bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds
Authors: Allinger Norman L. , Chen Kuo‐Hsiang , Lii Jenn‐Huei , Durkin Kathleen A. 
Published: July 2003

AbstractSimple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion–bend and torsion–torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm−1, as opposed to 38 cm−1 with MM3. Both the α and β bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the α and β electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol). © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1447–1472, 2003
Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect
Authors: Lii Jenn‐Huei , Chen Kuo‐Hsiang , Durkin Kathleen A. , Allinger Norman L. 
Published: July 2003

AbstractThe anomeric effect has been studied for a variety of compounds using the MM4 force field, and also using MP2/6‐311++G(2d,2p) ab initio calculations and experimental data for reference purposes. Geometries and energies, including conformational, rotational barriers, and heats of formation were examined. Overall, the agreement of MM4 with the experimental and ab initio data is good, and significantly better than the agreement obtained with the MM3 force field. The anomeric effect is represented in MM4 by various explicit terms in the force constant matrix. The bond length changes are accounted for with torsion‐stretch elements. The angle changes are accounted for with torsion‐bend elements. The energies are taken into account with a number of torsional terms in the usual way. A torsion‐torsion interaction is also of some importance. With all of these elements included in the calculation, the MM4 results now appear to be adequately accurate. The heats of formation were examined for a total of 12 anomeric compounds, and the experimental values were fit by MM4 with an RMS error of 0.42 kcal/mol. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1473–1489, 2003
Alcohols, ethers, carbohydrates, and related compounds. III. The 1,2‐dimethoxyethane system
Authors: Lii Jenn‐Huei , Chen Kuo‐Hsiang , Grindley T. Bruce , Allinger Norman L. 
Published: July 2003

AbstractEthylene glycol, its dimethyl ether, and some related compounds have been studied using the MM4 molecular mechanics force field. The MM4 calculated structural and energetic results have been brought into satisfactory agreement with a considerable number of experimental data and MP2/6‐311++G(2d,2p) ab initio calculations. The heats of formation of these compounds are also well calculated. The MM4 ethylene glycol conformations in particular are in good agreement, both geometrically and in terms of energy, with those from the ab initio calculations. The corresponding dimethyl ether is of special interest, because it has been suggested that the trans‐gauche conformation is unusually stable due to the hydrogen bonding of a hydrogen on a methyl group with the more distant oxygen. It is shown in the present work that while this conformation is more stable than might have been expected, the energy is adequately calculated by MM4 without using any hydrogen bonding between the CH bond and the oxygen. If such hydrogen bonding occurs, it amounts to no more than about 0.5 kcal/mol in energy, and is too small to detect with certainty. Additionally, energetic relationships in trans‐1,2‐dimethoxycyclohexane, 1,3,5,7‐tetraoxadecalin, and 3‐methoxytetrahydropyran have been studied, and the calculated results are compared with experimental information, which is adequately reproduced. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1490–1503, 2003
Alcohols, ethers, carbohydrates, and related compounds. IV. carbohydrates
Authors: Lii Jenn‐Huei , Chen Kuo‐Hsiang , Allinger Norman L. 
Published: July 2003

AbstractAb initio calculations [B3LYP/6‐311++G(2d,2p)] have been carried out on 84 conformations of 12 different sugars (hexoses), in both pyranose and furanose forms, with the idea of generating a data base for carbohydrate structural energies that may be used for developing the predictive value of molecular mechanics calculations for carbohydrates. The average value for the apparent gas phase anomeric effect for a series of 31 pairs of pyranose conformations was found to be 1.83 kcal/mol (vs. 2.67 kcal/mol with a smaller basis set used in earlier calculations). In developing MM4 to reproduce these data, it was necessary first to have good energies for simple alcohols and ethers, together with an adequate treatment of hydrogen bonding, and then to include the anomeric effect, and the ethylene glycol type system, as was previously recognized. It was also found that the so‐called delta‐2 effect, long recognized in carbohydrates, must be explicitly included, in order to obtain acceptable results. When a force field that included all of these items as developed from the small molecules based on the MM4 hydrocarbon force field was applied without any parameter adjustment to the set of hexopyranose and furanose conformations mentioned earlier, the Eβ − Eα was found to have an average value of 1.88 kcal/mol, versus 1.74 for the quantum calculations. The signed average and RMS deviations of the MM4 from the QM results were +0.15 and 0.87 kcal/mol. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1504–1513, 2003
Possible molecular hydrogen formation mediated by the radical cations of anthracene and pyrene
Authors: Hirama Mutsumi , Ishida Toshimasa , Aihara Jun‐Ichi 
Published: July 2003

