AGT gene polymorphisms was carried out using a PCR‐based restriction endonuclease digestion method. There was no significant difference in the distribution of the M235T and T174M variants between the two test groups and the control group. Association was also not seen when analysis was carried out in patients when subgrouped according to the extent of the severity of the disease. In addition, the risk was not restricted to subjects carrying the D allele of the ACE gene and T235T of AGT. M235T and T174M variants do not contribute to the increased risk of CHD or hypertension in the Indian population. J. Clin. Lab. Anal. 17:141–146, 2003. © 2003 Wiley‐Liss, Inc.
Development of a new method for measuring total urinary protein using acid violet 6B pigment
Authors: Iijima Shiro , Cho Hiroko , Sakai Nobue , Shiba Kiyoko , Toyoshima Yayoi , Nishida Kenji , Kobayashi Shizuko 
Published: August 2003

AbstractWe have developed a new method for measuring total urinary protein using acid violet 6B (AV6B) pigment. Nine purified components of human urinary proteins and urine samples collected randomly from 123 diabetic outpatients were used. There were 62, 36, and 25 cases of prenephropathy, early nephropathy, and overt nephropathy, respectively. All samples were measured by Coomassie brilliant blue G 250 (CBB), pyrogallol red‐molybdate (PRM), and AV6B methods using an optical photometer. In healthy subjects, the major components of urinary proteins, such as γ‐globulins, IgG, IgA Tamm‐Horsfall protein, and transferrin, the reactivity values of the AV6B and PRM methods were similar. The CBB method was the least sensitive of the three methods. In the urine samples from diabetic patients, the urinary protein values measured by the AV6B method were higher than those measured by the CBB method in the prenephropathy stage. The values obtained by the AV6B method (y) correlated well with those from the CBB method (x) (y = 1.243x+ 3.61, r = 0.904). When the values from the AV6B method (y) were compared to those from the PRM method (x), correlation was low (y = 1.406x−29.15, r = 0.786). In conclusion, the AV6B method was more useful than the CBB and PRM methods for low levels of urinary protein. J. Clin. Lab. Anal. 17: 147–154, 2003. © 2003 Wiley‐Liss, Inc.
Diagnosis of tuberculosis: Available technologies, limitations, and possibilities
Authors: Garg Sanjay K. , Tiwari R. P. , Tiwari Dileep , Singh Rupinder , Malhotra Dolly , Ramnani V. K. , Prasad G.B.K.S. , Chandra Ramesh , Fraziano M. , Colizzi V. , Bisen Prakash S. 
Published: August 2003

AbstractRapid diagnosis and treatment are important for preventing transmission of Mycobacterium tuberculosis. However, the diagnosis of tuberculosis continues to pose serious problems, mainly because of difficulties in differentiating between patients with active tuberculosis and those with healed lesions, normal mycobacterium boris BCG (Bacillus Calmette Guerin) vaccinated individuals, and unvaccinated Manteux positives. Physicians still rely on conventional methods such as Ziehl‐Neelsen (ZN) staining, fluorochrome staining, sputum culture, gastric lavage, and other non‐traditional methods. Although the tuberculin test has aided in the diagnosis of tuberculosis for more than 85 years, its interpretation is difficult because sensitization with nontuberculous mycobacteria leads to false‐positive tests. There have been numerous unsuccessful attempts to develop clinically useful serodiagnostic kits for tuberculosis. A number of proteinaceous and nonprotein antigens (such as acyltrehaloses and phenolglycolipids) have been explored from time to time for the development of such assays but they have not proved to be clinically useful. It has been difficult to develop an ELISA utilizing a suitable antigen because M. tuberculosis shares a large number of antigenic proteins with other microorganisms that may or may not be pathogenic. With the advent of molecular biology techniques, there have been significant advances in nucleic acid‐based amplification and hybridization, which are helping to rectify existing flaws in the diagnosis of tuberculosis. The detection of mycobacterial DNA in clinical samples by polymerase chain reaction (PCR) is a promising approach for the rapid diagnosis of tuberculous infection. However, the PCR results must be corrected for the presence of inhibitors as well as for DNA contamination. In the modern era of genetics, marked by proteomics and genomics, the day is not far off when DNA chip‐based hybridization assays will instantly reveal mycobacterial infections. J. Clin. Lab. Anal. 17: 155–163, 2003. © 2003 Wiley‐Liss, Inc.