bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational center–ligand couplings in transition metal complexes
Authors: Neugebauer Johannes , Reiher Markus 
Published: January 2004

AbstractThe mode‐tracking principle [J. Chem. Phys. 2003, 118, 1634] for the direct quantum chemical calculation of preselected, characteristic molecular vibrations makes vibrational analyses of very large molecules feasible. This is demonstrated here for the [(Ph3PAu)6C]2+ complex, in which 18 phenyl groups in the ligand sphere are explicitly taken into account. We are aiming at the motion of the endohedral carbon atom, which is in an extraordinary bonding situation because it is surrounded by an octahedral core of gold atoms in this cluster. Secondary effects of the full ligand sphere on the vibrations of the [Au6C] core embedded in [(R3PAu)6C]2+ clusters are investigated. For this purpose, local vibrations of the octahedral core are generated, and their long‐range couplings with the phosphine ligand sphere become visible in the mode‐tracking iterations. The exact normal modes of these characteristic vibrations of the cluster are then obtained after convergence of the mode‐tracking refinement. This protocol allows us to assess the coupling of the outer ligand sphere with the inner core of the cluster in terms of changes of the vibrational frequencies and of the collective motions of the atomic nuclei. The vibrational frequencies of the octahedral [Au6C] core split due to symmetry breaking in the C1‐symmetric [(Ph3PAu)6C]2+ cluster. Our study demonstrates how effects of the periphery of a large molecule on local vibrations can be quantified. Furthermore, we predict the first set of characteristic vibrational frequencies obtained with first‐principles methods for this gold cluster, whose vibrational spectra have not yet been recorded experimentally. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 587–597, 2004
Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium
Authors: Li Xiang‐Yuan , Fu Ke‐Xiang 
Published: January 2004

AbstractConsidering the influences of electrostatic potential Φ upon the change of solute charge distribution δρ and ρ upon the change δΦ at the same time, a more reasonable integral formula of dG = (1/2) ∫V (ρδΦ + Φδρ)dV is used to calculate the change of the electrostatic free energy in charging the solute–solvent system to a nonequilibrium state, instead of the one of dG = ∫V ΦδρdV used before. This modification improves the expressions of electrostatic free energy and solvation free energy, in which no quantity of the intermediate equilibrium state is explicitly involved. Detailed investigation reveals that the solvation free energy of nonequilibrium only contains the interaction energy between the field due to the solute charge in vacuum, and the dielectric polarization at the nonequilibrium state. The solvent reorganization energies of forward and backward electron transfer reactions have been redefined because the derivations lead to a remarkable feature that these quantities are direction‐dependent, unlike the theoretical models developed before. The deductions are given in the electric field‐displacement form. Relevant discussions on the reliability of theoretical models suggested in this work have also been presented © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 500–509, 2004
A practical valence bond method: A configuration interaction method approach with perturbation theoretic facility
Authors: Song Lingchun , Wu Wei , Zhang Qianer , Shaik Sason 
Published: January 2004

AbstractThe previously developed valence bond configuration interaction (VBCI) method (Wu, W.; Song, L.; Cao, Z.; Zhang, Q.; Shaik, S., J. Phys. Chem. A, 2002, 105, 2721) that borrows the general CI philosophy of the MO theory, is further extended in this article, and its methodological features are improved, resulting in three accurate and cost‐effective procedures: (a) the effect of quadruplet excitation is incorporated using the Davidson correction, such that the new procedure reduces size consistency problems, with due improvement in the quality of the computational results. (b) A cost‐effective procedure, named VBCI(D, S), is introduced. It includes doubly excited structures for active electrons and singly excited structures for inactive pairs. The computational results of VBCI(D, S) match those of VBCISD with much less computational effort than VBCISD. (c) Finally, a second‐order perturbation theory is utilized as a means of configuration selection, and lead to considerable reduction of the computational cost, with little or no loss in accuracy. Applications of the new procedures to bond energies and barriers of chemical reactions are presented and discussed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 472–478, 2004
Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking
Authors: Totrov Maxim 
Published: January 2004

