bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrostatic component of solvation: Comparison of SCRF continuum models
Authors: Curutchet Carles , Cramer Christopher J. , Truhlar Donald G. , Ruiz‐López; Manuel F. , Rinaldi Daniel , Orozco Modesto , Luque F. Javier 
Published: January 2003

AbstractWe report a systematic comparison of the electrostatic contributions to the free energy of solvation from three different kinds of quantum mechanical self‐consistent reaction field (SCRF) methods. We also compare the liquid‐phase dipole moments as a measure of the solute's response to the reaction field of the solvent. In particular, we compare these quantities for the generalized Born model as implemented in the SM5.42R method, the multipolar expansion model developed at Nancy, and the MST version of the polarizable continuum model. All calculations are carried out at the HF/6‐31G(d) level. The effects of various choices of solute cavities and representations of the charge density are examined. The test set consists of 18 molecules containing prototypical polar groups, and three different values of the dielectric permittivity are considered. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 284–297, 2003
Ground and excited state CASPT2 geometry optimizations of small organic molecules
Authors: Page Christopher S. , Olivucci Massimo 
Published: January 2003

AbstractA method for computing second‐order multiconfigurational perturbation theory (CASPT2) energy gradients numerically has been implemented and applied to a range of elementary organic chromophores, including 1,3 butadiene, acrolein, and two protonated Schiff bases. Geometries of ground and excited states—as well as conical intersections—are compared with the corresponding CASSCF structures, illustrating the effect of including the correction for dynamical electron correlation. It is shown that the differences between the two methods are not readily categorized, but that, while individual changes in bond lengths can be quite large (∼0.01–0.02 Å), the natures and CASPT2 energetics of the structures remain similar. Exceptions to this tend to be systems that have a strong ionic character and that are not well described at the CASSCF level. Basis set effects (double‐ vs. triple‐ζ) were examined for a limited number of examples, and found to be quite dramatic at both levels of theory. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 298–309, 2003
β‐Hairpins, α‐helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β‐hairpin of SH3 domain
Authors: Ikeda Kazuyoshi , Galzitskaya Oxana V. , Nakamura Haruki , Higo Junichi 
Published: January 2003

AbstractEnergy landscape of a peptide, extracted from a distal β‐hairpin of src SH3 domain, in explicit water was obtained with the multicanonical molecular dynamics. A variety of β‐hairpins with various strand–strand hydrogen bonds were found in the energy landscape at 300 K. There was no energy barrier between random‐coil and hairpins. Thus, the peptide conformation can easily change from the random‐coil to the hairpins in the thermal fluctuations at 300 K. The landscape also included two clusters of α‐helices, among which an energy barrier existed, and besides, these helix clusters were separated from the other conformations. Thus, the free‐energy barrier exists among the helices and the other conformations. Intermediate clusters were found between the helix and the hairpin clusters. The current study showed that the isolated state of this peptide in water fluctuates among random‐coil, β‐hairpin, and α‐helix. In SH3 domain, which has a topology of mainly β‐protein, the whole‐protein folding may proceed when the segment is folded in the β‐hairpin and the other parts of the protein are coupled with the β‐hairpin in an energetically or kinetically favorite way. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 310–318, 2003
Molecular mechanics (MM3) calculations on lithium amide compounds
Authors: Yoshida Takashi , Sakakibara Kazuhisa , Asami Masatoshi , Chen Kuo‐Hsiang , Lii Jenn‐Huei , Allinger Norman L. 
Published: January 2003

AbstractThe MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6‐31G* and/or DFT (B3LYP/6‐31G*, B3‐PW91/6‐31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 319–327, 2003
Nonspecific interaction forces at water–membrane interface by forced molecular dynamics simulations
Authors: Lorenzo Alicia C. , Pascutti Pedro G. , Bisch Paulo M. 
Published: January 2003