AbstractHydrogen molecules cannot be formed readily by the association of gaseous hydrogen atoms. Possible H2 formation mediated by the radical cations of typical polycyclic aromatic hydrocarbons (PAHs), anthracene and pyrene, was studied at the B3LYP/6‐31G** level of theory. We presumed that H2 is formed by way of two elementary reactions: the addition of an H atom to a PAH molecular cation, and the H abstraction from the resulting monohydro‐PAH cation (i.e., arenium ion) by a second H atom to yield H2. The first reaction takes place without any activation energy. The second reaction is also predicted to proceed along almost barrierless pathways, although it is far from being a typical ion–molecule reaction. There is a possibility that these reactions might constitute one of the mechanisms for H2 formation in extremely cold interstellar space. Deuterium enrichment in PAH cations is possibly accompanied by such H2 formation because deuteration lowers the energies of polyatomic PAH cations appreciably. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1378–1382, 2003
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9
Authors: Chong Lillian T. , Bandyopadhyay Pradipta , Scanlan Thomas S. , Kuntz Irwin D. , Kollman Peter A. 
Published: July 2003

AbstractDirect hydroxide attack on the scissile carbonyl of the substrate has been suggested as a likely mechanism for esterase antibodies elicited by phosphonate haptens, which mimic the transition states for the alkaline hydrolysis of esters.1 The unique amidase activity of esterase antibody 43C9 has been attributed to nucleophilic attack by an active‐site histidine residue.2 Yet, the active site of 43C9 is strikingly similar to those of other esterase antibodies, particularly 17E8. We have carried out quantum mechanical calculations, molecular dynamics simulations, and free energy calculations to assess the mechanism involving direct hydroxide attack for 43C9. Results support this mechanism and suggest that the mechanism is plausible for other antiphosphonate antibodies that catalyze the hydrolysis of (p‐nitro)phenyl esters. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1371–1377, 2003
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
Authors: Zagrovic Bojan , Pande Vijay 
Published: July 2003

AbstractBy using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20‐residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (γ). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low‐viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/γ for values from 1–10−1× that of water viscosity. However, for the regime between 10−4–10−1× that of water viscosity we observe power‐law dependence of the form k ∼ γ−1/5. These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1432–1436, 2003
Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC‐CI study
Authors: Das Abhijit K. , Hasegawa Jun‐Ya , Miyahara Tomoo , Ehara Masahiro , Nakatsuji Hiroshi 
Published: July 2003

AbstractTwo ground‐state protonation forms causing different absorption peaks of the green fluorescent protein chromophore were investigated by the quantum mechanical SAC/SAC‐CI method with regard to the excitation energy, fluorescence energy, and ground‐state stability. The environmental effect was taken into account by a continuum spherical cavity model. The first excited state, HOMO‐LUMO excitation, has the largest transition moment and thus is thought to be the source of the absorption. The neutral and anionic forms were assigned to the protonation states for the experimental A‐ and B‐forms, respectively. The present results support the previous experimental observations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1421–1431, 2003
Flexible effective fragment QM/MM method: Validation through the challenging tests
Authors: Nemukhin A. V. , Grigorenko B. L. , Topol I. A. , Burt S. K. 
Published: July 2003

AbstractA new version of the QM/MM method, which is based on the effective fragment potential (EFP) methodology [Gordon, M. et al., J Phys Chem A 2001, 105, 293] but allows flexible fragments, is verified through calculations of model molecular systems suggested by different authors as challenging tests for QM/MM approaches. For each example, the results of QM/MM calculations for a partitioned system are compared to the results of an all‐electron ab initio quantum chemical study of the entire system. In each case we were able to achieve approximately similar or better accuracy of the QM/MM results compared to those described in original publications. In all calculations we kept the same set of parameters of our QM/MM scheme. A new test example is considered when calculating the potential of internal rotation in the histidine dipeptide around the CαCβ side chain bond. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1410–1420, 2003
Multireference perturbation theory with optimized partitioning. II. Applications to molecular systems
Authors: Witek Henryk A. , Nakano Haruyuki , Hirao Kimihiko 
Published: July 2003

AbstractThe second‐order multireference perturbation theory using an optimized partitioning, denoted as MROPT(2), is applied to calculations of various molecular properties—excitation energies, spectroscopic parameters, and potential energy curves—for five molecules: ethylene, butadiene, benzene, N2, and O2. The calculated results are compared with those obtained with second‐ and third‐order multireference perturbation theory using the traditional partitioning techniques. We also give results from computations using the multireference configuration interaction (MRCI) method. The presented results show very close resemblance between the new method and MRCI with renormalized Davidson correction. The accuracy of the new method is good and is comparable to that of second‐order multireference perturbation theory using Møller‐Plesset partitioning. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1390–1400, 2003
Systematic and statistical error in histogram‐based free energy calculations
Authors: Kobrak Mark N. 
Published: July 2003

