The Magnitude of [C−H···O] Hydrogen Bonding in Molecular and Supramolecular Assemblies (original) (raw)
Related papers
Cations as hydrogen bond donors: A view of electrostatic interactions in DNA
2003
Cations are bound to nucleic acids in a solvated state. High-resolution X-ray diffraction studies of oligonucleotides provide a detailed view of Mg 2+ , and occasionally other ions bound to DNA. In a survey of several such structures, certain general observations emerge. First, cations bind preferentially to the guanine base in the major groove or to phosphate group oxygen atoms. Second, cations interact with DNA most frequently via water molecules in their primary solvation shell, direct ion-DNA contacts being only rarely observed. Thus, the solvated ions should be viewed as hydrogen bond donors in addition to point charges. Finally, ion interaction sites are readily exchangeable: The same site may be occupied by any ion, including spermine, as well as by a water molecule.
Inorganic Chemistry, 2005
This paper reports on the chemistry of platinum complexes containing bidentate pyridine-carboxylate (pyAc ) pyridin-2-yl-acetate and picEt ) pyridine-2-ethylcarboxylate, ethylpicolinate) (N,O) ligands. The pyridine-2-acetate and ethylpicolinate ligands form six-and five-membered chelates, respectively, upon formation of the Pt−carboxylate bond. In all reactions with picEt with various platinum complex starting materials, spontaneous de-esterification of the pendant carboxylate ester occurs to give directly the chelates K[PtCl 2 (pic-N,O)]-trans-[Pt(pic-N,O) 2 ] and SP-4,2-[PtCl(pic-N,O)(NH 3 )] without any evidence of intermediates. The de-esterification is solvent dependent, and molecular modeling was used to explain this reaction. The reactions of the geometric isomers of [PtCl(pyAc-N,O)-(NH 3 )] with 5′-guanosine monophosphate, 5′-GMP, and N-acetyl-L-methionine, AcMet, were investigated by NMR spectroscopy. The objective was to ascertain by model chemistry the feasibility of formation of ternary DNA−Pt− protein adducts in biology. Model nucleotide and peptide compounds were formed in situ by chloride displacement giving [PtL(pyAc-N,O)(NH 3 )] + (L ) 5′-GMP or AcMet). Competitive reactions were then examined by addition of the complementary ligand L. Sulfur displacement of coordinated 5′-GMP was slow. For SP-4,3-[Pt(AcMet)(NH 3 )-(PyAc-N,O)] + , a rapid displacement of the sulfur ligand by 5′-GMP was observed, giving SP-4,2-[Pt(5′-GMP-N7)-(pyAc-N,O)(NH 3 )] + .
This paper is a logical continuation of the theoretical survey of the CH⋯O/N specific contacts in the nucleobase pairs using a wide arsenal of the modern methods, which was initiated in our previous study [J. Biomol. Struct. & Dynam., 2014, 32, 993–1022]. It was established that 34 CH⋯O and 7 CH⋯N interactions, that were detected by quantum-chemical calculations in the 39 biologically important pairs involving modified nucleobases, completely satisfy all geometrical, vibrational, electron-topological, in particular Bader’s and “two-molecule” Koch and Popelier’s, Grunenberg’s compliance constants theory and natural bond orbital criteria indicating that they can be identified as true H-bonds. The geometrical criteria of the H-bond formation are fulfilled for all considered CH⋯O/N H-bonds without any exception. It was shown that the classical rule of the stretching vibration shifts does not work in the ~95% cases of the CH⋯O/N H-bonds. Furthermore, significant increase in the frequency of the out-of-plane deformation modes γ(CH) under the formation of CH⋯O/N H-bonds and corresponding changes of their intensities can be also considered as reliable indicators of the H-bonding. We revealed high linear mutual correlations between the electron density, Laplacian of the electron density, H-bond energy at the (3, −1) bond critical points of the CH⋯O/N H-bonds, and different physico-chemical parameters of the CH⋯O/N H-bonds. We suggested that the electron density ρ and the interaction energy E(2) of the lone orbital pairs are the most reliable descriptors of the H-bonding. The linear dependence of the H-bond energy ECH⋯O/N on the electron density ρ was established: ECH⋯O = 250.263∙ρ – .380/258.255∙ρ – .396 and ECH⋯N = 196.800∙ρ – .172/268.559∙ρ – .703 obtained at the density functional theory (DFT)/Møller−Plesset (MP2) levels of theory, respectively. The studies of the interaction energies show that the contribution of the CH⋯O and CH⋯N H-bonds into the base