AbstractNonspecific interactions are the main driving forces for the behavior of molecules with great affinity for biologic membranes. To investigate not only the molecular details of these interactions but to estimate their magnitude as well, the theoretical method of Forced Molecular Dynamics Simulations, based on the Atomic Force Spectroscopy experimental technique, was applied. In this approach, an additional one‐dimensional elastic force, representing the cantilever probe, was incorporated to the force field of a Molecular Dynamics computational program. This force represents a spring fixed on one end to a selected atom of the molecule; the other end of the spring is displaced at constant velocity to pull the molecule out of the membrane. The force experimented by the molecule due to the spring, is proportional to the spring elongation relative to its equilibrium position. This value is registered during the entire simulation, and its maximum value will determine the molecule–membrane interaction force. Nonexplicit medium simulations were carried out. Polar and apolar media were considered according to their polarizability degree and a specific dielectric constant value was assigned. In this approach, the membrane was considered as the apolar region limited by two flat surfaces with a polar aqueous medium. The potential energy discontinuity at the interfaces was smoothed by considering the polarization‐induced effects using the image method. The results of this methodology are presented using a small system, a single Alanine amino acid model, which enables extended simulations in a microsecond time scale. The confinement of this amino acid at the interface reduces its degrees of freedom and forces it to adopt one of the six defined conformations. A correlation between these stable structures at the water–membrane interface and the interaction force value was determined. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 328–339, 2003
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations
Authors: Kaminski George A. , Friesner Richard A. , Zhou Ruhong 
Published: January 2003

AbstractWe present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three‐body energies of molecular complexes with dipolar electrostatic probes, gas‐phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations—water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three‐body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies—within 0.43 kcal/mol (except for the special case of the CH3SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid‐state calculations with Monte Carlo technique. Comparison with the full‐scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full‐scale model accuracy, while the difference in energetic results between the full‐scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS‐AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 267–276, 2003
Correlation method for variance reduction of Monte Carlo integration in RS‐HDMR
Authors: Li Genyuan , Rabitz Herschel , Wang Sheng‐Wei , Georgopoulos Panos G. 
Published: January 2003

AbstractThe High Dimensional Model Representation (HDMR) technique is a procedure for efficiently representing high‐dimensional functions. A practical form of the technique, RS‐HDMR, is based on randomly sampling the overall function and utilizing orthonormal polynomial expansions. The determination of expansion coefficients employs Monte Carlo integration, which controls the accuracy of RS‐HDMR expansions. In this article, a correlation method is used to reduce the Monte Carlo integration error. The determination of the expansion coefficients becomes an iteration procedure, and the resultant RS‐HDMR expansion has much better accuracy than that achieved by direct Monte Carlo integration. For an illustration in four dimensions a few hundred random samples are sufficient to construct an RS‐HDMR expansion by the correlation method with an accuracy comparable to that obtained by direct Monte Carlo integration with thousands of samples. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 277–283, 2003
Density functional investigation on electron‐transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism
Authors: Qu Zheng‐Wang , Zhu Hui , Zhang Xing‐Kang , Zhang Qi‐Yuan 
Published: January 2003

AbstractThe mechanism of cycloreversion of cyclobutane radical anion (c‐C4H) has been investigated at the UB3LYP/6‐31++G(d,p) level, and compared with those of neutral c‐C4H8 and c‐C4H radical cation. Although both c‐C4H and C2H4 are shown to be Rydberg states unstable with respect to electron ejection, the activation barrier for the “rotating” cycloreversion of c‐C4H (37.3 kcal/mol) is lower by about 25.2 kcal/mol than that of c‐C4H8, and even the intervention of tetramethylene radical anion intermediate may reduce the activation barrier for the cycloreversion of c‐C4H8 by about 8.4 kcal/mol, mainly due to stronger electron‐deficiency of intermediate biradical species than close‐shell cyclobutanes. For the cycloreversion for c‐C4H, side isomerization reaction may be efficiently prevented by the low kinetic stability of tetramethylene radical anion intermediate towards dissociation, just different from the radical cation case. Our theoretical results have suggested the possibility of electron‐attachment catalysis of the cycloreversion of some electron‐deficient substituted cyclobutanes. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 340–344, 2003
Anab initiostudy of intermolecular interactions of nitromethane dimer and nitromethane trimer
Authors: Li Jinshan , Zhao Feng , Jing Fuqian 
Published: January 2003

