Convergence of the density functional one-centre expansion for the molecular continuum: N2 and (CH3)3N

A large-scale one-centre expansion with a radial B-spline basis set is implemented for bound and continuum states. A Kohn-Sham hamiltonian is employed with Hartree and exchange-correlation potentials calculated from the SCF electron density taken from a previous LCAO calculation. An inverse iteration method is used to obtain the continuum wavefunction, from which the cross section and asymmetry parameter are calculated. The convergence with respect to angular momentum and cut-off radius is analysed for N₂. The relevance of multipolar contributions even at large distances is shown and suggestions for further improvements are given. In order to show that the present method is suitable to treat systems of moderate size, the (CH₃)₃N molecule has also been calculated and the results are compared with experiment. Received: 19 May 1998 / Accepted: 20 August 1998 / Published online: 7 December 1998     

Production of soft core/hard shell composite polymer particles by the stepwise heterocoagulation method with heat treatment

Soft core/hard shell composite polymer particle was prepared by the stepwise heterocoagulation, which was proposed by authors in 1990, of many cationic hard small polymer particles (SPs) onto an anionic soft large polymer particle (LP). The powder was obtained by freeze-drying at 0 ^°C which was higher than glass transition temperature of LP (−7 ^°C) and lower than that of SP (90 ^°C). Received: 9 December 1997 Accepted: 12 May 1998     

Direct subduction of Q-conjugacy representations to give characteristic monomials for combinatorial enumeration

Characteristic monomials for a finite group are obtained by direct subductions of Q-conjugate representations. They are shown to give a generating function that is capable of solving enumeration problems. Received: 1 May 1998 / Accepted: 16 July 1998 / Published online: 18 September 1998     

Valence p functions for alkali and alkaline-earth atoms

Contracted Gaussian-type function (CGTF) basis sets are reported for valence p orbitals of the six alkali and alkaline-earth atoms Li, Be, Na, Mg, K, and Ca for molecular applications. These sets are constructed by Roothaan–Hartree–Fock calculations for the ns → np excited states of atoms, in which both linear and nonlinear parameters of CGTFs are variationally optimized. The present CGTF sets reproduce well the numerical Hartree–Fock ns → np excitation energies: the largest error is 0.0009 hartrees for Li. New CGTFs are tested with diatomic Li₂, Na₂, K₂, and MH molecules, where M = Li, Be, Na, Mg, K, and Ca, by self-consistent-field (SCF) and multiconfiguration SCF calculations. The resultant spectroscopic constants compare well with those of more elaborate calculations and are sufficiently close to experimental values, supporting the efficiency of the present set for the valence p orbitals. Received: 9 July 1998 / Accepted: 17 September 1998 / Published online: 1 February 1999     

Hydrophilic magnetic polymer latexes. 1. Adsorption of magnetic iron oxide nanoparticles onto various cationic latexes

With a view to preparing monosized hydrophilic functional magnetic latex particles based on a two-step strategy using anionic iron oxide and cationic polymer latexes, the adsorption step was systematically investigated for a better control of the subsequent encapsulation step. The iron oxide nanoparticles were first obtained according to the classical precipitation method of ferric and ferrous chloride salt using a concentrated sodium hydroxide solution, whereas the polystyrene (PS), P(S/N-isopropylacrylamide (NIPAM)) core–shell and PNIPAM latexes were produced via emulsion and precipitation polymerizations, respectively. The polymer and inorganic colloids were then characterised. The adsorption of iron oxide nanoparticles onto the three types of polymer latexes via electrostatic interaction was studied as a function of iron oxide particle concentration, charge density and the cross-linking density of the hydrophilic layer. The maximum amounts of magnetic nanoparticles adsorbed onto the various latexes were found to increase in the following order: PS < P(S/NIPAM) < P(NIPAM). This significant difference is discussed by taking into account the charge distribution in the hydrogel layer and diffusion phenomena inside the cross-linked hydrophilic shell. Received: 28 December 1998 Accepted in revised form: 15 April 1999     

Stabilization centers in various proteins

Interactions among residues together with their interactions with the surrounding medium determine the unique structure of globular proteins. An algorithm was recently developed to locate residues participating in cooperative long-range interactions, called stabilization center residues, that are primarily responsible for preventing the decay of the 3D structure. While our statistical analysis showed that interactions of stabilization center residues hardly influence the formation of the various secondary structure elements, the distribution of the stabilization center residues is rather uneven among the secondary structure elements. Here we analyzed the frequency and distribution of the stabilization center residues and their interacting pairs in secondary structure classes to learn about the effect of secondary structure on the formation and properties of stabilization centers and about the types of interactions responsible for stabilization of proteins of various secondary structure classes. It was found that residues from the same secondary structure tend to interact with each other in the stabilization centers of all classes. It is also suggested that the folding-unfolding equilibrium is governed by different principles for class all-α than for the rest of the classes. Received: 24 April 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998     