AbstractA novel method for fast and accurate evaluation of the generalized Born radii in macromolecular solvation electrostatics calculations is proposed, based on the solvent accessibility of the first two solvation layers around an atom. The reverse generalized Born radii calculated by the method have correlation coefficient of 98.7% and RMSD of 0.031 Å−1 with the values obtained using a precise but significantly slower numerical boundary element solution. The method is applied to derive an estimate of the free solvation energy difference between octanol and water and to predict LogP octanol–water. A nine‐parameter model is optimized on an 81 compound training set and applied to predict LogPow for an external evaluation set of 19 drug molecules with RMSD of 0.9. The new GB approximation is also tested in Monte Carlo docking simulations of the fully flexible p53 peptide fragment to MDM2. The best energy solution found in the simulations has RMSD of 2.8 Å to the X‐ray structure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 609–619, 2004
Modified Gaussian‐2 level investigation of the identity ion‐pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanisms
Authors: Ren Yi , Chu San‐Yan 
Published: January 2004

AbstractIdentity ion‐pair SN2 reactions LiX + CH3X → XCH3 + LiX (X = F, Cl, Br, and I) have been investigated in the gas phase and in solution at the level of the modified Gaussian‐2 theory. Two possible reaction mechanisms, inversion and retention, are discussed. The reaction barriers relative to the complexes for the inversion mechanism [ΔH(inv)] are found to be much higher than the corresponding values for the gas phase anionic SN2 reactions, decreasing in the following order: F (263.6 kJ mol−1) > Cl (203.3 kJ mol−1) > Br (174.7 kJ mol−1) > I (150.7 kJ mol−1). The barrier gaps between the two mechanisms [ΔH (ret) − ΔH (inv)] increase in the order F (−62.7 kJ mol−1) < Cl (4.4 kJ mol−1) < Br (24.9 kJ mol−1) < I (45.1 kJ mol−1). Thus, the retention mechanism is energetically favorable for fluorine and the inversion mechanism is favored for other halogens, in contrast to the anionic SN2 reactions at carbon where the inversion reaction channel is much more favorable for all of the halogens. The stabilization energies for the dipole–dipole complexes CH3X · · · LiX (ΔHcomp) are found to be similar for the entire set of systems with X = F, Cl, Br, and I, ranging from 53.4 kJ mol−1 for I up to 58.9 kJ mol−1 for F. The polarizable continuum model (PCM) has been used to evaluate the direct solvent effects on the energetics of the anionic and ion‐pair SN2 reactions. The energetic profiles are found to be still double‐well shaped for most of the ion‐pair SN2 reactions in the solution, but the potential profile for reaction LiI + CH3I is predicted to be unimodal in the protic solvent. Good correlations between central barriers [ΔH (inv)] with the geometric looseness of the inversion transition state %C—X≠, the dissociation energies of the C—X bond (DC—X) and Li—X bond (DLi—X) are observed, respectively. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 461–467, 2004
Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin
Authors: Ozkan S. Banu , Meirovitch Hagai 
Published: January 2004

AbstractThe energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM) structure, which corresponds approximately to the native structure, is a severe problem in global optimization. Recently we have proposed a conformational search technique based on the Monte Carlo minimization (MCM) method of Li and Scheraga, where trial dihedral angles are not selected at random within the range [−180°,180°] (as with MCM) but with biased probabilities depending on the increased structure‐energy correlations as the GEM is approached during the search. This method, called the Monte Carlo minimization with an adaptive bias (MCMAB), was applied initially to the pentapeptide Leu‐enkephalin. Here we study its properties further by applying it to the larger peptide with bulky side chains, deltorphin (H‐Tyr‐D‐Met‐Phe‐His‐Leu‐Met‐Asp‐NH2). We find that on average the number of energy minimizations required by MCMAB to locate the GEM for the first time is smaller by a factor of approximately three than the number required by MCM—in accord with results obtained for Leu‐enkephalin. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 565–572, 2004
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling
Authors: Gallicchio Emilio , Levy Ronald M. 
Published: January 2004

