A practical procedure for the determination of electrostatic charges of large molecules

Summary A practical procedure for the precise determination of electrostatic charges, which are evaluated by fitting the rigorous quantum mechanical molecular electrostatic potential to a monopole-monopole expression, is presented. The proposal of this procedure arises from the study of the minimum requirements necessary to obtain reliable electrostatic charges. Such a study is focused on: (i) the dependence of the electrostatic charges on the set of points where the quantum mechanical and the monopole-monopole molecular electrostatic potentials are fitted; thus, both the influence of the number of points and their distribution in layers located out of the van der Waals radii of the atoms are examined, and (ii) the reliability of the use of fractional models for the evaluation of electrostatic charges of large molecules. Results point out that the optimum number of points is defined by a density of points ranging from 0.45 to 0.60 points/Ų when four layers (separated by 0.2 Å) are considered. Nevertheless, the use of only two layers (separated by 0.4 Å) for large molecules is recommended, thus enabling one to obtain reliable charges at a reduced computational cost. Moreover, results justify the use of fractional models for the determination of electrostatic charges of extremely large molecules, even when aromatic structures exist.     

Solvent effects on tautomerism equilibria in heterocycles

. High-level ab initio quantum mechanical methods have been used to analyze the tautomeric preferences in the gas phase and in aqueous solution of three important five-member heterocycles: 4-(5-)methylimidazole, 5-hydroxyisoxazole, and 3-hydroxypyrazole. Solvent effects have been introduced by means of self-consistent reaction field (SCRF) calculations at the ab initio level using our parametrized version of the polarizable continuum model developed by Miertus, Scrocco and Tomasi (MST), including geometry relaxation upon solvation. The extent to which the MST model, and SCRF methods in general, are suitable for the study of processes of this type is discussed.     

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives

The structure of parallel-stranded duplexes of DNA-containing a mixture of guanines (G) and adenines (A) is studied by means of molecular dynamics (MD) simulation, as well as NMR and circular dichroism (CD) spectroscopy. Results demonstrate that the structure is based on the Hoogsteen motif rather than on the reverse Watson-Crick one. Molecular dynamics coupled to thermodynamic integration (MD/TI) calculations and melting experiments allowed us to determine the effect of 8-amino derivatives of A and G and of 8-amino-2'-deoxyinosine on the stability of parallel-stranded duplexes. The large stabilization of the parallel-stranded helix upon 8-amino substitution agrees with a Hoogsteen pairing, confirming MD, NMR, and CD data, and suggests new methods to obtain DNA triplexes for antigene and antisense purposes.     

Synthesis of enantiopure trans-3,4-disubstituted piperidines. An enantiodivergent synthesis of (+)- and (-)-paroxetine

Reaction of (R)-phenylglycinol with methyl 5-oxopentanoate gave either bicyclic lactam cis-1 (the kinetic product) or its isomer trans-1 (under equilibrating conditions) as the major products, which were converted to the corresponding (cis or trans) unsaturated lactams 4 and 5. On treatment with lithium alkyl (or aryl) cyanocuprates, these chiral building blocks undergo conjugate addition to give enantiopure trans-3,4-substituted 2-piperidone derivatives in high yield and stereoselectivity. The synthetic potential of this transformation is illustrated by the synthesis of (+)-femoxetine and the two enantiomers of the known antidepressant paroxetine.     

Magnetic polyoxometalates: anisotropic exchange interactions in the moiety of [(NaOH2)Co3(H2O)(P2W15O56)2]17-

