bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes of optical properties of dental nano‐filled resin composites after curing and thermocycling
Authors: Lee Yong‐Keun , Lim Bum‐Soon , Rhee Sang‐Hoon , Yang Hyeong‐Cheol , Powers John M 
Published: June 2004

AbstractThe objective was to evaluate the color changes after curing, polishing, and thermocycling of a nano‐filled resin composite. A nano‐filled composite was grouped into two shades of enamel (EN) and translucent (TL). One hybrid composite was used as a control (CL). Color of specimens of 10 mm in diameter and 2 mm in thickness was measured on a reflection spectrophotometer with SCE geometry under the D65 illumination over white and black backgrounds. Color before curing and after curing, polishing and thermocycling was measured. Color change (ΔE), translucency parameter (TP), and contrast ratio (CR) were compared. Average ΔE after curing was 4.6 in the EN group and 10.4 in the TL group compare to 2.9 in CL. Polishing caused average ΔE of 3.3–3.6, which was not different by the shade group (p > 0.05). After 2000 cycles of thermocycling, average ΔE was 1.4–1.8, which was not different by the shade group (p > 0.05). TP values increased after curing in the EN group, but decreased in the TL group (p < 0.05). TP values after thermocycling decreased in the EN group but did not change in TL (p = 0.05). TP values of TL shades were higher than those of EN regardless of specimen conditions (p < 0.05). Changes in CR values showed similar trends to those of TP values in translucency. Changes of color and translucency after curing, polishing, and thermocycling varied by the shade group. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 71B: 16–21, 2004
Influence of the aspect ratio of bioactive nanofillers on rheological behavior of PMMA‐based orthopedic materials
Authors: Liu Tse‐Ying , Chen San‐Yuan , Liu Dean‐Mo 
Published: June 2004

AbstractIn this investigation, calcium‐deficient hydroxyapatite (CDHA) nanocrystals with needle‐like geometry were synthesized and incorporated with Poly(methyl methacrylate), PMMA, to form CDHA–PMMA nanocomposites. Rheological behaviors of the PMMA–CDHA melting suspensions were systematically investigated in terms of solid loading and aspect ratio of the CDHA nanoparticles. The maximum solid loadings of nano‐CDHA particles with aspect ratios of 7.2, 10.4, and 17 were determined to be 28, 31, and 57%, respectively. An increase in solid concentrations causes pronounced shear‐thinning behavior. This result suggests that a strong interaction, including Van der Waals attraction and mechanical interlocking, between the nano‐CDHA particles makes the nanocomposite mixture more non‐Newtonian. Furthermore, it was found that packing efficiency and yield strength in the suspension were strongly influenced by the aspect ratio, especially above the critical value of 8.8. The obtained critical aspect ratio and solid content provide not only appropriate design in the PMMA–CDHA polymeric suspension for fabrication process but also optimal conditions for the fabrication of orthopedic devices via injection molding or extrusion. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 71B: 116–122, 2004
Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl
Authors: Sheng Li , Li Ze‐Sheng , Liu Jing‐Yao , Xiao Jing‐Fa , Sun Chia‐Chung 
Published: June 2004

AbstractThe multiple channel reaction H + CH3CH2Cl → products has been studied by the ab initio direct dynamics method. The potential energy surface information is calculated at the MP2/6‐311G(d,p) level of theory. The energies along the minimum energy path are further improved by single‐point energy calculations at the PMP4(SDTQ)/6‐311+G(3df,2p) level of theory. For the reaction, four reaction channels (one chlorine abstraction, one α‐hydrogen abstraction, and two β‐hydrogen abstractions) have been identified. The rate constants for each reaction channel are calculated by using canonical variational transition state theory incorporating the small‐curvature tunneling correction in the temperature range 298–5000 K. The total rate constants, which are calculated from the sum of the individual rate constants, are in good agreement with the experimental data. The calculated temperature dependence of the branching fractions indicates that for the title reaction, H‐abstraction reaction is the major reaction channel in the whole temperature range 298–5000 K. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 72–82, 2004
Peptide backbone reconstruction using dead‐end elimination and a knowledge‐based forcefield
Authors: Adcock Stewart A. 
Published: June 2004

AbstractA novel, yet simple and automated, protocol for reconstruction of complete peptide backbones from Cα coordinates only is described, validated, and benchmarked. The described method collates a set of possible backbone conformations for each set of residue triads from a structural library derived from the PDB. The optimal permutation of these three residue segments of backbone conformations is determined using the dead‐end elimination (DEE) algorithm. Putative conformations are evaluated using a pairwise‐additive knowledge‐based forcefield term and a fragment overlap term. The protocol described in this report is able to restore the full backbone coordinates to within 0.2–0.6 Å of the actual crystal structure from Cα coordinates only. In addition, it is insensitive to errors in the input Cα coordinates with RMSDs of 3.0 Å, and this is illustrated through application to deliberately distorted Cα traces. The entire process, as described, is rapid, requiring of the order of a few minutes for a typical protein on a typical desktop PC. Approximations enable this to be reduced to a few seconds, although this is at the expense of prediction accuracy. This compares very favorably to previously published methods, being sufficiently fast for general use and being one of the most accurate methods. Because the method is not restricted to the reconstruction from only Cα coordinates, reconstruction based on Cβ coordinates is also demonstrated. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 16–27, 2004
Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains
Authors: McQuaid Michael J. , Sun Huai , Rigby David 
Published: June 2004