pairs stability varies from 3.0/4.2 to 35.1/31.2% and from 3.0/4.3 to 44.4/46.5% at the DFT/MP2 levels of theory, accordingly. Energy decomposition analysis performed for all base pairs involving canonical and modified nucleobases defines the electrostatic attraction and Pauli repulsion as dominant stabilizing forces in all complexes. This observation was additionally confirmed by the results of the QTAIM delocalization indexes analysis. The studies reported here advance our understanding of the biological role of the weak CH⋯O/N H-bonds, that dictates the requirements for the structural and dynamical similarity of the canonical and mismatched pairs with Watson–Crick (WC) geometry, which facilitates their enzymatic incorporation into the DNA double helix during DNA replication. Thus, these H-bonds in the base pairs with WC geometry may be also considered as “the last drop” at the transmission of the electronic signal that launches the chemical incorporation of the incoming nucleoside triphosphate into DNA.
Journal of Molecular Biology, 2000
Cation-p interactions between an aromatic ring and a positive charge located above it have proven to be important in protein structures and biomolecule associations. Here, the role of these interactions at the interface of protein-DNA complexes is investigated, by means of ab initio quantum mechanics energy calculations and X-ray structure analyses. Ab initio energy calculations indicate that Na ions and DNA bases can form stable cation-p complexes, whose binding strength strongly depends on the type of base, on the position of the Na ion, and whether the base is isolated or included in a double-stranded B-DNA. A survey of protein-DNA complex structures using appropriate geometrical criteria revealed cation-p interactions in 71 % of the complexes. More than half of the cation-p pairs involve arginine residues, about one-third asparagine or glutamine residues that only carry a partial charge, and one-seventh lysine residues. The most frequently observed pair, which is also the most stable as monitored by ab initio energy calculations, is arginineguanine. Arginine-adenine interactions are also favorable in general, although to a lesser extent, whereas those with thymine and cytosine are not. Our calculations show that the major contribution to cation-p interactions with DNA bases is of electrostatic nature. These interactions often occur concomitantly with hydrogen bonds with adjacent bases; their strength is estimated to be from three to four times lower than that of hydrogen bonds. Finally, the role of cation-p interactions in the stability and speci®city of protein-DNA complexes is discussed.
Chemistry-a European Journal, 1999
The view that the hydrogen bonds in Watson ± Crick adenine ± thymine (AT) and guanine ± cytosine (GC) base pairs are in essence electrostatic interactions with substantial resonance assistance from the p electrons is questioned. Our investigation is based on a state-of-the-art density functional theoretical (DFT) approach (BP86/TZ2P) that has been shown to properly reproduce experimental data. Through a quantitative decomposition of the hydrogen bond energy into its various physical terms, we demonstrate that, contrary to the widespread belief, donor ± acceptor orbital interactions (i.e., charge transfer) in s symmetry between N or O lone pairs on one base and NÀH s*-acceptor orbitals on the other base do provide a substantial bonding contribution which is, in fact, of the same order of magnitude as the electrostatic interaction term. The overall orbital interactions are reinforced by a small p component which stems from polarization in the p-electron system of the individual bases. This p component is, however, one order of magnitude smaller than the s term. Furthermore, we have investigated the synergism in a base pair between charge transfer from one base to the other through one hydrogen bond and in the opposite direction through another hydrogen bond, as well as the cooperative effect between the donor ± acceptor interactions in the sand polarization in the pelectron system. The possibility of CÀH´´´O hydrogen bonding in AT is also examined. In the course of these analyses, we introduce an extension of the Voronoi deformation density (VDD) method which monitors the redistribution of the sand p-electron densities individually out of (DQ b 0) or into (DQ`0) the Voronoi cell of an atom upon formation of the base pair from the separate bases.