The magnetic exchange interactions in a C0(3)(11) moiety encapsulated in Na(17) [(NaOH(2))Co(3)(H(2)O)(P(2)W(15)O(56))(2)] (NaCo(3)) were studied by a combination of magnetic measurements (magnetic susceptibility and low-temperature magnetization), with a detailed Inelastic Neutron Scattering (INS) investigation. The novel structure of the salt was determined by X-ray crystallography. The ferromagnetic Co(3)O(14) triangular cluster core consists of three octahedrally oxo-coordinated Co(II) ions sharing edges. According to the single-ion anisotropy and spin-orbit coupling usually assumed for octahedral Co(II) ions, the appropiate exchange Hamiltonian to describe the ground-state properties of the isosceles triangular Co(3) spin cluster is anisotropic and is expressed as H = - 2sigma(alpha)(=)(x,y,z)(J(alpha)(12)S(1alpha)S(2alpha) + J(alpha)(23)S(2alpha)S(3alpha) + J(alpha)(13)S(1alpha)S(3alpha)), where J(alpha) are the components of the exchange interactions between the Co(II) ions. To reproduce the INS data, nonparallel anisotropic exchange tensors needed to be introduced, which were directly connected to the molecular symmetry of the complex. The following range of parameters (value +/- 0.5 cm(-1)) was found to reproduce all experimental information while taking magnetostructural relations into account: J(x)(12) = J(y)(13) = 8.6 cm(-1); J(y)(12) = J(x)(13) = 1.4 cm(-1); J(z)(12) = J(z)(13) = 10.0 cm(-1); J(x)(23) = J(y)(23) = 6.5 cm(-1) and = 3.4 cm(-1).     

Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility

The structure and dynamic properties of different antisense related duplexes (DNA x RNA, 2'O-Me-DNA x RNA, 2'F-ANA x RNA, C5(Y)-propynyl-DNA x RNA, ANA x RNA, and control duplexes DNA x DNA and RNA x RNA) have been determined by means of long molecular dynamics simulations (covering more than 0.5 micros of fully solvated unrestrained MD simulation). The massive analysis presented here allows us to determine the subtle differences between the different duplexes, which in all cases pertain to the same structural family. This analysis provides information on the molecular determinants that allow RNase H to recognize and degrade some of these duplexes, whereas others with apparently similar conformations are not affected. Subtle structural and deformability features define the key properties used by RNase H to discriminate between duplexes.     

Ab initio study of naphtho-homologated DNA bases

Naphtho-homologated DNA bases have been recently used to build a new type of size-expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naphtho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like forms of naphtho-thymine (yyT) and naphtho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naphtho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.     

Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian

The need to simulate large-sized molecules or to deal with large series of compounds is a challenging topic in computational chemistry, which has stimulated the development of accurate semiempirical methods, such as the recently reported Recife Model 1 (RM1; J Comput Chem 2006, 27, 1101). Even though RM1 may prove to be of value simply due to the enhanced quantitative accuracy in gas phase, it is unclear how the new parameters optimized for RM1 affect the suitability of this semiempirical Hamiltonian to study chemical processes in condensed phases. To address this question, we report the parametrization of the MST/RM1 continuum model for neutral solutes in water, octanol, chloroform and carbon tetrachloride, and for ions in water. The results are used to discuss the transferability of the solvation parameters implemented in previous MST/AM1 and MST/PM3 models.     

Biosynthesis of the cyclooligomer depsipeptide beauvericin, a virulence factor of the entomopathogenic fungus Beauveria bassiana

Beauvericin, a cyclohexadepsipeptide ionophore from the entomopathogen Beauveria bassiana, shows antibiotic, antifungal, insecticidal, and cancer cell antiproliferative and antihaptotactic (cell motility inhibitory) activity in vitro. The bbBeas gene encoding the BbBEAS nonribosomal peptide synthetase was isolated from B. bassiana and confirmed to be responsible for beauvericin biosynthesis by targeted disruption. BbBEAS utilizes D-2-hydroxyisovalerate (D-Hiv) and L-phenylalanine (Phe) for the iterative synthesis of a predicted N-methyl-dipeptidol intermediate, and forms the cyclic trimeric ester beauvericin from this intermediate in an unusual recursive process. Heterologous expression of the bbBeas gene in Escherichia coli to produce the 3189 amino acid, 351.9 kDa BbBEAS enzyme provided a strain proficient in beauvericin biosynthesis. Comparative infection assays with a BbBEAS knockout B. bassiana strain against three insect hosts revealed that beauvericin plays a highly significant but not indispensable role in virulence.     

Effect of oxide films on formation of Fe-rich intermetallic phases in aluminum alloys

Journal of Thermal Analysis and Calorimetry - The aim of the present work was to study the effect of the α-Al2O3 and MgAl2O4 oxide films, normally found in cast aluminum alloys, on formation...