Theoretical pKa calculations of proteins; the tyrosine and lysine residues of b-elicitin

Elicitins are small proteins that are secreted by plant pathogenic fungi. In this work we have used a computer program that utilizes the boundary element method for heterogeneous dielectrics with ionic strength to calculate the pK _a of all titrating groups in the 98-residue protein β-cryptogein. Our results are in reasonable agreement with the experimentally determined pK _a values for the Tyr residues in the protein. We find that the functionally important Lys13 residue has a normal pK _a of 10.3. Our work also shows that there is no direct correlation between the exposure of an amino acid sidechain and its pK _a. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 11 November 1998     

Calculation of ground- and excited-state potential energy curves for barium-rare gas complexes in a pseudopotential approach

Adiabatic potential curves for the ground state and several low-lying excited states of the barium atom interacting with Ne, Ar, Kr and Xe have been obtained from valence ab initio configuration-interaction calculations. Atomic cores are replaced by scalar-relativistic l-dependent pseudopotentials, while core-polarization potentials are used for describing correlation contributions of the rare-gas atoms and the Ba²⁺ cores. Implications of the resulting potential curves for the interpretation of experimental data are discussed, together with first applications of the curves for calculating absorption profiles of the (6s ²)¹S→(6p)¹P Ba transition. Received: 7 April 1998 / Accepted: 27 July 1998 / Published online: 12 October 1998     

Molecular dynamics simulation in aqueous solution of N-methylazetidinone as a model of β-lactam antibiotics

In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having similar energy barriers at the rate-limiting step of the reaction path. In the first type, the β-lactam-water interaction takes place through the oxygen carbonyl atom and there is agreement between the maxima of the RDFs obtained here and the ab initio structure of the complexes previously reported. In the second type, the interaction takes place through the nitrogen atom and we do not predict a coordination layer around the β-lactam nitrogen atom. The results suggest that in aqueous solution hydrolysis of the carbonyl group is the most probable starting point for the overall hydrolysis reaction. Some discussion on the use of cluster models to represent the solvent effect is included. Received: 29 July 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999     

Transition state structure invariance to model system size and calculation levels: a QM/MM study of the carboxylation step catalyzed by Rubisco

The present study elucidates structural features related to the molecular mechanism in the carboxylation step of the reaction catalyzed by Rubisco. Starting from the initial X-ray Protein Data Bank structure of a Rubisco monomer, the reactive subsystem in vacuo is subjected to quantum chemical semiempirical and ab initio studies, while the effects of the protein environments are included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. The QM/MM is used to characterize the transition structure for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme. Comparisons between the in vacuo and in situ transition structures show remarkable invariance with respect to geometric parameters, index and transition vector amplitudes. The transition state couples the carbon dioxide attack to the C2 center of the substrate in its dienol form with a simultaneous intramolecular hydrogen transfer from the C2 atom to the hydroxyl group linked to the C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 center in the enzyme. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Density functional study on zerovalent lanthanide bis(arene)-sandwich complexes

Several zerovalent lanthanide bis(arene)-sandwich complexes, Ln(η⁶-C₆H₆)₂, Ln = La, Ce, Eu, Gd and Lu, have been studied by means of density functional theory. The calculated geometries are in good agreement with experiment. The calculated dissociation energies of the bond Ln-(η⁶-C₆H₆) may be considerably underestimated, but they correctly reveal the variation regularity. The bonding in these molecules can be described in terms of a relatively weak π-electron donation from benzene to Ln and a stronger electron back-donation from Ln 5d to the benzene π* orbitals. During bond formation, there is electron promotion from Ln 6s to 5d instead of from 4f to 5d, in opposition to the proposal of Anderson et al. The relativistic effect only slightly influences the molecular geometry, but decreases the bonding energy considerably through lowering the Ln 6s level and raising the 5d level. It enhances the trend of the bonding energy to decrease along the lanthanide series. Received: 22 June 1998 / Accepted: 9 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     

Ab initio MO study of ethylene insertion into the Sm–C bond of H2SiCp2SmCH3

Ethylene insertion into the Sm–C bond of H₂SiCp₂SmCH₃, a model reaction of an olefin polymerization propagation step, has been studied by ab initio molecular orbital methods. The small electronegativity of the Sm atom makes the Sm–C bond ionic, the methyl group being negatively charged by −0.75. The reaction passes through a loose ethylene complex with a binding energy of 15 kcal/mol and then a tight four-centered transition state with an agostic interaction between the Sm atom and one of the methyl CH bonds. A small activation energy of 14 kcal/mol is required to pass through this transition state, indicating that this is an easy reaction. Compared with the reactions with group 4 cationic silylene-bridged metallocenes the activation energy is higher and the reaction is less exothermic. The origin of these differences is discussed. The results of molecular mechanics calculations on regio- and stereoselectivities in the insertion reaction of propylene are also reported. Received: 13 July 1998 / Accepted: 28 August 1998 / Published online: 2 November 1998     

