bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free energy of solvation from molecular dynamics simulations for low dielectric solvents
Authors: Gonçalves Paulo F. B. , Stassen Hubert 
Published: September 2003

AbstractUsing molecular dynamics simulation, we present new results for the free energy of solvation for solvents with low dielectric constants (CCl4, CHCl3, benzene). The solvation free energy is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute–solvent repulsion and dispersion interactions, and the electrostatic solvation of the solute. The cavitational contribution has been obtained from the Claverie–Pierotti model applied to excluded volumes obtained from distances for nearest neighbor configurations between the solute's atoms and a spherical solvent description. An electrostatic continuum model has been adapted for the computation of the electrostatic free energy of solvation, whereas the van der Waals contribution has been calculated directly from the intermolecular interactions defined by the force fields applied to the simulations. For each solvent, a large set of solute molecules containing most of the chemically interesting functionalities has been treated. The simulated solvation free energies are in very good agreement with experimental data, although a small systematical overestimation of the free energy of solvation indicates a failure of the spherical approach to the solvent molecules in the case of benzene. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1758–1765, 2003
Low‐ and high‐spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics
Authors: Darkhovskii M. B. , Pletnev I. V. , Tchougréeff A. L. 
Published: September 2003

AbstractA computational method targeted to Werner‐type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie–Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d‐shell. The quantum mechanical EHCF part is limited to the metal ion d‐shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. © 2003 Wiley Periodicals, Inc. J Comput Chem 14: 1703–1719, 2003
Single‐step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character
Authors: Oostenbrink Chris , Van Gunsteren Wilfred F. 
Published: September 2003

AbstractRelative free energies for a series of not too different compounds can be estimated accurately from a single simulation of an unphysical reference state that encompasses the characteristic molecular features of the compounds. Previously, this method has been applied to the calculation of free energies of solvation and of ligand binding for small molecules. In the present study we investigate the limits to the accuracy of the method by applying it to a realistic model of the binding of a set of rather large ligands to the protein factor Xa, a key protein in current efforts to design anticoagulation drugs. The evaluation of the binding free energies and conformations of nine derivatives of a biphenylamidino inhibitor leads to insights regarding the effect of the size, flexibility, and character of the unphysical part of the ligand in the reference state on the accuracy of the predicted binding free energies. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1730–1739, 2003
Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution
Authors: Rajamani Ramkumar , Naidoo Kevin J. , Gao Jiali 
Published: September 2003

AbstractWe describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H3N—H—NH3]+ using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1775–1781, 2003
An improvement of the resolution of the identity approximation for the formation of the Coulomb matrix
Authors: Neese Frank 
Published: September 2003

AbstractA straightforward modification of the resolution of the identity (RI) approximation to the Coulomb interaction is described. In the limit of basis sets that are dominated by high angular momentum functions the observed speedups in realistic test systems reach a factor of 2 compared to the standard RI algorithm, and a factor of up to 300 compared to the standard algorithm to form the Coulomb matrix. More moderate savings on the order of 0–20% are obtained for the more commonly used smaller basis sets. A series of test calculations is reported to illustrate the efficiency of the algorithm. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1740–1747, 2003
Generalized born model with a simple smoothing function
Authors: Im Wonpil , Lee Michael S. , Brooks Charles L. 
Published: September 2003

AbstractBased on recent developments in generalized Born (GB) theory that employ rapid volume integration schemes (M. S. Lee, F. R. Salabury, Jr., and C. L. Brooks III, J Chem Phys 2002, 116, 10606) we have recast the calculation of the self‐electrostatic solvation energy to utilize a simple smoothing function at the dielectric boundary. The present GB model is formulated in this manner to provide consistency with the Poisson–Boltzmann (PB) theory previously developed to yield numerically stable electrostatic solvation forces based on finite‐difference methods (W. Im, D. Beglov, and B. Roux, Comp Phys Commun 1998, 111, 59). Our comparisons show that the present GB model is indeed an efficient and accurate approach to reproduce corresponding PB solvation energies and forces. With only two adjustable parameters—a0 to modulate the Coulomb field term, and a1 to include a correction term beyond Coulomb field—the PB solvation energies are reproduced within 1% error on average for a variety of proteins. Detailed analysis shows that the PB energy can be reproduced within 2% absolute error with a confidence of about 95%. In addition, the solvent‐exposed surface area of a biomolecule, as commonly used in calculations of the nonpolar solvation energy, can be calculated accurately and efficiently using the simple smoothing function and the volume integration method. Our implicit solvent GB calculations are about 4.5 times slower than the corresponding vacuum calculations. Using the simple smoothing function makes the present GB model roughly three times faster than GB models, which attempt to mimic the Lee–Richards molecular volume. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1691–1702, 2003
Development of a multipopulation parallel genetic algorithm for structure solution from powder diffraction data
Authors: Habershon Scott , Harris Kenneth D. M. , Johnston Roy L. 
Published: September 2003

