Solvent effects on electron-driven proton-transfer processes: adenine-thymine base pairs

Time-Dependent Density Functional Theory (TD-DFT) computations, with M05-2X and PBE0 functionals, have been employed for a detailed study of the Electron-Driven Proton-Transfer (PT) processes in an Adenine-Thymine Watson-Crick Base Pair in the gas phase and in solution, with the bulk solvent described by the polarizable continuum model. In the gas phase, TD-DFT computations predict that the Adenine → Thymine Charge Transfer (CT) excited state undergoes a barrierless PT reaction, in agreement with CC2 computations (S. Perun, A. Sobolewski, W. Domcke, J. Phys. Chem. A, 2006, 110, 9031.). The good agreement between the TD-DFT approach and CC2 results validates the former for the studies of excited state properties, excited state proton transfer reaction, and deactivation mechanisms in the DNA base pairs. Next, it is shown that inclusion of solvent effects significantly influences the possibility of both barrier-less excited state proton transfer and radiation-less deactivation through conical intersection with the ground state, affecting the energy of the CT excited state in the Franck-Condon region, the energy barrier associated to the PT process and the energy gap with the ground electronic state. These findings clearly indicate that environmental effects, with a special attention to proper treatment of dynamical solvation effects, have to be included for reliable computational analysis of photophysical and photochemical processes occurring in condensed phases.     

Metal-metabolomics of microalga Chlorella sorokiniana growing in selenium- and iodine-enriched media

The microalga Chlorella sorokiniana has been used to accumulate selenium and iodine from culture media enriched with these elements as a first stage in the production of supplemented foods. The microalgal colony was grown in a conventional culture medium containing iodine (KI) at concentrations in the range of 150?C4000 ??g mL^?1. Similar experiments were performed with selenium (SeO ₄ ^2? ) at concentrations in the range of 20?C500 ??g mL^?1. The concentration of iodine and selenium in the culture medium was analytically monitored daily and the viability of the colony was checked by biomass concentration measurement and by evaluation of the total content of chlorophyll and carotenoids. In addition, photosynthetic activity and the number of cells were also monitored. Iodine accumulation in the algal biomass increased rapidly with time and reached a steady state after 4 h of exposure. With Se exposure the colony viability decreased, although the culture grew well with concentrations of the element of 50 ??g mL^?1 in the culture medium; this experiment produced Se-enrichment in the alga (3 ??g g^?1) within 100 h. Sequential extraction of an algal pellet was performed in order to separate Se compounds according to their affinity with the following solvents: hot water to recover low molecular mass Se species, enzymatic extraction with driselase for species associated with the cell wall, sodium dodecyl sulphate (SDS) for water insoluble selenoproteins and, finally, enzymolysis with lipase and pronase that release and fragment residual selenoproteinsproducing compounds with low molecular mass. Size-exclusion chromatography (SEC) coupled with an ICP-MS detector showed the preponderance of Se-containing molecules with low molecular mass, possibly seleno-amino acids. Only a peak of low intensity located at 10 min was observed in the SDS extract that could be associated with a protein with molecular mass of 67 kDa. Finally, analysis of the aqueous extract of alga by reverse-phase chromatography with inductively-coupled plasma mass-spectrometry (RPC-ICP-MS) detection revealed the presence of selenocysteine (SeCys₂), selenomethylselenocysteine (SeMetSeCys), selenomethionine (SeMet), and Se(VI), particularly the last two species.     

Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)(n) polypeptides

The importance of vicinal and long-range interresidue effects in determining the stability of the collagen triple helix has been investigated by quantum mechanical (QM) and molecular mechanical (MM) computations on suitable model polypeptides, taking into account solvent effects by the polarizable continuum model (PCM). At the QM level, the PII conformation corresponds to an energy minimum for pentapeptide analogues incorporating the sequence Gly-Pro-Pro-Gly, irrespective of the down or up puckering of the pyrrolidine ring. However, our computations indicate that the alternation of down and up prolines characterizing collagen and collagen-like peptides is not due to an intrinsic preference of the Pro-Pro-Gly sequence. This result is confirmed by MM computations of longer polypeptides. Next, MM computations on model triple helices show that a better packing is obtained for specific values of backbone dihedrals, which, in turn, favor the alternation of down and up prolines along each chain.     