Examining ligand-protein interactions with binding-energy landscapes

Binding-energy landscapes are used to investigate the thermodynamics of molecular recognition for the pteridine ring, a recognition anchor in binding with dihydrofolate reductase, and two molecules with the same shape but different heteroatom substitutions. The relative importance of hydrogen bonding and hydrophobic interactions in this system is analyzed by comparing these three different decorations of the pteridine scaffold. Received: 5 May 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998     

Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric

The conformational change associated with the interfacial activation of Rhizomucor miehei lipase involves the displacement of an α-helical lid (residues 82–96) away from the active site on moving from water (high dielectric) to lipid (low dielectric). The presence of two media of very different dielectric properties suggests that electrostatic interactions play an important role in this process. We have used linearized Poisson–Boltzmann calculations to examine the key electrostatic interactions which contribute to lid stability in the closed and open states. It is the two charged residues of the lid, Arg86 and Asp91, that form the strongest electrostatic interactions with the rest of the protein. We identify key residues whose interactions with the lid are significantly perturbed by the change in the dielectric of the medium: Asp61, Arg80, Lys109, Glu117 and the active-site residues Asp203 and Asp256, all of which lie within approximately 20 ? of the lid. We suggest that these residues are good candidates for site-specific mutation studies, which could help elucidate their role in the lipase activation mechanism. Received: 27 May 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998     

Grid-free DFT implementation of local and gradient-corrected XC functionals

Following an approach to density functional theory calculations based on the matrix representation of operators, we implemented a scheme as an alternative to traditional grid-based methods. These techniques allow integrals over exchange-correlation operators to be evaluated through matrix manipulations. Both local and gradient-corrected functionals can be treated in a similar way. After deriving all the required expressions, selected examples with various functionals are given. Received: 7 March 1998 / Accepted: 21 May 1998 / Published on line: 6 August 1998     

Contracted Gaussian-type basis functions revisited. III. Atoms K through Kr

Six minimal basis sets of contracted Gaussian-type functions (GTFs) are developed for the third-row atoms K through Kr. The smallest and largest sets for transition metal atoms are (3333/33/3) and (8433/84/8), respectively, where a slash distinguishes the s, p, and d symmetries and single-digit figures in the parentheses denote the numbers of primitive GTFs. The two largest sets, (7433/74/7) and (8433/84/8), surpass the (62111111/33111/311) set of Schaefer et al. in the associated total energies. Our (8433/84/8) set is also superior to their (842111/631/411) set. The quality of the present basis sets is tested by self-consistent field (SCF) and configuration interaction (CI) calculations on the Cu₂ molecule. As the accuracy of the basis set increases, SCF calculations show a decrease in the dissociation energy and an increase in the equilibrium internuclear distance. The same tendencies are found in the results of CI calculations with and without a Davidson correction. All the present basis sets are freely available at the internet address: http://202.35.198.41/∼htatewak/. Received: 17 June 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998     

Degenerate symmetry-adapted perturbation theory of weak interactions between closed- and open-shell monomers: application to Rydberg states of helium hydride

Symmetry-adapted perturbation theory is extended to the (quasi) degenerate, open-shell case. The new formalism is tested in calculations of the interaction energies for a helium atom in the ground state interacting with an excited hydrogen atom. It is shown that the method gives satisfactory results if the coupling with higher Rydberg states of the dimer is small, as is the case for the A²Σ⁺,B²Π,E²Π,3²Π, and 1²Δ states of HeH. For the C²Σ⁺ state convergence of the method is very slow, but it can be improved by including the n=3 states in the model space. Received: 3 June 1998 / Accepted: 9 September 1998 / Published online: 7 December 1998     

Multireference perturbation CI III. Fast evaluation of the one-particle density matrix

Within the frame of multireference perturbation configuration interaction we have developed a fast algorithm, based on diagrammatic techniques, for the calculation of the first-order correction to the one-particle density matrix. As an example of an application we have chosen the evaluation of the dipole moment of the CO molecule, where utilization of the first-order density is shown to corroborate the variational calculation. Received: 4 August 1998 / Accepted: 21 September 1998 / Published online: 16 November 1998     

Peptides in membranes: assessment of environmental effects via simulations using an implicit solvation model

