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.     

Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes

Molecular dynamics and thermodynamic integration calculations have been carried out on a set of G-rich single-strand, duplex, triplex, and quadruplex DNAs to study the structural and stability changes connected with the guanine --> 6-thioguanine (G --> S) mutation. The presence of 6-thioguanine leads to a shift of the geometry from the B/A intermediate to the pure B-form in duplex DNA. The G --> S mutation does not largely affect the structure of the antiparallel triplex when it is located at the reverse-Hoogsteen position, but leads to a non-negligible local distortion in the structure when it is located at the Watson-Crick position. The G --> S mutation leads to destabilization of all studied structures: the lowest effect has been observed for the G --> S mutation in the reverse-Hoogsteen strand of the triplex, a medium effect has been observed in the Watson-Crick strand of the triplex and duplex, and the highest influence of the G -->S mutation has been found for the quadruplex structures.     

A new scaling procedure to correct semiempirical MEP and MEP-derived properties

Summary The MNDO, AM1, PM3, and ab initio 6–31G^* and 6–31+G^* MEPs for 21 neutral and 12 charged molecules were computed in layers ranging from 1.2 to 2.0 times the van der Waals radii of atoms. Semiempirical and ab initio MEPs for each layer and two groups of layers were compared to gain insight into the relationships between semiempirical and ab initio MEPs. A detailed statistical study allowed us to obtain a new set of scaling coefficients able to correct the semiempirical MEPs to provide better representations of the ab initio values. The corrected semiempirical MEPs were used to obtain electrostatic charges, whose quality was tested by the comparison between semiempirical Coulombic MEPs and ab initio quantum mechanical MEPs.     

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).     

Combined PIXE and X‐ray diffraction analysis of accretionary lapilli from the Cretaceous/Paleogene boundary El Guayal Section,Tabasco, Mexico

By employing the techniques, X‐ray powder diffraction (XRPD) and particle‐induced X‐ray emission (PIXE), it could be obtained in a simply way an overall vision of the structure and chemical composition of a spheroid (lapillus) collected in the K/Pg deposit located at the place called El Guayal in Tabasco, Mexico. The XRPD analysis indicates the presence of an amorphous and four crystalline phases (quartz, calcite, ankerite, and montmorillonite) in the spheroid. None sulfur crystalline phases were detected. PIXE results show the presence of different atoms in a weight percentage that follows the sequence: Si > Al > Ca > Fe > Sr > Cu > Ti > Mn > Y > Rb > Zn > Pb. None of platinum group elements were detected. PIXE analysis by of the lapillus shows the presence of the most abundant atoms in the Earth's crust, but in this case, the relative abundance Fe‐Ca is inverted, and the Sr/Rb proportion is considerably higher than that observed in the crust. Additionally, nor sulfur or any of the platinum group elements was detected in the lapillus. Except for the case of trace elements detected, in general, no characteristic pattern is observed in the distribution of the most abundant elements. Copyright © 2015 John Wiley & Sons, Ltd.     

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.