AbstractPreviously, the genetic algorithm (GA) approach for direct‐space crystal structure solution from powder diffraction data has been applied successfully in the structure determination of a range of organic molecular materials. In this article, we present a further development of our approach, namely a multipopulation parallel GA (PGA), which is shown to give rise to increased speed, efficiency, and reliability of structure solution calculations, as well as providing new opportunities for further optimizing our GA methodology. The multipopulation PGA is based on the independent evolution of different subpopulations, with occasional interaction (e.g., transfer of structures) allowed to occur between the different subpopulations. Different strategies for carrying out this interpopulation communication are considered in this article, and comparisons are made to the conventional single‐population GA. The increased power offered by the PGA approach creates the opportunity for structure determination of molecular crystals of increasing complexity. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1766–1774, 2003
Hydrolysis of cyclic phosphates by ribonuclease A: A computational study using a simplified ab initio quantum model
Authors: Wladkowski Brian D. , Ostazeski Paul , Chenoweth Sarah , Broadwater Steven J. , Krauss Morris 
Published: September 2003

AbstractThe second step in the enzyme‐catalyzed hydrolysis of phosphate esters by ribonuclease A (RNase A) was studied using an ab initio quantum‐based model of the active site including constrained parts of three critical residues, His‐12, His‐119, and Lys‐41, and a small substrate. The competition between release of the cyclic phosphate intermediate and subsequent hydrolysis following transphosphorylation was explored to determine the electronic factors that contribute to preferential intermediate product release observed experimentally. The structural and energetic results obtained at both the RHF and MP2 levels reveal several contributing factors consistent with experimental observation. Although the intrinsic electronic effects tend to favor hydrolysis slightly with an overall activation free energy of approximately 70 kJ mol−1, entropic and environmental effects favor release of the cyclic phosphate intermediate over hydrolysis. Exploration of the second, hydrolysis step also revealed interesting similarity with the transphosphorylation step, including the observation of autocatalysis by the substrate. Moreover, both steps of the overall RNase A reaction reveal multiple pathways involving proton transfers to sites of similar proton affinities. The anionic phosphate in both steps can act as a stable proton binding site as protons are moved around the active site throughout the progress of the reaction. These results suggest autocatalysis may be representative of more general behavior in enzymes containing highly charged substrates, especially phosphates. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1803–1811, 2003
Direct INDO/SCI method for excited state calculations
Authors: Tomlinson Aimée , Yaron David 
Published: September 2003

AbstractIntermediate neglect of differential overlap (INDO) is the most commonly utilized semiempirical technique for performing excited state calculations on large organic systems such as organic semiconductors and fluorescent dyes. The calculations are typically done at the singles‐configuration interaction (SCI) level. Direct methods provide a more efficient means of performing configuration interaction (CI) calculations, and the computational trade offs associated with various approaches to direct‐CI theory have been well characterized for ab initio Hamiltonians and high‐order CI. However, the INDO and SCI approximations lead to a new set of trade offs. In particular, application of the electron‐electron interactions in the atomic basis leads to savings in computational time that scale as the number of atomic orbitals, which for a large organic system can be two to three orders of magnitude. These savings are largest when only a few low‐lying excited states are generated and when a full SCI basis, which includes excitations between all filled and empty molecular orbitals, is used. In addition, substantial memory savings are achieved in the direct method by avoiding the evaluation of the two electron integrals in the molecular orbital basis. The method is demonstrated by calculating the absorption spectrum of a poly(paraphenylenevinylene) oligomer containing 16 phenyl rings. © 2003 Wiley Periodicals, Inc. J Comput Chem 14: 1782–1788, 2003
Novel topological indexFbased on incidence matrix
Authors: Yang Feng , Wang Zhen‐Dong , Huang Yun‐Ping , Zhu Hai‐Liang 
Published: September 2003