AbstractDifferent geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6‐31++G** basis set. Three‐body interaction energy has been obtained with theab initiosupermolecular approach at the levels of MP2/6‐31++G**//B3LYP/6‐31++G** and MP2/aug‐cc‐pVDZ//B3LYP/6‐31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of CH…ON H‐bond ranges from −9.0 to −12.4 kJ mol−1at the MP2/aug‐cc‐pVDZ//B3LYP/6‐31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6‐31++G**//B3LYP/6‐31++G** calculated ΔECis within 2.5 kJ mol−1of the corresponding value at the MP4(SDTQ)/6‐31G**//B3LYP/6‐31++G** level. The analytic atom–atom intermolecular potential has been successfully regressed by using the MP2/6‐31++G**//B3LYP/6‐31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three‐body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three‐body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 Å. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 345–352, 2003
Ab initio study on the structures of fluorinated formates and hydrogen abstraction reaction with OH radical
Authors: Chandra Asit K. , Uchimaru Tadafumi , Sugie Masaaki , Sekiya Akira 
Published: January 2003

AbstractThe conformational potential energy surfaces for mono‐ and difluoromethyl formate have been determined by using a modified G2(MP2) level of calculations. The structures and vibrational frequencies for the conformers of mono‐ and difluoromethyl formate have been reported. The hydrogen abstraction reaction channels between these two formates and OH radicals have been studied at the same level of theory. Using the standard transition state theory and taking into account the effect of tunneling across the reaction barrier, we have estimated the rate constant for hydrogen abstraction by OH radical. The effect of successive fluorine substitution for methyl hydrogen on the conformational stability and on the hydrogen abstraction rate has been analyzed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 396–407, 2003
Extended method for adiabatic mode reordering
Authors: Tautermann Christofer S. , Voegele Andreas F. , Loerting Thomas , Kaps Peter , Liedl Klaus R. 
Published: January 2003

AbstractThe task of vibrational mode reordering is very important for reaction valley studies and for the determination of small curvature tunneling effects. An extended algorithm for adiabatic mode reordering is presented. It is based on the method introduced by Konkoli et al. [J Comput Chem 1997, 18, 1282], which is shown to suffer from numerical problems in the region of frequency‐crossings and avoided crossings. One improvement is the use of cubic splines for the interpolation of the projected matrix of force constants, which allows larger step sizes between the discrete points along the reaction path, where vibrational analysis is performed. The main improvement is the use of perturbation theory to resolve crossings and avoided crossings. Within this theoretical framework it becomes clear why the method of the maximal overlap between the normal modes cannot work properly, as eigenvectors associated with nearby eigenvalues tend to become “wobbly”. Thus a perturbative procedure is designed that is used for all cases where two harmonic frequencies approach each other and the overlap of the associated normal modes is of no practical use. Advantages of the new procedure are the use of larger step sizes along the minimum energy path and the much more reliable resolution of mode‐crossings and avoided crossings independent of the systems symmetry. In addition to that it is shown that one should be very cautious in all computational situations when working with eigenvectors associated with nearby eigenvalues. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 386–395, 2003
A practical and efficient method to calculate AIM localization and delocalization indices at post‐HF levels of theory
Authors: Wang Yi‐Gui , Werstiuk Nick Henry 
Published: January 2003

AbstractA practical and efficient method is proposed for calculating localization and delocalization indices at post‐Hartree‐Fock levels, and the method is tested at the CISD/6‐311G++(2d,2p) level for a large set of molecules. Our method, which utilizes wave functions written in the natural molecular orbital format and obtained with GAUSSIAN 94 or GAUSSIAN 98, convincingly extends the concepts established at the HF level. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 379–385, 2003
Boundary element solution of the linear Poisson–Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
Authors: Bordner A. J. , Huber G. A. 
Published: January 2003

