Medium-size polarized basis sets for high-level-correlated calculations of molecular electric properties

Summary The first-order polarized basis sets for the use in high-level-correlated investigations of molecular electric properties have been generated for Pb, Bi, Po, and At. The performance of the standard [10.17.14.5/13.11.8.2] and extended [20.17.14.9/13.11.8.4] basis sets has been examined in nonrelativistic and quasirelativistic calculations for atoms and simple closed-shell hydrides. The relativistic contributions to electric dipole properties of those systems have been evaluated by using the recently developed quasirelativistic scheme. The predicted dipole polarizability of At is in good agreement with the results of other relativistic calculations. The calculated quasirelativistic dipole moments of BiH₃ (–0.499 a.u.), PoH₂ (–0.207 a.u.), and AtH (+0.036 a.u.) involve a significant relativistic contribution which amounts to —0.230 a.u., –0.177 a.u., and –0.097 a.u., respectively. The basis set details append this paper. They are also available as a part of the basis set library of the MOLCAS system.     

Synthesis and characterisation of PEG-peptide surfaces for proteolytic enzyme detection

Peptide surfaces were obtained by the covalent immobilisation of fluorescently labelled pentapeptides carboxyfluorescein–glycine–arginine–methionine–leucine–glycine, either directly or through a poly(ethylene glycol) (PEG) linker on modified silicon wafers. Each step during the preparation of the peptide surfaces was confirmed by several surface characterisation techniques. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy were used to determine the surface composition, the wafers philicity was measured by contact angle and atomic force microscopy was used to investigate the surface morphology. Exposure of the peptide surfaces to trypsin resulted in the release of a fluorescently labelled peptide product, which allowed the kinetics of the enzymatic reaction to be followed with the aid of fluorescence spectroscopy. The electrospray ionisation mass spectrometry analysis of the post-digestion solution confirmed that the pentapeptides attached to the solid support undergo specific trypsin hydrolysis at the C-terminus of the arginine residues. Detailed surface analyses before and after the enzyme action was performed using ToF-SIMS. Because of the limited accessibility of the short peptide directly attached to the surface, a quantitative yield of enzymatic hydrolysis was observed only in case when the peptide was bound through the PEG linker. The insertion of the PEG linker increased the number of immobilised peptides and the rate of enzymatic digestion which consequently improved the quality of the enzyme assays. The described approach may be used for different peptide sequences designed for other proteases.

Morphology and molecular organisation of liquid-crystalline perylene-3,4,9,10-tetra-(n-hexylester) deposited on a solid substrate

Liquid-crystalline perylene-3,4,9,10-tetra-(n-hexylester) forms characteristic dendritic or flower-like structures at room temperature when it is deposited on a hydrophilic glass substrate using the zone-casting technique. It was found that such unique structures were not possible to be created simply by recrystallisation of this dye from a liquid-crystalline columnar phase. On the basis of the observations using a confocal microscope and the study of wide angle X-ray scattering (WAXS) as well as the analysis of the absorption and fluorescence spectra, some conclusions, concerning the molecular organisation in the dendritic structure, are drawn. Based on the research, one can assume that the dendrites are formed by columnar molecular aggregates with the column axes parallel to the substrate. Such an organisation of the molecules can be interesting from the point of view of organic electronics.     

Radical processes initiated by ionizing radiation in PEEK and their macroscopic consequences

Poly (ether ether ketone) was irradiated with gamma rays or electron beam to investigate the radical process. The generated paramagnetic species were observed by electron spin resonance spectroscopy at ambient temperature and in liquid nitrogen. The effect of microwave power on saturation of the particular spectra and thermal annealing effects were determined. The following radicals were identified: radical anion, phenoxyl radical, and phenylperoxy radical. Despite the fact that the intermediates were formed as a result of backbone cleavage causing degradation, the macroscopic features were almost unaffected by irradiation up to dose of 1500 kGy.     

Chiral molecular glass: synthesis and characterization of enantiomerically pure thiophene-based [7]helicene

Synthesis of thiophene-based [7]helicenes, which are functionalized for both design of organic chiral glasses with strong chiroptical properties and for further homologation to higher [n]helicenes, is reported. The key synthetic transformations are kinetic resolution of the intermediate diketone and the annelation step forming the center benzene ring by means of an intramolecular McMurry reaction. Based upon X-ray crystallographic determinations of the absolute configurations for (+)-enantiomers of the diketone and the [7]helicene, stereochemical correlation between the (R) axial chirality of the diketone and the (M) helical chirality of the [7]helicene is established. One such enantiopure trimethylsilyl-substituted [7]helicene possesses enchanced chiroptical properties and forms a chiral molecular glass.     

Methane-to-methanol oxidation by the hydrated iron(IV) oxo species in aqueous solution: a combined DFT and car-parrinello molecular dynamics study

Previously, we have shown that the ferryl ion ([FeIVO]2+) is easily produced from Fenton's reagent (i.e., a mixture of Fe2+ ions and H2O2 in aqueous solution), using DFT and Car-Parrinello MD calculations. To verify that the ferryl ion can indeed act as the active species in oxidation reactions with Fenton's reagent, we study in the present paper the reactivity of the ferryl ion toward an organic substrate, in particular the oxidation of methane to methanol. In the first part of this paper, we perform static DFT calculations on the reaction of CH4 with the [(H2O)5FeIVO]2+ complex in vacuo that show a strong prevalence of the oxygen-rebound mechanism over the methane coordination mechanism. This is in agreement with the static DFT results for methane oxidation by biocatalysts MMO and P450, but not with those for methane oxidation by bare metal-oxo ions, where the methane coordination mechanism prevails. The highest energy barrier in the oxygen-rebound mechanism is only 3 kcal/mol in vacuo, whereas in the methane coordination mechanism the highest barrier is 23 kcal/mol. Overall the oxidation reaction energy is downhill by 47 kcal/mol. We conclude that the ferryl ion can indeed act as the oxidative intermediate in the Fenton oxidation of organic species. In the second part of this paper, we perform a preliminary assessment of solvent effects on the oxidation by the ferryl ion in aqueous solution using the method of constrained (first principles) molecular dynamics. The free energy barrier of the H-abstraction reaction from methane by the ferryl ion (i.e., the first step in the rebound mechanism) in aqueous solution is, with 22 kcal/mol in solution, significantly higher than in vacuo. Given the fact that methane has a relatively strong C-H bond (ca. 10 kcal/mol stronger than the C-H bonds in the more typical Fenton's reagent substrates), we infer that for many organic substrates oxidation with the ferryl ion as an active intermediate may be a perfectly viable route.     

Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala-->Lac

A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.     

Monomer basis-set truncation effects in calculations of interaction energies: A model study

Supermolecular interaction energies are analyzed in terms of the symmetry-adapted perturbation theory and operators defining the inaccuracy of the monomer wave functions. The basis set truncation effects are shown to be of first order in the monomer inaccuracy operators. On the contrary, the usual counterpoise correction schemes are of second order in these operators. Recognition of this difference is used to suggest an approach to corrections for basis-set truncation effects. Also earlier claims--that dimer-centered basis sets may lead to interaction energies free of basis-set superposition effects--are shown to be misleading. According to the present study the basis-set truncation contributions, evaluated by means of the symmetry-adapted perturbation theory with monomer-centered basis sets, provide physically and mathematically justified corrections to supermolecular results for interaction energies.