AbstractBased on incidence matrixW, the novel topological indexFis defined by the matricesL,W,XasF=LWX. The properties, the chemical environments, and the interaction of the vertexes in a molecule are taken into account in this definition. Several good QSPR models in the hetero‐atom‐containing organic compounds and inorganic compounds are obtained. Moreover, based on the definition ofFand the valuesCiof the vertexes or the valuesmFijof the chemical bonds, we have obtained serial indices,mFv,mFb, andFw. They are successfully applied to QSPR models and good correlation results have been obtained as well. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1812–1820, 2003
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer
Authors: Balta Bülent , Aviyente Viktorya 
Published: September 2003

AbstractThe relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine‐water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute‐solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono‐ and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute‐solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1789–1802, 2003
Comparison of localization and delocalization indices obtained with Hartree–Fock and conventional correlated methods: Effect of Coulomb correlation
Authors: Wang Yi‐Gui , Matta Cherif , Werstiuk Nick Henry 
Published: September 2003

AbstractAtomic populations and localization [λ(A)] and delocalization [δ(A,B)] indices (LIs and DIs) are calculated for a large set of molecules at the Hartree–Fock (HF), MP2, MP4(SDQ), CISD, and QCISD levels with the 6‐311++G(2d,2p) basis set. The HF method and the conventional correlation methods [MP2, MP4(SDQ), CISD, and QCISD] yield distinct sets of LIs and DIs. Yet, within the four conventional correlation methods the differences in atomic populations and LIs and DIs are small. Relative to HF, the conventional correlation methods [MP2, MP4(SDQ), CISD, QCISD] yield virtually the same LIs and DIs for molecules with large charge separations while LIs and DIs that differ significantly from the HF values—the LIs are increased and DIs decreased—are obtained for bonds with no or small charge separations. Such is the case in the archetypal homopolar molecules HCCH, H2CCH2, CH3CH3, and “protonated cyclopropane” C3H, in which case the bonding may be atypical. Relative to HF, the typical effect of the conventional correlation methods is to decrease the DI between atoms. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1720–1729, 2003
The neuroarchitecture of the circadian clock in the brain of Drosophila melanogaster
Authors: Helfrich‐Förster Charlotte 
Published: September 2003

AbstractNeuroethologists try to assign behavioral functions to certain brain centers, if possible down to individual neurons and to the expression of specific genes. This approach has been successfully applied for the control of circadian rhythmic behavior in the fruit fly Drosophila melanogaster. Several so‐called “clock genes” are expressed in specific neurons in the lateral and dorsal brain where they generate cell‐autonomous molecular circadian oscillations. These clusters are connected with each other and contribute differentially to the control of behavioral rhythmicity. This report reviews the latest work on characterizing individual circadian pacemaker neurons in the fruit fly's brain that control activity and pupal eclosion, leading to the questions by which neuronal pathways they are synchronized to the external light‐dark cycle, and how they impose periodicity on behavior. Microsc. Res. Tech. 62:94–102, 2003. © 2003 Wiley‐Liss, Inc.
Development of PDF‐immunoreactive cells, possible clock neurons, in the housefly Musca domestica
Authors: Pyza Elzbieta , Siuta Tomasz , Tanimura Teiichi 
Published: September 2003