AbstractThe Poisson–Boltzmann equation is widely used to describe the electrostatic potential of molecules in an ionic solution that is treated as a continuous dielectric medium. The linearized form of this equation, applicable to many biologic macromolecules, may be solved using the boundary element method. A single‐layer formulation of the boundary element method, which yields simpler integral equations than the direct formulations previously discussed in the literature, is given. It is shown that the electrostatic force and torque on a molecule may be calculated using its boundary element representation and also the polarization charge for two rigid molecules may be rapidly calculated using a noniterative scheme. An algorithm based on a fast adaptive multipole method is introduced to further increase the speed of the calculation. This method is particularly suited for Brownian dynamics or molecular dynamics simulations of large molecules, in which the electrostatic forces must be calculated for many different relative positions and orientations of the molecules. It has been implemented as a set of programs in C++, which are used to study the accuracy and speed of this method for two actin monomers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 353–367, 2003
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
Authors: Koca Jaroslav , Zhan Chang‐Guo , Rittenhouse Robert C. , Ornstein Rick L. 
Published: January 2003

AbstractWe have run several molecular dynamics (MD) simulations on zinc‐containing phosphotriesterase (PTE) with two bound substrates, sarin and paraoxon, and with the substrate analog diethyl 4‐methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa‐coordinated. The hexa‐coordination of this zinc ion was not seen in the deposited X‐ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the hexa‐coordinated zinc ion in PTE is only present in solution and not in the crystal; and the hexa‐coordinated zinc ion in PTE is an artifact of the force field used. A charge of +1.5 leads to a coordination number (CN) of 5 on both zinc ions, which is consistent with the results from ab initio and DFT calculations and with the latest high resolution X‐ray crystal structure. The commonly used charge of +2 produces a CN of 6 on the less buried zinc. The CN on the more buried zinc ion is 5 when the substrate/inhibitor is present in the simulation, and increases to 6 when the substrate/inhibitor is removed prior to the simulation. The results of both of the MD and quantum mechanical calculations lead to the conclusion that the zinc ions in the PTE active site are both penta‐coordinated, and that the MD simulations performed with the charge of +2 overestimate the CN of the zinc ions in the PTE active site. The overall protein structures in the simulations remain unaffected by the change in zinc charge from +2 to +1.5. The results also suggest that the charge +1.5 is the most appropriate for the molecular dynamics simulations on zinc‐containing PTE when a nonbonded model is used and no global thermodynamic conclusion is sought. We also show that the standard nonbonded model is not able to properly treat the CN and energy at the same time. A preliminary, promising charge‐transfer model is discussed with the use of the zinc charge of +1.5. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 368–378, 2003
INI1 expression induces cell cycle arrest and markers of senescence in malignant rhabdoid tumor cells
Authors: Reincke Britta S. , Rosson Gary B. , Oswald Betty W. , Wright Cynthia F. 
Published: January 2003

AbstractThe INI1 gene, which encodes a functionally uncharacterized protein component of the hSWI/SNF chromatin remodeling complex, is often mutated or deleted in malignant rhabdoid tumor (MRT). Two isoforms of INI1, that differ by the variable inclusion of nine amino acids, potentially are produced by differential RNA splicing. To determine the effect of the two INI1 isoforms on cell growth, INI1‐devoid (MRT) and INI1‐expressing cell lines were transfected separately with mammalian expression vectors or transduced with adenoviruses. Transfection of the short form of INI1 into either INI1‐deficient or expressing cell lines resulted in complete suppression of cell growth in colony formation assays. The longer splice variant induced moderate to severe growth suppression of MRT cells, but had a far milder effect on non‐MRT cells. Transduction of MRT cells with adenoviruses expressing either isoform of INI1 led to a dramatic change in morphology, growth suppression, and cell cycle arrest. Furthermore, senescence‐associated proteins were up‐regulated after transduction, while levels of proteins implicated in cell cycle progression were down‐regulated. Adenoviral delivery of INI1 into a non‐MRT cell line, however, had no demonstrable effect on any of these parameters. These results support the genetic evidence that INI1 is a tumor suppressor gene gone awry in MRT cells, and also suggest that delivery of the INI1 gene to MRT cells by adenoviruses may lead to a more effective treatment of this highly aggressive malignancy. © 2003 Wiley‐Liss, Inc.