AbstractWe have developed an implicit solvent effective potential (AGBNP) that is suitable for molecular dynamics simulations and high‐resolution modeling. It is based on a novel implementation of the pairwise descreening Generalized Born model for the electrostatic component and a new nonpolar hydration free energy estimator. The nonpolar term consists of an estimator for the solute‐solvent van der Waals dispersion energy designed to mimic the continuum solvent solute‐solvent van der Waals interaction energy, in addition to a surface area term corresponding to the work of cavity formation. AGBNP makes use of a new parameter‐free algorithm to calculate the scaling coefficients used in the pairwise descreening scheme to take into account atomic overlaps. The same algorithm is also used to calculate atomic surface areas. We show that excellent agreement is achieved for the GB self‐energies and surface areas in comparison to accurate, but much more expensive, numerical evaluations. The parameter‐free approach used in AGBNP and the sensitivity of the AGBNP model with respect to large and small conformational changes makes the model suitable for high‐resolution modeling of protein loops and receptor sites as well as high‐resolution prediction of the structure and thermodynamics of protein‐ligand complexes. We present illustrative results for these kinds of benchmarks. The model is fully analytical with first derivatives and is computationally efficient. It has been incorporated into the IMPACT molecular simulation program. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 479–499, 2004
Partial rigid‐body dynamics in NPT, NPAT and NPγT ensembles for proteins and membranes
Authors: Ikeguchi Mitsunori 
Published: January 2004

AbstractA partial rigid‐body method of molecular dynamics simulations for proteins and membranes is presented. In this method, the symplectic integrator for rigid bodies is combined with the equations of motion for the NPT ensemble. The standard NPT ensemble is extended to the membrane‐specific ensembles, the NPAT (constant normal pressure and lateral surface area of membranes and constant temperature) and NPγT (constant normal pressure and lateral surface tension of membranes and constant temperature) ensembles. By more than 30‐ns simulations of aqueous proteins and hydrated lipid bilayers, the results of the partial rigid‐body method demonstrated excellent conservation of total energy and consistent behavior with the traditional constraint method in terms of structural distribution and fluctuation of proteins and lipids. The efficient implementation of the partial rigid‐body method in parallel computation is presented, which is shown to work well in large‐scale molecular dynamics simulations. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 529–541, 2004
Direct ab initio dynamics studies on the hydrogen‐abstraction reactions of OH radicals with HOX (X = F, Cl, and Br)
Authors: Wang Li , Liu Jing‐Yao , Li Ze‐Sheng , Sun Chia‐Chung 
Published: January 2004

AbstractThe hydrogen abstract reactions of OH radicals with HOF (R1), HOCl (R2), and HOBr (R3) have been studied systematically by a dual‐level direct‐dynamics method. The geometries and frequencies of all the stationary points are optimized at the MP2/6‐311+G(2d, 2p) level of theory. A hydrogen‐bonded complex is located at the product channel for the OH + HOBr reaction. To improve the energetics information along the minimum energy path (MEP), single‐point energy calculations are carried out at the CCSD(T)/6‐311++G(3df, 3pd) level of theory. Interpolated single‐point energy (ISPE) method is employed to correct the energy profiles for the three reactions. It is found that neither the barrier heights (ΔE) nor the H—O bond dissociation energies [D(H—O)] exhibit any clear‐cut linear correlations with the halogen electronegative. The decrease of ΔE and D(H—O) for the three reactions are in order of HOF > HOBr > HOCl. Rate constants for each reaction are calculated by canonical variational transition‐state theory (CVT) with a small‐curvature tunneling correction (SCT) within 200–2000 K. The agreement of the rate constants with available experimental values for reactions R2 and R3 at 298 K is good. Our results show that the variational effect is small while the tunneling correction has an important contribution in the calculation of rate constants in the low‐temperature range. Due to the lack of the kinetic data of these reactions, the present theoretical results are expected to be useful and reasonable to estimate the dynamical properties of these reactions over a wide temperature range where no experimental value is available. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 558–564, 2004
An AM1 semiempirical study of host–guest complexation in hemicarcerand complexes
Authors: Liddell Michael J. , Margetic Davor , Mitchell Anthony S. , Warrener Ronald N. 
Published: January 2004