Weighted HOMO-LUMO energy separation as an index of kinetic stability for fullerenes

A very simple but general index of kinetic stability, T, is proposed for π-electron systems, which is defined as a highest occupied molecular orbital (HOMO)- lowest unoccupied molecular orbital (LUMO) energy separation multiplied by the number of conjugated atoms. This new index can be justified by relating it to the approximate form of the superdelocalizability, an index of chemical reactivity defined by Fukui et al. It is best suited for predicting the kinetic stability of fullerenes. All isolable fullerene isomers have T values larger than 13. Received: 24 June 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998     

META 4. Prediction of the metabolism of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and are often implicated as potential carcinogens. It is generally believed that the carcinogenic potential of polycyclic aromatic hydrocarbons is linked to the formation of ultimate carcinogens generated by metabolic biotransformations. In this paper we propose a methodology that consists of using both quantum chemical properties and structural features of the reaction sites to predict PAH metabolism. Two essential questions have been answered: at which sites will the reaction take place and does the transformation consist of epoxidation or hydroxylation? This methodology has been successfully implemented into an expert system, META, for the evaluation of metabolic transformations of new chemicals. Received: 3 April 1998 / Accepted: 6 July 1998 / Published online: 7 October 1998     

Bis-periazulene: a simple Kekulé biradical with a triplet ground state

B3LYP/6-31G* calculations on bis-periazulene (cyclohepta[def]-fluorene) predict a triplet ground state for this molecule. The singlet has an aromatic 14π-electron periphery but is 2 kcal/mol higher in energy. The results agree with earlier predictions by Heilbronner. Received: 19 August 1998 / Accepted: 6 October 1998 / Published online: 23 February 1999     

Density functional study of ethylene oxidation on an Ag(111) surface

The mechanism of ethylene epoxidation on Ag surfaces has been investigated using the density functional method and Ag _n clusters (n = 3 to 10) modeling the Ag(111) surface. The adsorption energy of O₂ to the Ag clusters was strongly dependent on the HOMO level of the cluster, and the clusters with higher HOMO levels afforded larger O₂ adsorption energies. The energetics was investigated for both the molecular and atomic oxygen epoxidation mechanisms. For the atomic oxygen mechanism, epoxidation was found to proceed without an activation energy, whereas a small amount of activation energy (about 5 kcal/mol) was calculated for the molecular oxygen mechanism. Received: 2 July 1998 / Accepted: 9 September 1998 / Published online: 8 February 1999     

Chemical potential inequality principle

Regional density functional theory has been extended to treat irreversible thermodynamic electronic processes for application to adiabatic electron-transfer processes of chemical reactions. Onsager's local equilibrium hypothesis is slightly modified to take into account the quantum mechanical nature of the electron. The quantum mechanical interference effect has been demonstrated to be included in the entropy production rate formula associated with electron transfer through an interface. A new formula for the determination of the transition state of a chemical reaction has been postulated that corresponds to the maximum of the regional electron transferability. A quantum mechanical law of mass action has been established and applied to prove the regional electrochemical potential inequality principle. Received: 1 July 1998 / Accepted: 2 September 1998 / Published online: 8 February 1999     

An implementation of the conductor-like screening model of solvation within the Amsterdam density functional package

The conductor-like screening model (COSMO) of solvation has been implemented in the Amsterdam density functional program with maximum flexibility in mind. Four cavity definitions have been incorporated. Several iterative schemes have been tested for solving the COSMO equations. The biconjugate gradient method proves to be both robust and memory-conserving. The interaction between the surface charges and the electron density may be calculated by integrating over either the fitted or exact density, or by calculating the molecular potential. A disk-smearing algorithm is applied in the former case to avoid singularities. Several self-consistent field/COSMO coupling schemes were examined in an attempt to reduce computational effort. A gradient-preserving algorithm for removing outlying charge has been implemented. Preliminary optimized radii are given. Applications to the benzene oxide-oxepin valence tautomerization and to glycine conformation are presented. Received: 13 November 1998 / Accepted: 16 December 1998 / Published online: 16 March 1999     

Electron affinities, excitation energies and ionization potentials of the transition metals (I) Sc and Ti

