bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical solution of a partial differential equation system describing chemical kinetics and diffusion in a cell with the aid of compartmentalization
Authors: Salzner U. , Otto P. , Ladik J. 
Published: January 2005

AbstractTo build a kinetic model of a cell with diffusion one has to solve a coupled nonlinear partial differential equation system consisting of several hundred equations. (Several hundred chemical components undergoing several hundred reactions.) To solve this formidable mathematical problem the division of the model cell into compartments (most biochemical reactions take place in a certain part of the cell) was suggested.1 Solving the differential equation system in one compartment, the results can be used as input at other compartments until mutually consistent solutions are achieved.To test this suggestion 10 coupled chemical reactions with diffusion were investigated in a model that contains three compartments. The results in the case of pure diffusion are in excellent agreement with and without compartmentalization. After this the full problem was treated by compartmentalization using for the solution of the differential equation system a discretization of the concentrations as functions of space and time and the Newton–Raphson iterative procedure. The results obtained give reasonable space and time dependence for the concentrations of all 10 components.
Relaxed potential energy surfaces of N‐linked oligosaccharides: The mannose‐α(1 → 3)‐mannose case
Authors: Imberty Anne , Tran Vinh , Pérez Serge 
Published: January 2005

AbstractWe report calculations of potential energy surfaces where all the internal coordinates of the disaccharide Man‐α(1 → 3)‐Man‐α‐O‐Me were relaxed and minimized through an extensive molecular mechanics scheme. Flexibility within the mannopyranose rings plays a crucial role. Introduction of the relaxed principle into the conformational description of the disaccharide does not greatly alter the overall shape of the low‐energy domains but it reveals new local minima. However, its principle effect is the lowering of energy barriers in the potential energy surface. New conformational transitions about the glycosidic bonds appear, permiting pathways among the low energy sections. This occurs with only little variation of the classical 4C1 conformation of the mannopyranose residues. All the conformations observed in the solid state, along with those already predicted through the joint use of NMR and modeling techniques, fall into the populations of stable conformers calculated in the present work. Moreover, a satisfactory agreement is reached between previously observed NOE values, and the theoretical one, calculated from the averaging of more than 500 microstates. The present results reconciliate most of the apparently conflicting data previously reported; they provide strong support for the application of the concept of conformational averaging to solution behavior. Some limitations of the proposed methodology are also discussed.
On the enumeration and generation of polyhex hydrocarbons
Authors: Müller W. R. , Szymanski K. , Knop J. V. , Nikolić S. , Trinajstić N. 
Published: January 2005

AbstractA novel efficient computer‐oriented approach, based on the DAST (dualist angle‐restricted spanning tree) code, is introduced for enumeration and generation of planar polyhex hydrocarbons. It is much faster than other approaches in the literature. The numbers of planar polyhex hydrocarbons with 14 hexagons are reported for the first time.
Effects of computational variations for determining binding energies of diastereomeric complexes when using MM2
Authors: Still Miron G. , Rogers L. B. 
Published: January 2005

AbstractVariations of a procedure have been examined for minimization of the energies, calculated using MM2, of two docked molecules. After doing the intramolecular minimization of the individual molecules, randomized orientations of the rigid molecules were brought together to form complexes and the nonbonded energies of interaction were then minimized. Next, pairs having energies within 4.0 kcal/mol of the most stable pair were minimized further by atom‐by‐atom relaxation of the complex. Only two repetitions of the last two steps were found to give values within 0.001 kcal/mol in more than 90% of the cases. Compared to two other variations of the procedure, this method appeared to avoid erroneous (local, not global) minima. Finally, this overall procedure was tested against chromatographic data in the literature. Using only the most stable comformer of each species, the results appeared to be in qualitative agreement with fractionation data for enantiomeric aminoethanes on a chiral packing very similar to the one modeled here.
Coordination numbers for biomolecular hydration: A quantitative method based on pattern recognition analysis of Monte Carlo simulations of aqueous solutions
Authors: Marchese Francis T. 
Published: January 2005

AbstractA coordination number model (CNM) has been developed that reproduces coordination numbers generated by rigorous Monte Carlo simulations of dilute aqueous solutions. The molecular coordination number is calculated by using the volume of the Voronoi polyhedron surrounding each solute atom and a set of linear least squares fitted parameters. Agreement with simulation data is good, with average deviation of less than 5%. Although CNM is presently parameterized against a simulation database founded on the potential functions of Clementi and coworkers, the method is perfectly general and can be applied to simulation data derived from any potential function form. Finally, the method is fast and can predict coordination numbers within minutes on a microcomputer.
Diazonium ions. Topological electron density analysis of cyclopropeniumyldiazonium dications and of their stability toward dediazoniation
Authors: Glaser Rainer 
Published: January 2005