AbstractSemiempirical AM1 calculations have been carried out on host–guest complexes of model hemicarcerands 1a and 2a. The justification for the choice of the AM1 Hamiltonian was based on a comparison between reported X‐ray data for the smaller tetrabromocavitand 4a and computational results obtained using several different Hamiltonians. The complexation behavior of hemicarcerands 1a and 2a have been compared with experimental results reported by Cram et al. for the related hemicarcerands 1b and 2b. Based on this comparison, a criterion for predicting guest encapsulation was developed, Ecomplexation, which relies on the calculation of AM1 heats of formation for host, guest, and hemicarceplex. If Ecomplexation is lower than 10 kcal/mol, then a guest will be encapsulated, while if it is greater than 30 kcal/mol, a guest will not be encapsulated. The use of constrained‐path AM1 optimizations to determine the energy barriers to guest entry and exit from the host was found to be a useful tool for examining suitable host–guest combinations when the Ecomplexation criteria does not hold. We have computed the barriers to exit of N, N‐dimethylformamide (dmf) and furan from the hemicarcerand 1a, the former has been compared with the experiment and shows excellent agreement. Based on the success of the above computational methods in predicting which host–guest combinations will form stable hemicarceplexes we have synthesized a new target hemicarceplex 1b.furan. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 542–557, 2004
A hydration study of (1→4) and (1→6) linked α‐glucans by comparative 10 ns molecular dynamics simulations and 500‐MHz NMR
Authors: Corzana Francisco , Motawia Mohammed S. , Du Penhoat Catherine Hervé , Perez Serge , Tschampel Sarah M. , Woods Robert J. , Engelsen Søren B. 
Published: January 2004

AbstractThe hydration behavior of two model disaccharides, methyl‐α‐D‐maltoside (1) and methyl‐α‐D‐isomaltoside (2), has been investigated by a comparative 10 ns molecular dynamics study. The detailed hydration of the two disaccharides was described using three force fields especially developed for modeling of carbohydrates in explicit solvent. To validate the theoretical results the two compounds were synthesized and subjected to 500 MHz NMR spectroscopy, including pulsed field gradient diffusion measurements (1: 4.0 · 10−6 cm2 · s−1; 2: 4.2 · 10−6 cm2 · s−1). In short, the older CHARMM‐based force field exhibited a more structured carbohydrate–water interaction leading to better agreement with the diffusional properties of the two compounds, whereas especially the α‐(1→6) linkage and the primary hydroxyl groups were inaccurately modeled. In contrast, the new generation of the CHARMM‐based force field (CSFF) and the most recent version of the AMBER‐based force field (GLYCAM‐2000a) exhibited less structured carbohydrate–water interactions with the result that the diffusional properties of the two disaccharides were underestimated, whereas the simulations of the α‐(1→6) linkage and the primary hydroxyl groups were significantly improved and in excellent agreement with homo‐ and heteronuclear coupling constants. The difference between the two classes of force field (more structured and less structured carbohydrate–water interaction) was underlined by calculation of the isotropic hydration as calculated by radial pair distributions. At one extreme, the radial O…O pair distribution function yielded a peak density of 2.3 times the bulk density in the first hydration shell when using the older CHARMM force field, whereas the maximum density observed in the GLYCAM force field was calculated to be 1.0, at the other extreme. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 573–586, 2004
A computational study of the role of hydrogen bonds in SN1 and E1 reactions
Authors: Yamabe Shinichi , Tsuchida Noriko 
Published: January 2004

AbstractThe reaction between tertiary butyl chloride and water clusters was examined by applying density functional theory calculations. The carbonium ion t‐Bu+ that is normally sandwiched between the water clusters was found to be absent, such that a CO covalent bond was formed in the intermediate (Int1) after heterolysis. An (H2O)4 cluster is able to bridge the front and rear of the central carbon and promotes heterolysis. A correlation between bond interchanges at the central carbon and proton relays is presented. Stereochemical scrambling in the solvolysis products is discussed in terms of this correlation. In addition, an E1 pathway for the elimination product, iso‐butene, is found from Int1. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 598–608, 2004
Local round robin test for determination of aromatics in diesel fuels by HPLC
Authors: Šegudović Nikola , Tomić Tatjana , Škrobonja Liviana , Kontić Ljubica 
Published: January 2004

