The molecular electrostatic potentials for the nucleic acid bases: Adenine, thymine, and cytosine

Bonaccorsi, Rosanna; Pullman, Alberte; Scrocco, Eolo; Tomasi, Jacopo

doi:10.1007/bf00528310

Cited by 190 publications

(62 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In agreement with previous results [31], the MEP presents four minima with similar energy (-60 kcal/mol), associated with the lone pairs of the two carbonyl oxygens attached to C2 and C4, respectively. Regarding the maxima of the MEP, as can be seen in Figure 2(a), there are, principally, three dark regions to the map.…”

Section: Thyminesupporting

confidence: 90%

Molecular polarization potential maps of the nucleic acid bases

Alkorta

Pérez²

1996

Int. J. Quantum Chem.

167

View full text Add to dashboard Cite

-Ab initio calculations at the SCF level were carried out to compute the polarization potential map (MPP) of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine. For this purpose, the Dunning's 9s5p basis set contracted to a split-valence, was selected to perform the calculations. The molecular polarization potential (MPP) at each point was elaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (MEP) at that p2int. MEPS and MPPS for the different molecules were computed with a density of 5 points/A* on the van der Waals surface of each molecule, defined using the van der Waals radii. Due to the symmetry of the molecules, only half the points were computed. The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, have been focused on the properties of the isolated molecules. Thus, a suite of properties for the free bases have been computed in the past, including equilibrium geometries and relative energies of the different tautomers [l-161, electronic properties like charge density 117-191, dipole moments and polarizabilities [201, hydrophobicity profiles [21], pK,'s [221, absorption spectra 1231, and, more re-

show abstract

Section: Thyminesupporting

confidence: 90%

Molecular polarization potential maps of the nucleic acid bases

Alkorta

Pérez²

1996

Int. J. Quantum Chem.

167

View full text Add to dashboard Cite

show abstract

“…The constancy of the geometrical parameters in this interaction in the range of complexes studied [Cu-N(3)Av~ 1.99 (1), 1.979 (3) A in this study; Cu...O(2)Aw 2.77 (1), 2.819 (3) A in this study; angle Cu...O(2)-C(2)AVV 76 (1) °, 75"5 (2) ° in this study] suggests that this type of interaction may be specific for square-planar copper(II) complexes of cytosine (cytidine) and may play some role in the recognition of cytosine residues in nucleic acids by copper(II). Furthermore, there would seem to be some theoretical justification for the semi-chelation of cytosine (cytidine) to Cu(II) ions: a molecular electrostatic potential calculation for cytosine (Bonaccorsi, Pullman, Scrocco & Tomasi, 1972) shows that the presence of the carbonyl group, C(2)-O(2), adjacent to the pyrimidine nitrogen, N(3), establishes a wide attractive region for electrophilic agents with two deep minima, one in the direction of the lone pair at N(3) and one at an angle of 55 ° to the C(2)-O(2) bond. The minima at N(3) and 0(2) are deeper than similar sites in adenine or thymine, respectively, and the simultaneous interaction of Cu(II) ions with N(3) and 0(2) may be thought of then as a natural consequence of the electrostatic potential distribution inherent to the cytosine framework.…”

Section: Discussionmentioning

confidence: 99%

[(Glycylglycinato)(cytosine)copper(II)]. A model for enzyme–metal–nucleic acid ternary complexes

Kistenmacher¹,

Szalda²,

Marzillï³

1975

Acta Crystallogr Sect B

View full text Add to dashboard Cite

show abstract

“…In contrast, that angle is restricted to -85" in chelates. Pullman and co-workers (29) have calculated an, electrostatic molecular potential-energy map for cytosine. They have predicted maximum basicity at 55" from the C=O bond.…”

Section: Role Of Exocyclic Groupsmentioning

confidence: 99%

Crystal structure of dichlorobis(1-methylcytosine)cadmium(II)

Gagnon¹,

Beauchamp²,

Tranqui³

1979

Can. J. Chem.

View full text Add to dashboard Cite

Crystals of CdCl2(1-methylcytosine)2 belong to space group Cc, with a = 10.571(7), b = 24.35(2), c = 7.097(3) Å, β = 57.33(4)°, and Z = 4. The structure was refined over 1988 independent reflections to an R factor of 0.026. The structure consists of monomeric molecules in which cadmium has a (4 + 2)-coordination. Four strong bonds, two Cd—Cl (2.497, 2.485 Å) and two Cd—N(3) (2.281, 2.296 Å), define an approximate tetrahedron around the metal. Two carbonyl oxygens take part in weak Cd—O bonding interactions (2.677, 2.780 Å). The amino groups form only very weak intramolecular hydrogen bonds with chlorine and the difference >30° between angles Cd—N(3)—C(4) and Cd—N(3)—C(2) is ascribed to Cd—O bonding. Similar effects for other metal complexes are discussed in terms of steric hindrance of the amino group and bonding of the carbonyl group.

show abstract

The molecular electrostatic potentials for the nucleic acid bases: Adenine, thymine, and cytosine

Cited by 190 publications

References 19 publications

Molecular polarization potential maps of the nucleic acid bases

Molecular polarization potential maps of the nucleic acid bases

[(Glycylglycinato)(cytosine)copper(II)]. A model for enzyme–metal–nucleic acid ternary complexes

Crystal structure of dichlorobis(1-methylcytosine)cadmium(II)

Contact Info

Product

Resources

About