AbstractResults are presented of topological analyses of the electron density functions of cyclopropeniumyldiazonium dication, 1, of its 2,3‐diamino derivative, 2, and of their products 3 and 4, respectively, formed by dediazoniative ring‐opening. The new CN‐bonding type in 1 and 2, recently realized synthetically in derivatives of 2, is compared to prototypical aliphatic diazonium ions with regard to electronic structure and thermodynamic stability, factors that both are crucial for the appreciation of the mechanisms of deamination reactions of chemical and biochemical significance. Association of the dication with N2 involves density accumulation in the CN bonding region, occurs without major overall charge transfer, and leads to an electrostatically favorable quadrupolar charge distribution in the diazonium ion. The CN‐bonding model recently proposed for aliphatic diazonium ions also applies to these dications. 1 is thermodynamically stable while the dediazoniation of 2 is exothermic but kinetically hindered. Our best estimates for the reaction energies of the dediazoniations 1 → 3 + N2 and 2 → 4 + N2, respectively, are 65.5 and −7.2 kcal/mol, respectively. We have found that, in general, the cation is destabilized and that N2 is stabilized upon CN‐bond cleavage. Cations force N2 to form diazonium ions. The remarkable difference between the stabilities of 1 and 2 is primarily due to the larger destabilization of the open dication 3 compared to 4. Push‐pull interactions between the diazo‐ and the overall electron‐withdrawing amino‐functions characterize the electronic structure of 2. CN‐Bonding and the overall electronic structure of 2 are incompatible with the usual Lewis resonance notations. Instead of dismissing the Lewis notations, it is shown that the topological description can be reconciled with the Lewis notations if the resonance forms are interpreted in a way that appropriately reflects the atom populations and first moments. Implications of the model with regard to reactivity are discussed.
Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride‐ion transfer between the NADH analogue, 1‐methyl‐dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase
Authors: Cummins Peter L. , Gready Jill E. 
Published: January 2005

AbstractAs part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1‐methyl‐dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter‐ring coupling. The influence of carboxamide side‐chain conformation of nicotinamide on the energetics of the hydride‐ion transfer, and on the structures of the transition states and stable intermolecular‐interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants‐complex, and transition‐state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO‐3G and SCF/3‐21G single‐point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants‐complex and transition‐state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H‐bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product‐like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H‐bond which is present for the dihydrofolate reaction, and consequently the reactants‐complex and transition state are less stable.
ARGOS, a vectorized general molecular dynamics program
Authors: Straatsma T. P. , McCammon J. A. 
Published: January 2005

AbstractThe organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX‐2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX‐2/400 than on the VAX 8650.
Molecular mechanics parameterization: Bond lengths and angles for nitrogen and phosphorus containing compounds
Authors: Leonard Joseph M. , Ashman William P. 
Published: January 2005

AbstractMolecular mechanics provides an excellent means of generating reasonable chemical structures in a short amount of time. Using a classical representation, a molecule can be partitioned into a collection of n‐fold atomic interactions, each with an associated force constant. In order for a calculation to proceed, all of the required force constants must be known. This article presents a method of rapidly determining the values for missing parameters using appropriately scaled quantum chemical techniques.
AM1 study of acid‐catalyzed hydrolysis of maleamic (4‐amino‐4‐oxo‐2‐butenoic) acids
Authors: Katagi Toshiyuki 
Published: January 2005

AbstractThe acid‐catalyzed hydrolysis mechanisms of maleamic (4‐amino‐4‐oxo‐2‐butenoic) acids were studied using AM1 method. The reaction proceeded mainly in two steps: (1) nucleophilic attack of the undissociated carboxyl group on the adjacent aminocarbonyl carbon via a zwitterionic intermediate; and (2) the rate‐determining proton transfer to form the zwitterionic tetrahedral intermediate. In each step, the hydration of water and hydronium ion molecules was important in stabilizing the polarized intermediates. The substituent effects at the amide moiety and the 2,3‐positions of the maleamic acids were qualitatively estimated for each step.
An improved empirical force field for saturated hydrocarbons
Authors: Dillen Jan L. M. 
Published: January 2005