AbstractDetermination of aromatics in diesel fuels by HPLC is covered by European Standard EN 12916 (April 2000). The Standard is based on former standards IP 391/90 and IP 391/95. The method used for measurements is NP HPLC and separation is performed on silica or modified silica columns with RI detection. The precision of the method was checked by determining the repeatability and reproducibility. The content of aromatics was measured in a number of commercial samples. The measurements have been performed in three different laboratories and under different working and instrumental conditions. Satisfactory agreement was established for repeatability and was slightly poorer for reproducibility. The content of polyaromatics is within the tolerance range (IP 590/99) and the content of tricyclic and higher aromatics (tri+) is close to the limit of quantitition in some samples. Clear differences in the content of polycyclic aromatics in domestic diesel and eurodiesel fuels were observed. The results have confirmed the ruggedness and robustness of the measuring method.
Pressurized hot water extraction of insecticides from process dust – Comparison with supercritical fluid extraction
Authors: Eskilsson Cecilia Sparr , Hartonen Kari , Mathiasson Lennart , Riekkola Marja‐Liisa 
Published: January 2004

AbstractPressurized hot liquid water and steam were used to investigate the possibilities of extracting insecticides (carbofuran, carbosulfan, and imidacloprid) from contaminated process dust remaining from seed‐pellet production. Extraction temperature was the most important parameter in influencing the extraction efficiency and rate of extraction, while varying the pressure had no profound effect. A clean‐up procedure of the water extracts using solid phase extraction (SPE) was found to be necessary prior to final analysis by high‐performance liquid chromatography (HPLC). Quantitative extraction (compared to a validated organic solvent extraction method) of imidacloprid was obtained at temperatures of 100–150°C within 30 min extraction time. Temperatures above 150°C were required to extract carbofuran efficiently. The most non‐polar analyte of the investigated compounds, carbosulfan, gave no detectable concentrations with pressurized hot water extraction (PHWE). One reason might be its low solubility in water, and when attempts are made to increase its solubility by increasing the temperature it may degrade to carbofuran. This can explain recovery values above 100% for carbofuran at higher temperatures. A comparison of the PHWE results and those obtained with supercritical fluid extraction (SFE) revealed that PHWE is advantageous for polar compounds, where the solubility of the analyte in water is high enough that lower temperatures can be used. For non‐polar compounds carbon dioxide based extraction is preferred unless the target analyte is highly thermostable.
Development of a solid phase extraction method for simultaneous determination of corticoids and tranquilizers in serum samples
Authors: Quintana M. Carmen , Ramos Lourdes , González M. Jose , Blanco Manuel H. , Hernández Lucas 
Published: January 2004

AbstractA simple and fast solid phase extraction (SPE) method allowing the preconcentration, clean‐up, and subsequent separate elution of phenothiazines (chlorpromazine hydrochloride, acetopromazine, and propionylpromazine hydrochloride) and glucocorticoids (dexamethasone, betamethasone acetate, and phenylbutazone) from serum samples has been developed. Both fractions were separately collected and analyzed without any additional treatment by high performance liquid chromatography with UV‐Vis. The performance of the complete procedure was satisfactory irrespective of the spiking level with recoveries in the range 64–85% for all analytes investigated but for phenylbutazone (20%). Repeatability, evaluated as the relative standard deviation, was globally better than 12%. LC‐MS was used for final confirmation of the results.
Using analytical multidimensional isocratic HPLC methods of separation to isolate active constituents in natural products
Authors: Wong Victor , Sweeney Alan P. , Shalliker R. Andrew 
Published: January 2004

AbstractMultidimensional reversed‐phase HPLC was employed to isolate the active constituents from a crude extract of Clerodendrum floribundum R. Br. These active constituents were known to have bioactivity against the enzyme xanthine oxidase and potentially could be employed in the treatment of gout. Using a multidimensional separation approach, rapid isolation of the active constituents was achieved from a complex sample matrix. As each separation dimension was isocratic, no equilibration time was required and consequently the technique shows promise in the scale up to preparative levels where high throughput is important.