N-(6-Amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl) derivatives of glycine, valine, serine, threonine and methionine: interplay of molecular, molecular–electronic and supramolecular structures

Abstract

In each of N-(6-amino-3, 4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)valine, C(10)H(15)N(5)O(4) (3) (orthorhombic, P2(1)2(1)2(1)), N-(6-amino-3, 4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)serine monohydrate, C(8)H(11)N(5)O(5).H(2)O (4) (orthorhombic, P2(1)2(1)2(1)), and N-(6-amino-3, 4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)threonine, C(9)H(13)N(5)O(5)(5) (monoclinic, P2(1)), the C-nitroso fragments exhibit almost equal C-N and N-O bond lengths: the C-N range is 1. 315 (3)-1.329 (3) A and the N-O range is 1.293 (3)-1.326 (3) A. In each compound there are also very short intermolecular O-H.O hydrogen bonds, in which carboxyl groups act as hydrogen-bond donors to the nitrosyl O atoms: the O.O distances range from 2.440 (2) to 2. 504 (4) A and the O-H.O angles lie between 161 and 163 degrees. An interpretation of the relationship between the unusual intramolecular bond lengths and the very short intermolecular hydrogen bonds has been developed based on database analysis and computational modelling. In each of (3)-(5) there is an extensive network of intermolecular hydrogen bonds, generating three-dimensional frameworks in (3) and (5), and two-dimensional sheets in (4).

Study of protonation and Zn(II), Cd(II), Cu(II) and Mn(II) complexation with a glutamic acid N-pyrimidine derivative: Crystal structure of a neutral Cd(II) complex of the bianionic ligand

“…It is noteworthy that the N3 py position displays no affinity to any of the studied metal-ions. This fact, which is consistent with previous observations done with other analogous pyrimidine derivatives [5,19], agrees with the typical low electron density existing at the -NH-(C2-N3-C4) py -NH 2 moiety [8,10].…”

“…The somewhat long bond length values in the NH-C2-N3-C4-NH 2 fragment and the short bond distances in the C5NO grouping point out the location of a positive charge at the former fragment, and a negative charge at the latter; for example, the bipolar character of the aromatic moiety. These features have already been observed in the case of analogous amino acid derivatives [10] (Scheme 2).…”

“…The pyrimidine moiety shows alike structural and electronic features to a series of analogous compounds obtained by condensation of the above-mentioned pyrimidine derivatives with a series of single amino acids [10]. These data show extensive p-electron delocalization at the cyclic moiety which also involves the C2NH 2 , C6O, C5NO and C4NH 2 exocyclic substituents.…”

Adsorption of Metal Ions on an Activated Carbon/L‐Lysine Derivative Hybrid Compound

“…The pyrimidine moiety shows similar structural and electronic features to analogous compounds mentioned above. [12][13][14] The C(5)NO group is oriented trans to C(6) in such a way that its oxygen atom O(5) is able to form an intramolecular N-H···O hydrogen bond in an S(6) motif, which is coplanar with the pyrimidine ring. However, the N-amino acid side-chain deviates from this plane.…”

“…Scheme 1. Structural studies on these type of derivatives have shown the existence of a strong dipole at the aromatic moieties due to the electron-withdrawing character of their C(5) NO and C(6)O substituents. [12][13][14] The existence of such a dipole is common to all compounds of this class as the polymethylene separators (S) are not conjugated with the pyrimidine residues. This bipolar character means that the energy differences between their HOMO and LUMOs are small and that the energy of these orbitals is close to the energy values calculated for the frontier orbitals of modelled arene active sites present on the surface of an activated carbon (AC).…”