AbstractA common technique for the numerical calculation of free energies involves estimation of the probability density along a given coordinate from a set of configurations generated via simulation. The process requires discretization of one or more reaction coordinates to generate a histogram from which the continuous probability density is inferred. We show that the finite size of the intervals used to construct the histogram leads to quantifiable systematic error. The width of these intervals also determines the statistical error in the free energy, and the choice of the appropriate interval is therefore driven by the need to balance the two sources of error. We present a method for the construction of the optimal histogram for a given system, and show that the use of this technique requires little additional computational expense. We demonstrate the efficacy of the technique for a model system, and discuss how the principles governing the choice of discretization interval could be used to improve extended sampling techniques. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1437–1446, 2003
Immersion fixation with Carnoy solution for conventional immunohistochemical detection of particular N‐methyl‐D‐aspartate receptor subunits in murine hippocampus
Authors: Yoneyama Masanori , Kitayama Tomoya , Taniura Hideo , Yoneda Yukio 
Published: July 2003

AbstractImmunoblotting analysis revealed heterologous distribution profiles of the N‐methyl‐D‐aspartate (NMDA) receptor subunits GluR ζ‐1, GluR ϵ‐1, and GluR ϵ‐2 in membrane preparations of different murine brain structures, with exclusive detection of GluR ϵ‐3 subunit in cerebellar preparations. Mice were anesthetized and perfused with 4% paraformaldehyde (PA), Zamboni, or Carnoy solution for subsequent immunohistochemical detection of these NMDA receptor subunits. In coronal brain sections from animals perfused with 4% PA and Zamboni solutions, high immunoreactivity was detected exclusively with GluR ζ‐1, GluR ϵ‐1, GluR ϵ‐2, and GluR ϵ‐3 subunits in the pyramidal and dentate granular layers, where the GluR ϵ‐3 subunit is supposed to be absent. By contrast, high immunoreactivity was detected with GluR ζ‐1, GluR ϵ‐1, and GluR ϵ‐2, but not GluR ϵ‐3, subunits in the strata oriens and radiatum of the CA1 subfield without immunoreactivity along the pyramidal and granular layers when sections were prepared by immersion fixation with Carnoy solution after dissection from brains of mice decapitated. On these sections, relatively high immunoreactivity was found also with GluR ζ‐1, GluR ϵ‐1, and GluR ϵ‐2 subunits in the stratum lacunosum‐moleculare of the CA1 region, the strata oriens, radiatum, and lacunosum‐moleculare of the CA3 region, and the stratum moleculare of the dentate gyrus, respectively. The systemic administration of kainate led to significant decreases in immunoreactivity to GluR ζ‐1, GluR ϵ‐1, and GluR ϵ‐2 subunits in the CA1 and CA3 subfields on brain sections prepared by immersion fixation with Carnoy solution. These results suggest that immersion fixation with Carnoy solution may be suitable and appropriate for reproducible and quantitative immunohistochemical detection of particular NMDA receptor subunits in murine hippocampus. © 2003 Wiley‐Liss, Inc.
Developmental and cell type‐specific expression of the neuronal marker NeuN in the murine cerebellum
Authors: Weyer Anja , Schilling Karl 
Published: July 2003

AbstractNeuN is a 46/48‐kD nuclear protein antigen used widely to identify postmitotic neurons in both research and diagnostics. It is expressed by neurons throughout the nervous system of a variety of species, including birds, rodents, and man (Mullen et al. [1992] Development 116:201–211). When we sought to use NeuN to follow the developmental progression of murine cerebellar interneurons, we observed that expression of this antigen in the cerebellum was restricted to granule neurons and a small population of cells present in the lower molecular layer of the adult cerebellum. In an attempt to identify these cells, we combined immunostaining for NeuN with a panel of cell type‐specific markers to unambiguously identify neurons that express NeuN in the adult and developing cerebellum. In contrast to postmitotic granule neurons, NeuN was not expressed by any other immunocytochemically identified cerebellar interneurons, which comprised basket and stellate cells, Golgi neurons, unipolar brush cells, and Lugaro cells. NeuN‐positive cells in the molecular layer failed to express any cell type‐specific markers tested. They may represent ectopic granule cells; alternatively, they may represent a hitherto unknown population of cerebellar cells. In vitro experiments suggest that NeuN expression is related closely to granule cell axogenesis. This approach also revealed that the level of NeuN expression could be modulated by chronically depolarizing these cells. Thus, whereas NeuN expression per se is a reliable marker of proliferative capacity, levels of NeuN expression may also be indicative of the physiological status of a postmitotic neuron. © 2003 Wiley‐Liss, Inc.
Intravenous versus intrastriatal cord blood administration in a rodent model of stroke
Authors: Willing A.E. , Lixian J. , Milliken M. , Poulos S. , Zigova T. , Song S. , Hart C. , Sanchez‐Ramos J. , Sanberg P.R. 
Published: July 2003