Crystal Growth & Design, 2020
Salts and ionic cocrystals simultaneously comprising N-oxide and carboxylic acid functional groups constitute a very fertile ground for the investigation of various proton transfer phenomena. This is because such compounds combine two types of proton transfer: that is, inter-and intramolecular hydrogen bonding in acid−base systems. To this end, a series of novel salts based on pyridine-2,5-dicarboxylic acid N-oxide (H 2 pydco) as an organic acid and 2,4,6-triamino-1,3,5-triazine (tata), 2-aminopyrimidine (2a-pym), 2-amino-6-methylpyridine (2a-6mpy), 1,10phenanthroline (phen), and 9-aminoacridine (9a-acr) as organic bases have been synthesized and characterized by elemental analyses, infrared spectroscopy, and single-crystal X-ray diffraction: (Htata) + (Hpydco) − (1), (H2a-pym) + (Hpydco) − (2), (H2a-6mpy) + (Hpydco) − (3A,B), [(Hphen) + (Hpydco) − ](H 2 pydco) (4), and [(H9a-acr) + (Hpydco) − ]•EtOH (5). The unit cells of 3A and 3B differ slightly; however, 3A crystallizes in a chiral orthorhombic space group P2 1 2 1 2 1 , while 3B crystallizes in the achiral space group P2 1 /n. In both cases, the asymmetric unit comprises one cation and one anion. The influence of different organic cations on the packing of Hpydco − in the crystal lattice is studied. The most important feature of these crystals is the presence of extensive O− H•••O, N−H•••O, N−H•••N, and C−H•••O hydrogen bond networks, which form base-dependent supramolecular synthons: 1, 2, and 3A,B comprise an α-aminopyridinium moiety, and all involve the hydrogen-bonded motif R 2 2 (8) with the Hpydco − anion. Compounds 4 and 5, which lack the α-aminopyridinium moiety, reveal different hydrogen-bonding patterns. The interaction energies of each individual hydrogen bond have been estimated using the quantum theory of "atoms-in-molecules", which led us to the identification of the energetically favorable antielectrostatic N−H•••N hydrogen bonds (stabilization energy of 4.0 kcal/mol) between positively charged melaminium species in 1. It has been also established that charge-assisted hydrogen bonding does not always offer an energetic advantage over "noncharged" hydrogen bonds. With the use of Hirshfeld surface (HS) analysis we have also explored the influence of the protonation state of pydco species on the composition of contact contributions, as well as established specific properties of their 2D fingerprint plots. Finally, a comment is provided on the applicability of HS analysis for the exploration of polymorphs featuring intramolecular proton transfer.
Hydrogen bonding, stacking and cation binding of DNA bases
Journal of Molecular Structure-theochem, 2001
Ab initio quantum chemical calculations with inclusion of electron correlation effects significantly contributed to our understanding of molecular interactions of DNA bases. Some of the most important findings are introduced in the present overview: nonplanarity of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions, structures and energies of hydrogen bonded base pairs, nature of base stacking, and interactions between metal
Biopolymers, 1972
Electrostatic interactions between the DNA bases in the Watson-Crick hydrogen bonding configuration are examined in both the molecular and the atomic multipole representations using three different methods of calculation: (a) CNDO wave functions and definitions of moments, (b) IEHT wave functions and division of two-center densities and (c) IHET wave functions with equally divided overlap densities. It is shown that the inclusion in the interaction series of terms at least as high as the quadrupole-quadrupole is required to quantitatively characterize the interactions. Convergence is more rapid with the atomic multipole representation and is unaffected by the type of assignment of formal charges. A quantitative approach to the problem of the role of electrostatic interactions in hydrogen bonding in DNA is thus provided, with obvious impact on the investigation of molecular recognition processes.