AbstractEven though the housefly Musca domestica shows clear circadian rhythms in its behavioural and physiological processes, a circadian pacemaker system controlling these rhythms has not yet been described morphologically in this species. In M. domestica, neurons immunoreactive to pigment‐dispersing factor (PDF), a neurotransmitter/neuromodulator of circadian information arising from a circadian clock and transmitted to target cells, are similar in their number and distribution to the PDF neurons of Drosophila melanogaster. In D. melanogaster these neurons co‐localize PER protein and have been identified as clock neurons in that species. Here we report PDF‐immunoreactive cells in the housefly's brain during postembryonic development in the larval and pupal stages, as well as in the adult fly soon after eclosion. In the housefly's brain, there are three groups of PDF‐immunoreactive neurons: two groups with small (sPDFMe) and large (lPDFMe) cell bodies in the proximal medulla of the optic lobe; and one group in the dorsal protocerebrum (PDFD). Three out of four sPDFMe can be detected during the first hour of larval development, but the fourth sPDFMe is observed in the larva only from 48 hours after hatching, along with five lPDFMe neurons, seen first as two subgroups, and three out of four PDFD neurons. During postembryonic development these neurons show changes in their structure and immunoreactivity. New PDF neurons are observed during pupal development but these neurons mostly do not survive into adulthood. In the adult fly's brain, the PDF neurons have also been examined in double‐labelled preparations made with a second antibody directed against the product of one of several clock genes: period (per), timeless (tim), or cryptochrome (cry). Among them, only immunoreactivity to CRY‐like protein has been detected in the brain of M. domestica and has shown a daily rhythm in its concentration, as examined immunocytochemically. CRY was co‐localized with PDF in the sPDFMe of the housefly's brain fixed during the day. The possibility that the sPDFMe neurons are the housefly's clock neurons is discussed. Microsc. Res. Tech. 62:103–113, 2003. © 2003 Wiley‐Liss, Inc.
Anatomical organization of retinotopic motion‐sensitive pathways in the optic lobes of flies
Authors: Douglass John K. , Strausfeld Nicholas J. 
Published: September 2003

AbstractAnatomical methods have identified conserved neuronal morphologies and synaptic relationships among small‐field retinotopic neurons in insect optic lobes. These conserved cell shapes occur across many species of dipteran insects and are also shared by Lepidoptera and Hymenoptera. The suggestion that such conserved neurons should participate in motion computing circuits finds support from intracellular recordings as well as older studies that used radioactive deoxyglucose labeling to reveal strata with motion‐specific activity in an achromatic neuropil called the lobula plate. While intracellular recordings provide detailed information about the motion‐sensitive or motion‐selective responses of identified neurons, a full understanding of how arrangements of identified neurons compute and integrate information about visual motion will come from a multidisciplinary approach that includes morphological circuit analysis, the use of genetic mutants that exhibit specific deficits in motion processing, and biomimetic models. The latter must be based on the organization and connections of real neurons, yet provide output properties similar to those of more traditional theoretical models based on behavioral observations that date from the 1950s. Microsc. Res. Tech. 62:132–150, 2003. © 2003 Wiley‐Liss, Inc.
The mushroom bodies of Drosophila melanogaster: An immunocytological and golgi study of Kenyon cell organization in the calyces and lobes
Authors: Strausfeld Nicholas J. , Sinakevitch Irina , Vilinsky Ilya 
Published: September 2003

AbstractGolgi impregnations reveal a variety of dendritic morphologies amongst Kenyon cells in the mushroom bodies of Drosophila melanogaster. Different morphological types of Kenyon cells contribute axon‐like processes to five divisions of the medial and vertical lobes. Four of these divisions have characteristic affinities to antibodies raised against aspartate, glutamate, and taurine. A newly described posterior subdivision of the medial lobe, here named the βc lobe with its vertical branch αc, comprises glutamatergic Kenyon cells that are probably homologous to glutamatergic Kenyon cells in the cockroach and honey bee, and are the last neurons to differentiate. The first neurons to differentiate, which supply the γ lobe, are equipped with clawed dendritic specializations and are the structural homologues of clawed class II Kenyon cells supplying the γ lobes in cockroaches and honey bees. Three intermediate divisions lie between the βc lobe and γ lobe. These are, from the back towards the front, the β lobe, the β′ lobe, and a narrow division between β′ and γ called the β″ lobe. The fused calyx of the Drosophila mushroom body is comparable to the double calyces of Hymenoptera, here exemplified by a basal taxon, Diprion pini. Further similarities between the hymenopteran calyces and those of Drosophila are suggested by the segregation of different types of Kenyon cell dendrites within the calyx neuropil. The organization of afferents from the antennal lobes also defines regions in the Drosophila calyx that may be homologous to the lip and basal ring regions of the honey bee calyces. As in honey bees, GABAergic processes densely invade Drosophila's calyces, which also contain a sparse but uniform distribution of octopaminergic elements. Microsc. Res. Tech. 62:151–169, 2003. © 2003 Wiley‐Liss, Inc.