AbstractHuman umbilical cord blood (hUCB) is a rich source of hematopoietic stem cells that have been used to reconstitute immune cells and blood lineages. Cells from another hematopoietic source, bone marrow, have been found to differentiate into neural cells and are effective in the treatment of stroke. In this study, we administered hUCB cells intravenously into the femoral vein or directly into the striatum and assessed which route of cell administration produced the greatest behavioral recovery in rats with permanent middle cerebral artery occlusion (MCAO). All animals were immunosuppressed with cyclosporine (CSA). When spontaneous activity was measured using the Digiscan automated system, it was found to be significantly less when hUCB was transplanted 24 hr after stroke compared with nontransplanted, stroked animals (P < 0.01). Furthermore, behavioral recovery was similar with both striatal and femoral hUCB delivery. This is in contrast to the step test, in which significant improvements were found only after femoral delivery of the hUCB cells. In the passive avoidance test, transplanted animals learned the task faster than nontransplanted animals (P < 0.05). Together, these results suggest that hUCB transplantation may be an effective treatment for brain injuries, such as stroke, or neurodegenerative disorders. In addition, intravenous delivery may be more effective than striatal delivery in producing long‐term functional benefits to the stroked animal. © 2003 Wiley‐Liss, Inc.
Human Aβ1–42 reduces iron‐induced toxicity in rat cerebral cortex
Authors: Bishop Glenda M. , Robinson Stephen R. 
Published: July 2003

AbstractSenile plaques, the major neuropathological lesions of Alzheimer's disease (AD), are composed primarily of amyloid‐β (Aβ) peptide and contain high concentrations of iron (1.0 mM). We have previously shown that intracortical injections of 1.0 mM iron to adult rats produce significantly more neuronal loss than control injections of saline vehicle, whereas injections of Aβ do not. Because iron has been shown to increase the in vitro toxicity of Aβ, the present study was undertaken to determine whether iron can make Aβ neurotoxic in vivo. Aβ and 1.0 mM iron (as ferric ammonium citrate) were coinjected into rat cerebral cortex, and the neuronal loss was compared with that produced by pure Aβ or pure iron. The human and rat variants of Aβ1–42 were compared to determine whether they produce the same amount of neuronal loss when combined with iron. Coinjection of iron with either Aβ variant caused significantly more neuronal loss than Aβ peptide alone, suggesting that iron may contribute to the toxicity associated with senile plaques. Rat Aβ1–42 combined with iron was as toxic as iron alone, whereas iron combined with human Aβ1–42 was significantly less toxic. This latter finding indicates that fibrillar human Aβ is able to reduce iron‐induced neurotoxicity in vivo and raises the interesting possibility that senile plaques in AD may represent a neuroprotective response to the presence of elevated metal ions. © 2003 Wiley‐Liss, Inc.
Dopamine induces autophagic cell death and α‐synuclein increase in human neuroblastoma SH‐SY5Y cells
Authors: Gómez‐Santos Cristina , Ferrer Isidre , Santidrián Antonio F. , Barrachina Marta , Gil Joan , Ambrosio Santiago 
Published: July 2003

AbstractFree cytoplasmic dopamine may be involved in the genesis of neuronal degeneration in Parkinson's disease and other such diseases. We used SH‐SY5Y human neuroblastoma cells to study the effect of dopamine on cell death, activation of stress‐induced pathways, and expression of α‐synuclein, the characteristic protein accumulated in Lewy bodies. We show that 100 and 500 μM dopamine causes a 40% and 60% decrease of viability, respectively, and triggers autophagy after 24 hr of exposure, characterized by the presence of numerous cytoplasmic vacuoles with inclusions. Dopamine causes mitochondrial aggregation in adherent cells prior to the loss of functionality. Plasma membrane and nucleus also maintain their integrity. Cell viability is protected by the dopamine transporter blocker nomifensine and the antioxidants N‐acetylcysteine and ascorbic acid. Dopamine activates the stress‐response kinases, SAPK/JNK and p38, but not ERK/MAPK or MEK, and increases α‐synuclein expression. Both cell viability and the increase in α‐synuclein expression are prevented by antioxidants; by the specific inhibitors of p38 and SAPK/JNK, SB203580 and SP600125, respectively; and by the inhibitor of autophagy 3‐methyladenine. This indicates that oxidative stress, stress‐activated kinases, and factors involved in autophagy up‐regulate α‐synuclein content. The results show that nonapoptotic death pathways are triggered by dopamine, leading to autophagy. These findings should be taken into account in the search for strategies to protect dopaminergic neurons from degeneration. © 2003 Wiley‐Liss, Inc.