AbstractA new molecular mechanics force field for alkanes is presented. The force field aims to eliminate some identified failures of the well‐known MM2 force field. The new energy function gives an improved prediction of the rotational barriers of highly congested molecules, a better calculation of short nonbonded contacts, and the correct reproduction of bond elongation in small torsion angles. The calculation of sublimation enthalpies is also improved. The standard deviation of the formation enthalpies for a set of 54 compounds is 0.63 kcal/mol; this compares with the reported value of 0.42 calculated with MM2 and MM3 for different sets. The force field parameters were obtained using a least squares method.
Construction and molecular modeling of phospholipid surfaces
Authors: Charifson Paul S. , Hiskey Richard G. , Pedersen Lee G. 
Published: January 2005

AbstractA protocol is given for the construction of phospholipid surfaces that possess variable head groups and thus variable net charge. Ab initio quantum mechanical calculations are performed to establish the necessary force field (AMBER) parameters. The charge distribution is defined by an electrostatic potential method consistent with the ab initio wave function. As a model calculation, a monolayer surface with head groups of phosphatidylserine and phosphatidylcholine derived from the crystal structure of 1,2‐dilauroyl‐DL‐phosphatidylethanolamine (DLPE) is placed in a water bath with two Ca(II) ions present. The resultant surface is energy‐optimized followed by 64 ps of molecular dynamics integration. Evaluation of calcium ion coordination environments, characterization of the P‐N dipole inclination with respect ot the plane of the monolayer, and calculation of molecular surface area is performed and compared with experimental data.
Minimization and molecular dynamics studies of guanosine and Z‐DNA modified by N‐2‐acetylaminofluorene
Authors: Fritsch V. , Westhof E. 
Published: January 2005

AbstractThe modeling program AMBER 3.0 was used to study the conformations adopted by the C8‐substituted guanosine adduct of the carcinogen N‐2‐acetylaminofluorene (AAF), called dGuo‐AAF. This conformational study was extended to the hexamer d(CGCGCG)2 in the Z form, modified by AAF at guanine G4 with the carcinogen situated at the helix exterior in two different orientations (named ZAAF‐5′ and ZAAF‐3′). Considering the importance of electrostatic interactions in case of charged molecules like nucleic acids, minimization and molecular dynamics (MD) were performed using different electrostatic parameters (dielectric functions and scale factors). For that purpose, a subroutine allowing the use of a sigmoidal distance‐dependent dielectric function εcal has been added to the program. For dGuo‐AAF, the results show a great importance of the starting conformation and of the force field parameters on the minimization and MD behaviors. For the AAF‐modified Z‐DNA, the results display a pronouned dependence on the choice of the set of electrostatic parameters as well. With the distance‐dependent dielectric function ε = r, the force field parameters favor the formation of intramolecular H bonds, which can lead to important distortions of Z‐DNA. The use of ε = 4r or ε = εcal attenuates effectively such a tendency, except in full MD simulations. The dielectric function εcal is computing intense, but often similar results are obtained with ε = 4r, especially with the use of the BELLY option. AAF appears to prefer the ZAAF‐5′ conformation, i.e., with the fluorene ring stacking on the sugar phosphate backbone of the following 5′ C‐G bases. Such a conformation is further stabilized by an intramolecular hydrogen bond between the amino group of the 3′ cytosine and the carbonyl group of AAF. The fluorene ring, although mobile around its long axis, does not flip‐flop between its two main orientations, ZAAF‐5′ and ZAAF‐3′. The presence of the AAF does not prevent the ZI to ZII transitions. Whatever the electrostatic parameters, the presence or absence of AAF, the cytosine sugars stay in the C2′‐endo pucker domain. In unmodified Z‐DNA, the guanine sugars stay in the C3′‐endo region, except for the terminal guanines which transit to the C2′endo region. In modified Z‐DNA, the sugar of the modified guanine behaves as a terminal guanine sugar.
Comparison of compuational methods for simulating nuclear Overhauser effects in NMR spectroscopy
Authors: Forster Mark J. 
Published: January 2005