A recently developed implicit solvation model is applied to Monte Carlo simulations of peptides in bilayer-mimetic and polar environments. The model employs the formalism of atomic solvation parameters and reproduces experimental data. Solvent effects on the␣structure of the following peptides were studied: 20-residue poly-Leu and poly-Val, transmembrane helix A of bacteriorhodopsin, magainin2. It was shown that a␣membrane-like environment considerably promotes α-helix formation (all the peptides were found to be α-helical), while simulations in water reveal helix distortion. Consistency of the results with experimental data and further implications of the model are discussed. Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Interaction energy anisotropy of the pyrrole dimer: ab initio theoretical study

The van der Waals pyrrole dimer is studied using supermolecular and perturbation ab initio treatment with inclusion of correlation energy. The influence of selected geometry variations on the interaction energy components is investigated. Our calculations verified the minimum on the potential energy surface deduced from microwave spectra. Its stability is possibly related not to the extremal values of the selected interaction energy contributions but its physical origin is connected with the delicate equilibrium between the repulsive and attractive forces. Any structure variation connected with the extremal attraction energy is more than compensated for by the repulsion energy. Received: 11 June 1998 / Accepted: 6 October 1998 / Published online: 1 February 1999     

Dynamics of the transmembrane domain of the ErbB-2 receptor

The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both in vacuum and within an explicit hydrated L-α-dilauroyl-phosphatidyl-ethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition occurs frequently within the α-helical transmembrane domain which converts to local π-helices. We show that the α-helix alteration does not depend upon the force field or initial side-chain conformations but is intimately related to the sequence. The membrane-like environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the appearance of a π-bulge is not an artifact of the vacuum approximation. The consequences of π-helix formation could be very huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar local structures are also observed experimentally. Received: 9 May 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998     

Computation of stationary points via a homotopy method

A homotopy method is presented that locates both minimizers and saddle points of energy functions in an efficient manner. In contrast to other methods, it makes possible the exploration of large parts of potential energy surfaces. Along a homotopy path stationary points of odd and even order occur alternately. A path tracing procedure requiring only gradients and at most one evaluation of the Hessian matrix is given. Test results on a model potential and three MINDO/3 potentials are reported. Received: 6 May 1996 / Accepted: 2 April 1998 / Published online: 23 June 1998     

Transition structures and exo/endo stereoselectivities of concerted [6 + 4] cycloadditions with density functional theory

Density functional theory transition structures were located for three concerted [6 + 4] cycloaddition reactions involving cis-hexatriene and butadiene, cyclopentadiene and cycloheptatriene, and cyclopentadiene and tropone. Geometries, energies, and entropies were computed at the Becke3LYP/6-31G* level. The activation energy of the concerted [6 + 4] cycloaddition of hexatriene and butadiene is 33.3 kcal/mol, about 8 kcal/mol above the activation energy of the butadiene plus ethylene [4 + 2] cycloaddition. The endo concerted [6 + 4] transition state is 1.1 kcal/mol higher than the exo. The [6 + 4] reaction of cyclopentadiene and cycloheptatriene has a barrier of 25.9 kcal/mol, while the cyclopentadiene–tropone barrier drops to 20.7 kcal/mol. Received: 3 December 1998 / Accepted: 18 February 1999 / Published online: 7 June 1999     

Possible long-lived quartet resonance states of CO−

Two states of CO⁻ which are expected to live longer than the well-known ²Π shape resonance are examined and the results obtained are compared with the analogous states of the isoelectronic N₂ ⁻ system. The ⁴Σ⁻ and ⁴Π states are found to be stable with respect to dissociation. The latter state is also stable with respect to single-electron loss to its parent neutral state. The lifetime of this state is supposed to be long, but not necessarily long enough to allow detection in a mass spectrometer. Received: 28 May 1998 / Accepted: 23 July 1998 / Published online: 9 October 1998     

A new “hydrophobic template” method detects segments forming transmembrane α-helical bundles in ion channels

We present a “hydrophobic template” method enabling recognition of α-helix bundles in membrane channels from sequence analysis. Inspection of hydrophobic properties of pore-forming helices in proteins with known structure (A-B₅ toxins) permits delineation of a common polarity motif: two hydrophobic surface stretches separated by polar areas. The bundles are stabilized by nonpolar interhelical contacts. A number of transmembrane segments were checked for presence of this motif, and it was detected for pore-forming helices of several ion transporters (segments M2 of acetylcholine and GABA_A receptors, α5 peptide of δ-endotoxin), which reveal five α-helix bundle architecture. Applications of the method to modeling of membrane channels are discussed. Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998