Determination of the substituent effect on the O-H bond dissociation enthalpies of phenolic antioxidants by the EPR radical equilibration technique

The bond dissociation enthalpies (BDE) of several phenols containing electron-withdrawing substituents in the para position have been determined by means of the EPR radical equilibration technique. It has been found that CN, NO(2), CHO, COOR, and COOH induce an increase of the BDE value of the O-H bond, thus producing a worsening of the antioxidant activity of phenols, while Cl, Ph, and CH[double bond]CHPh show an opposite effect. The contributions of these substituents for the calculation of the BDE values in polysubstituted phenols by using the group additivity rule have also been derived. It is shown that this rule provides quite reliable predictions of bond strengths, so that the method can be conveniently used to estimate new data on substituted phenols.     

DFT description of the magnetic properties and electron localization in dinuclear di-mu-oxo-bridged manganese complexes

Density functional theory (DFT) was applied to describe the magnetic and electron-transfer properties of dinuclear systems containing the [MnO2Mn]n+ core, with n=0,1,2,3,4. The calculation of the potential energy surfaces (PESs) of the mixed-valence species (n=1,3) allowed the classification of these systems according to the extent of valence localization as Class II compounds, in the Robin-Day classification scheme. The fundamental frequencies corresponding to the asymmetric breathing vibration were also computed.     

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: glycyl radical as a case study

An integrated quantum mechanical approach for the structural and magnetic characterization of flexible free radicals in solution has been applied to a model of the glycyl radical engaged in peptidic chains. The hyperfine couplings computed using hybrid density functionals and purposely tailored basis sets are in good agreement with experiment when vibrational averaging effects from low frequency motions and solvent effects (both direct H bonding and bulk) are taken into the proper account. The g tensor shows a smaller dependence on the specific form of the density functional, the extension of the basis set over a standard double-zeta+polarization level, vibrational averaging, and bulk solvent effects. However, hydrogen bridges with solvent molecules belonging to the first solvation shell play a significant role. Together with their intrinsic interest, our results show that a comprehensive and reliable computational approach is becoming available for the complete characterization of open-shell systems of biological interest in their natural environment.     

Thiazolidin-4-one formation. Mechanistic and synthetic aspects of the reaction of imines and mercaptoacetic acid under microwave and conventional heating

Microwave irradiation of a mixture of benzylidene-anilines and mercaptoacetic acid in benzene gives 1,3-thiazolidin-4-ones in very high yield (65-90%), whereas the same reaction performed through using the conventional method, at reflux temperature, requires a much longer time and gives a much lower yield (25-69%). This difference seems to be due to some intermediates and by-products formed during the conventional reaction. On the basis of 1H NMR studies, two different mechanisms, acting in benzene and in DMF, respectively, have been hypothesized for the thiazolidin-4-one system formation.     

Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution

The conformational behavior of the title compounds has been investigated by Hartree-Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed gamma turn (gammal), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4-0.5 kcal/mol for helical structures and about 2 kcal/mol for gammal structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for gammal structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation.     

Phase equilibrium measurements for semi-clathrate hydrates of the (CO2 + N2 + tetra-n-butylammonium bromide) aqueous solution system

The application of semi-clathrate hydrate formation technology for gas separation purposes has gained much attention in recent years. Consequently, there is a demand for experimental data for relevant semi-clathrate hydrate phase equilibria. In this work, semi-clathrate hydrate dissociation conditions for the system comprising mixtures of {CO₂ (0.151/0.399 mole fraction) + N₂ (0.849/0.601 mole fraction) + 0.05, 0.15, and 0.30 mass fraction tetra-n-butylammonium bromide (TBAB)} aqueous solutions have been measured and are reported. An experimental apparatus which was designed and built in-house was used for the measurements using the isochoric pressure-search method. The range of conditions for the measurements was from 277.1 K to 293.2 K for temperature and pressures up to 16.21 MPa. The phase equilibrium data measured demonstrate the high hydrate promotion effects of TBAB aqueous solutions.     

Implementation and validation of the Lacks-Gordon exchange functional in conventional density functional and adiabatic connection methods

We present an analysis of the numerical performances of the exchange functional proposed by Lacks and Gordon, which we have implemented in the Gaussian series of programs. This functional has been built with the double aim of respecting most of the known scaling and asymptotic properties and of giving good numerical performances, especially as concerns noncovalent interactions. We have found that the coupling of the Lacks-Gordon exchange and Lee-Yang-Parr correlation functionals provides a reliable conventional density functional approach. The corresponding parameter-free adiabatic connection model, in which the ratio between Hartree-Fock and Lacks-Gordon exchange is determined a priori from purely theoretical considerations, allows us to obtain remarkable results for both covalent and noncovalent interactions in a satisfactory theoretical scheme, encompassing the free electron gas limit and most of the known scaling conditions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 418–429, 1998