AbstractVarious algorithms for solving the Solomon equations describing nuclear Overhauser effects (nOes) in NMR spectroscopy have been compared. The applicability of the eigenvalue/eigenvector and the numerical integration approaches have been investigated. The eigenvalue/eigenvector approach is not a computationally efficient means of simulating nOe experiments in which a saturating radiofrequency field is applied during the time course. For experiments in which nOes develop in the absence of an RF field, this approach should only be used in simulating a full NOESY spectrum. Integration schemes have been found to be more efficient at simulating nOe experiments in which the nOe evolves in the presence of a saturating field, at simulating a partial set of initial perturbation experiments and at simulating a few rows or columns in a NOESY spectrum. Various integration schemes were applied to a two‐spin system for which an analytic solution is available and to a model B‐DNA oligonucleotide hexamer. The previously unused Taylor series algorithm was found to be superior to the Euler, midpoint, and fourth‐order Runge–Kutta methods with regard to integration accuracy/computation time. An adaptive step size control routine for the Taylor series integration scheme was developed. Integration schemes can be speeded up in a simple fashion by introducing a distance cutoff for the dipolar interaction. Using a cutoff of 8 Å the Taylor series algorithm was able to compute the NOESY spectrum more rapidly than the eigenvalue/eigenvector algorithm for large spin systems at short mixing times. At longer mixing times the eigenvalue/eigenvector approach becomes the more efficient scheme.
Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of deca‐alanine
Authors: Kitao Akio , Gō Nobuhiro 
Published: January 2005

AbstractEffects of different treatments of the degrees of freedom of bond length stretching and bond angle bending in computational analysis of conformational dynamics of proteins and polypeptides are assessed. More specifically, the normal mode analysis of conformational dynamics of α‐helix of deca‐alanine has been carried out both in the dihedral angle space (DAS) and in the Cartesian coordinate space (CCS). Almost perfect one‐to‐one correspondence has been found between normal modes in the CCS with frequencies less than 128 cm−1 and those in the DAS with frequencies less than 164 cm−1. Patterns of atomic displacements in the corresponding modes are very similar. This indicates that the effects of fixing degrees of freedom of bond length stretching and bond angle bending on the very‐low‐frequency normal modes in the CCS with frequencies less than 128 cm−1 are almost solely to increase the frequencies by about 20%. The conclusion indicates that the different treatment of these degree does not lead to qualitatively different results as long as low‐frequency motions are concerned. Based on the results of calculation, mechanical property of the α‐helix of deca‐alanine is discussed.
New development on energetic approach to the packing in proteins
Authors: Carlacci Louis , Chou Kuo‐Chen 
Published: January 2005

AbstractThe energy minimization in the computer program PACK established for investigating interactions of secondary structures in proteins was based on the finite deference method. It is well known that a minimizer of finite difference method is less efficient than that of analytical gradient method. In this article the equations of the analytical energy gradients for a multiple chain system have been derived and they can be directly incorporated into the PACK program. The revised version, PACK/2, thus obtained is much more efficient. Energy minimizations carried out on the theoretical models of 4‐helix bundle, sheet‐sheet packing, and β‐barrel indicated that the CPU times were reduced 15‐ to 20‐fold if the revised PACK/2 algorithm was used. In general, the more complicated the computed structure was, the more significantly the computation time was reduced. Furthermore, for the cases demonstrated here, the final minimized energies were always lower than those obtained by the original version of PACK, indicating that a better packing structure was achieved by means of the revised program PACK/2.
A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation
Authors: Nicholls Anthony , Honig Barry 
Published: January 2005

AbstractAn efficient algorithm is presented for the numerical solution of the Poisson–Boltzmann equation by the finite difference method of successive over‐relaxation. Improvements include the rapid estimation of the optimum relaxation parameter, reduction in number of operations per iteration, and vector‐oriented array mapping. The algorithm has been incorporated into the electrostatic program DelPhi, reducing the required computing time by between one and two orders of magnitude. As a result the estimation of electrostatic effects such as solvent screening, ion distributions, and solvation energies of small solutes and biological macromolecules in solution, can be performed rapidly, and with minimal computing facilities.
Atomic multipoles and perpendicular electrostatic forces in diatomic and planar molecules
Authors: Dinur Uri 
Published: January 2005

AbstractCurrent methods for assigning atomic multipoles focus on reproduction of the molecular electrostatic potential. Another aspect of electrostatic interaction, which is usually overlooked, is the forces that an external electric field exerts on the nuclei of a molecule. In a self‐consistent theory, both the electrostatic potential and force should be accounted for. However, in general it is not easy to meet this requirement for the force. For planar molecules, though, a formal solution is available in terms of atomic multipoles that are extracted from the molecular multipolar tensors. These Force‐Related (FR) atomic multipoles are discussed in detail for some typical diatomics and planar polyatomics, and are shown to provide a solid uniform framework for treating both aspects of the electrostatics. In contrast, the commonly used potential‐derived charges (i.e., the atomic charges obtained by fitting the electrostatic potential) can yield large deviations with respect to electrostatic forces on the nuclei, even when the electrostatic potential is very well reproduced.