The electron affinities of the Sc and Ti atoms have been obtained by configuration interaction calculations. Energy convergence with respect to the systematic expansion of both the one-electron basis set and the configuration space was investigated for valence electrons, and the inclusion of correlation contributions from core electrons and relativistic effects gave the electron affinities of 0.181 eV and 0.163 eV for Sc and Ti, respectively. These are in excellent agreement with the observed values of 0.189 ± 0.020 eV and 0.080 eV. The same approach was applied for the first excited states and positive ions of both atoms. Excellent agreement with the experimental results was also obtained for these states. Received: 16 February 1998 / Accepted: 2 April 1998 / Published online: 23 June 1998     

A theoretical study on the first ionic states of vinyl fluoride, vinyl chloride, trifluoroethylene, and trichloroethylene with an analysis of the vibrational structures of the photoelectron spectra

Ab initio calculations have been performed to study the molecular structures and the vibrational levels of the first ionic states of vinyl fluoride, vinyl chloride, trifluoroethylene, and trichloroethylene. The equilibrium molecular structures and vibrational modes of these states are presented. The theoretical ionization intensity curves including the vibrational structures are also presented and compared with the photoelectron spectra. Received: 11 September 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999     

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     

Pseudopotential study of the ground and excited states of Yb2

The ground state of the van der Waals-type lanthanide dimer Yb₂ has been studied by means of relativistic energy-consistent ab initio pseudopotentials using three different core definitions. Electron correlation was treated by coupled-cluster theory, whereby core-valence correlation effects have been accounted for either explicitly by correlating the energetically highest coreorbitals or implicitly by means of an effective core-polarization potential. Results for the first and second atomic ionization potentials, the atomic dipole polarizability, and the spectroscopic constants of the molecular ground state are reported. Low-lying excited states have been investigated with spin-orbit configuration interaction calculations. It is also demonstrated for the whole lanthanide series that correlation effects due to the atomic-like, possibly open 4f-shell in lanthanides can be modeled effectively by adding a core-polarization potential to pseudopotentials attributing the 4f-shell to the core. Received: 3 April 1998 / Accepted: 27 July 1998 / Published online: 9 October 1998     

Ab initio molecular orbital study of the flavin-catalyzed dehydrogenation reaction of glycine - protein transport channel driving hydride-transfer mechanism

The reaction mechanism of flavin-catalyzed dehydrogenation of glycine has been studied by ab initio molecular orbital calculations using the 6-31G* basis set. 10-Methyl isoalloxazine (10-MIA) has been used as the flavin model compound. The results showed that when we assume a proton transport channel in amino acid oxidase, which is switched on by the substrate anion, the O12-protonated 10-MIA [10-MIAH⁺(O12)] is generated. The main structure of 10-MIAH⁺(O12) is one in which the central ring is expressed by an NAD⁺-like structure, which is favorable for driving the hydride-transfer reaction, i.e., the abstraction of the α-hydrogen of glycine by the hydride-transfer mechanism. We have found that this protonation results in a dramatic lowering of the activation energy of the reaction. The proposed mechanism is summarized as follows: the hydride transfer proceeds via two-electron transfer and synchronous intramolecular proton transfer → intermolecular proton transfer. Received: 10 August 1998 / Accepted: 17 September 1998 / Published online: 8 February 1999     

Theoretical study of group 11 metal–silonyl complexes: M–SiO and M–(SiO)2 (M = Cu, Ag, or Au)

 The spectroscopic properties of M–SiO and M–(SiO)₂ (1–1 and 1–2 complexes with M = Cu, Ag, or Au) have been theoretically studied. It has been shown that both M–SiO and M–(SiO)₂ compounds in their ground state are bent with a metal–Si bonded structure. The calculated M(ns) spin density agrees well with the electron spin resonance experimental data. From a topological analysis, it has been shown that a rather large charge transfer occurs from the metal towards the SiO moiety, and that the M–Si bond energy correlates with the electron density located at the M–Si bond path (bond critical point). Received: 6 July 2000 / Accepted: 11 October 2000 / Published online: 19 January 2001     

A statistical analytical approach to predict the secondary structure of proteins from amino acid sequence information

A statistical analytical approach has been used to analyze the secondary structure (SS) of amino acids as a function of the sequence of amino acid residues. We have used 306 non-homologous best-resolved protein structures from the Protein Data Bank for the analysis. A sequence region of 32 amino acids on either side of the residue is considered in order to calculate single amino acid propensities, di-amino acid potentials and tri-amino acid potentials. A weighted sum of predictions obtained using these properties is used to suggest a final prediction method. Our method is as good as the best-known SS prediction methods, is the simplest of all the methods, and uses no homologous sequence/family alignment data, yet gives 72% SS prediction accuracy. Since the method did not use many other factors that may increase the prediction accuracy there is scope to achieve greater accuracy using this approach. Received: 4 May 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998