AbstractTo establish force‐field‐based (molecular) modeling capability that will accurately predict condensed‐phase thermophysical properties for materials containing aliphatic azide chains, potential parameters for atom types unique to such chains have been developed and added to the COMPASS force field. The development effort identified the need to define four new atom types: one for each of the three azide nitrogen atoms and one for the carbon atom bonded to the azide. Calculations performed with the expanded force field yield (gas‐phase) molecular structures and vibrational frequencies for hydrazoic acid, azidomethane, and the anti and gauche forms of azidoethane in good agreement with values determined experimentally and/or through computational quantum mechanics. Liquid densities calculated via molecular dynamics (MD) simulations were also in good agreement with published values for 13 of 15 training set compounds, the exceptions being hydrazoic acid and azidomethane. Of the 13 compounds whose densities are well simulated, nine have experimentally determined heats of vaporization reported in the open literature, and in all of these cases, MD simulated values for this property are in reasonable agreement with the published values. Simulations with the force field also yielded reasonable density estimates for a series of 2‐azidoethanamines that have been synthesized and tested for use as hydrazine‐alternative fuels. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 61–71, 2004
DFT‐GIAO calculations of 19F NMR chemical shifts for perfluoro compounds
Authors: Fukaya Haruhiko , Ono Taizo 
Published: June 2004

AbstractThe 19F NMR shieldings for 53 kinds of perfluoro compounds were calculated by the B3LYP‐GIAO method using the 6‐31G(d), 6‐31+G(d), 6‐31G(d,p), 6‐31++G(d,p), 6‐311G(d,p), 6‐311++G(d,p), 6‐311G(2d,2p), 6‐311++G(2d,2p), 6‐311++G(2df,2p), 6‐311++G(3d,2p), and 6‐311++G(3df,2p) basis sets. The diffuse functions markedly reduce the difference between the calculated and experimental chemical shifts. The calculations using the 6‐31++G(d,p) basis set give the chemical shifts within 10 ppm deviations from experimental values except for the fluorine nuclei attached to an oxygen atom, a four‐ and a six‐coordinated sulfur atom, and FC(CF3)2 attached to a sulfur atom. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 51–60, 2004
Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results
Authors: Linnanto Juha , Korppi‐Tommola Jouko 
Published: June 2004

AbstractThe semiempirical PM5 method has been used to calculate fully optimized structures of magnesium‐bacteriochlorin, magnesium‐chlorin, magnesium‐porphin, mesochlorophyll a, chlorophylls a, b, c1, c2, c3, and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree‐Fock/6‐31G* ab initio and density functional B3LYP/6‐31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c1, and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self‐consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6‐31G* or Hartree‐Fock/6‐31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree‐Fock/6‐31G* and B3LYP/6‐31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin‐like molecules. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 123–137, 2004
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
Authors: Patel Sandeep , Brooks Charles L. 
Published: June 2004

AbstractA first‐generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT‐based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom‐typing scheme are determined via simultaneously optimizing vacuum water‐solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute‐water geometries, specifically hydrogen bond distances, are fit to 0.19 Å r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P‐FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1–0.2 Debye in keeping with previously reported work. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 1–15, 2004
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens
Authors: Tubert‐Brohman Ivan , Guimarães Cristiano Ruch Werneck , Repasky Matthew P. , Jorgensen William L. 
Published: June 2004

AbstractThe new semiempirical methods, PDDG/PM3 and PDDG/MNDO, have been parameterized for halogens. For comparison, the original MNDO and PM3 were also reoptimized for the halogens using the same training set; these modified methods are referred to as MNDO′ and PM3′. For 442 halogen‐containing molecules, the smallest mean absolute error (MAE) in heats of formation is obtained with PDDG/PM3 (5.6 kcal/mol), followed by PM3′ (6.1 kcal/mol), PDDG/MNDO (6.6 kcal/mol), PM3 (8.1 kcal/mol), MNDO′ (8.5 kcal/mol), AM1 (11.1 kcal/mol), and MNDO (14.0 kcal/mol). For normal‐valent halogen‐containing molecules, the PDDG methods also provide improved heats of formation over MNDO/d. Hypervalent compounds were not included in the training set and improvements over the standard NDDO methods with sp basis sets were not obtained. For small haloalkanes, the PDDG methods yield more accurate heats of formation than are obtained from density functional theory (DFT) with the B3LYP and B3PW91 functionals using large basis sets. PDDG/PM3 and PM3′ also give improved binding energies over the standard NDDO methods for complexes involving halide anions, and they are competitive with B3LYP/6‐311++G(d,p) results including thermal corrections. Among the semiempirical methods studied, PDDG/PM3 also generates the best agreement with high‐level ab initio G2 and CCSD(T) intrinsic activation energies for SN2 reactions involving methyl halides and halide anions. Finally, the MAEs in ionization potentials, dipole moments, and molecular geometries show that the parameter sets for the PDDG and reoptimized NDDO methods reduce the MAEs in heats of formation without compromising the other important QM observables. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 138–150, 2004
New reaction simulator “LUMMOX” and its application for prediction of catalytic activities
Authors: Motoki Takao , Shiga Akinobu 
Published: June 2004

AbstractWe developed a new reaction simulator, “LUMMOX.” It is an intermolecular interaction analyzer based on the theories of paired interacting orbitals (PIOs) and localized frontier orbitals (LFOs) that have been developed by Fujimoto et al. (Fukui, K.; Koga, N.; Fujimoto, H. J Am Chem Soc 1981, 103, 196; Fujimoto, H.; Koga, N.; Fukui, K. J Am Chem Soc 1981, 103, 7452; Fujimoto, H.; Satoh, S. J Phys Chem 1994, 98, 1436). LUMMOX runs on a Windows PC and displays graphic representation of orbital interactions. Prediction of activities, selectivities, and molecular weight of olefin polymerization catalysts are presented using PIO analysis and LFO calculation. Not only computational chemists but also experimental chemists can easily use this new system for catalyst design or molecular design from the point of view of orbital interaction. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 106–111, 2004
Systematic quantum chemical study of DNA‐base tautomers
Authors: Piacenza M. , Grimme S. 
Published: June 2004

AbstractThe relative energies of the energetically low‐lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso‐cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B‐LYP, B3‐LYP, and BH‐LYP, and the ab initio methods Hartree‐Fock (HF), standard second‐order Møller‐Plesset perturbation theory (MP2), an improved version of it (SCS‐MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple‐ζ quality including f‐functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3‐LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH‐LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS‐MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 83–98, 2004
Theoretical study of the internal conversion of sulfoxide precursors of poly‐isothianaphthene and related polymers
Authors: Claes Luc , François Jean‐Pierre , Deleuze Michael S. 
Published: June 2004

AbstractIn the present contribution, we theoretically investigate the suitability of the sulfoxide route for the synthesis of conjugated polymers of relevance for the fabrication of low‐band gap materials with improved characteristics. The study focuses specifically on the internal elimination (Ei) reactions of sulfoxide precursors of model oligomers of trans‐ and cis‐poly‐isothianaphtene (PITN), trans‐poly‐isothianaphtene vinylene (PITNV), and trans‐poly‐(ethylene dioxythiophene vinylene) (PEDOTV). These reactions have been characterized in detail by means of Density Functional Theory, along with the MPW1K functional (Modified Perdew‐Wang 1‐parameter model for kinetics). © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 40–50, 2004
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
Authors: Lu Nandou , Kofke David A. , Woolf Thomas B. 
Published: June 2004

AbstractA challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free‐energy results in an efficient way. The formalism of the OS method is based on ensuring sampling of important overlapping phase space during perturbation calculations. This technique samples both forward and reverse free energy perturbation (FEP) to improve the free‐energy calculation. It considers the asymmetry of the FEP calculation and features an ability to optimize both the precision and the accuracy of the measurement without affecting the simulation process itself. The OS method is tested at two optimization levels: no optimization (simple OS), and full optimization (equivalent to Bennett's method), and compared to conventional FEP techniques, including the widely used direct FEP averaging method, on three alchemical mutation systems: (a) an anion transformation in water solution, (b) mutation between methanol and ethane, and (c) alchemical change of an adenosine molecule. It is consistently shown that the reliability of free‐energy estimates can be greatly improved using the OS techniques at both optimization levels, while the performance of Bennett's method is particularly striking. In addition, the efficiency of a calculation can be significantly improved because the method is able to (a) converge to the right answer quickly, and (b) work for large perturbations. The basic two‐stage OS method can be extended to admit additional stages, if needed. We suggest that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 28–39, 2004
Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry
Authors: Casadesús Ricard , Moreno Miquel , González‐Lafont àngels , Lluch José M. , Repasky Matthew P. 
Published: June 2004

AbstractIn this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2‐(2′‐hydroxyphenyl)‐4‐methyloxazole (HPMO) encapsulated in β‐cyclodextrin (β‐CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H · · · H intermolecular interactions between guest (HPMO) and host (β‐CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H · · · H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H · · · H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H · · · H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(β‐CD)‐guest(HPMO) system. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 99–105, 2004