Characterizing the Cooperativity in H-Bonded Amino Structures

Experimental and theoretical investigation of intramolecular cooperativity in cyclic benzene trimer motif

A series of new symmetrical tripodal molecules 1a–4b with a central benzene scaffold substituted with methyl/ethyl groups and three benzimidazolyl units having a bithiophene/biphenyl/5-alkylthiophene motif at the 2-position via a –CH₂– unit were synthesized and characterized by elemental analysis, HR-MS, and NMR spectroscopy. NMR spectral data reveal that all molecules adopt a cyclic benzene trimer (CBT) using three benzimidazolyl units. Intramolecular cooperative edge-to-face C–H⋯π interactions stabilize the CBT motif in solution and are strong in ethyl substituted molecules (1b–4b) compared to methyl substituted (1a–4a) ones. However, the strength of the CBT unit in the tripodal molecule is independent of the length of the substituent at the 2-position of the benzimidazolyl unit. The relative ¹H NMR chemical shift calculated at the MPW1PW91/6-311+G(d,p) level of theory corroborates the experimental values, and the calculations predict the distribution of the structures into syn isomers. The relative change in the NMR chemical shift is justified by the relative change in the magnitude of the (3,+3) critical point (CP) in the molecular electrostatic potential (MESP) topography. Also, a linear correlation of the intramolecular C–H⋯π interactions evaluated at M062X/6-311+G(d,p) with the relative NMR chemical shift suggest the latter as a measure of intramolecular cooperativity.

A family of biaryl/alkylthiophene (R–R) benzimidazolyl-based tripodal molecules with cyclic benzene trimer (CBT) motif was synthesized and studied by NMR spectroscopy and MPW1PW91/6-311+G(d,p) theory.

Intermolecular magnetic interactions in stacked DNA base pairs

The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.

Modified Guanines as Constituents of Smart Ligands for Nucleic Acid Quadruplexes

Repetitive guanine-rich nucleic acid sequences play a crucial role in maintaining genome stability and the cell life cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that guanine-based ligands with a porphyrin core can be used as markers of G-quadruplex assemblies in cell tissues. Herein, model systems of guanine-based ligands are explored by DFT methods. The energies of formation of modified guanine tetrads and those of modified tetrads stacked on the top of natural guanine tetrads have been calculated. The interaction energy has been decomposed into contributions from hydrogen bonding, stacking, and ion coordination and a twist-rise potential energy scan has been performed to find the individual local minima. Energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe2 ) on individual energy terms. In addition, cooperative reinforcement in forming the modified and stacked tetrads, as well as the frontier orbitals participating in the hydrogen-bonding framework involving the HOMO-LUMO gap between the occupied σHOMO on the proton-accepting C=O and =N- groups and unoccupied σLUMO on the N-H groups, has been studied. The investigated systems are demonstrated to have a potential in ligand development, mainly due to stacking enhancement compared with natural guanine, which is used as a reference.

A B3LYP and MP2(full) theoretical investigation into cooperativity effects, aromaticity and thermodynamic properties in the Na(+)⋯benzonitrile⋯H2O ternary complex

The cooperativity effects between H-bonding and Na(+)⋯π or Na(+)⋯σ interactions in Na(+)⋯benzonitrile⋯H2O complexes were investigated using the B3LYP and MP2(full) methods with 6-311++G(2d,p) and aug-cc-pVTZ basis sets. The thermodynamic cooperativity and the influence of this cooperativity on aromaticity was evaluated by nucleus-independent chemical shifts (NICS). The results showed that the influence of the Na(+)⋯σ or Na(+)⋯π interaction on the hydrogen bond is more pronounced than that of the latter on the former. The cooperativity effect appeared in the Na(+)⋯σ interaction complex while the anti-cooperativity effect tended to be in the Na(+)⋯π system. The change in enthalpy is the major factor driving cooperativity. Thermodynamic cooperativity is not in accordance with the cooperativity effect evaluated by the change of interaction energy. The ring aromaticity of is weakened while the bond dissociation energy (BDE) of the C-CN bond increases upon ternary complex formation. The cooperativity effect (E coop) correlates with R c (NICS(1)ternary/NICS(1)binary) and ΔΔδ (Δδ ternary - Δδ binary) involving the ring and C ≡ N bond, as well as R BDE(C-CN) [BDE(C-CN)ternary/BDE(C-CN)binary], respectively. AIM (atoms in molecules) analysis confirms the existence of cooperativity.

Computational study of interactions and nuclear magnetic shielding constants in linear chains of formamide clusters

We investigated the energetic, structural, dielectric, and nuclear magnetic shielding properties of linear n-formamide clusters, with n up to 6, to quantitatively characterize cooperative effects in model biological systems. The geometries of the complexes were optimized at the MP2 and DFT/B3LYP levels by using the pc-2 and pc-3 basis sets, while the nuclear magnetic shielding constants were calculated by employing pcS-n type basis sets, which have been optimized specifically for density functional calculations of these properties. The interaction energies show the cooperative effect, which favors the successive addition of monomers. In addition, by analyzing structural changes in the intermolecular C=O, C-N and hydrogen O⋯H bonds, as well as in the average dipole moments as cluster size increases, we found that the cooperative interaction far exceeds that expected for electrostatic interactions. Such non-pairwise-additive effects are also reflected in the changes of the nuclear magnetic shielding constants. In particular, the negativity of O shielding decreases around 23% from the monomer to the 6-formamide chain. It is possible to note the decrease in the shielding of H and in the deshielding of O as a result of their hydrogen bonding. However, the results obtained show that these variations in the extremes of formamide chains tend to zero, and the respective shielding values tend to stabilize as the number of monomers increases in the chain. Also, the cooperative effect increases in the middle of the chains, by decreasing the shielding for all atoms except that of O, which decreases its deshielding. These results could serve to guide improvements in current conventional models for simulating hydrogen bonded systems.

Characterization of cooperative effects in linear alpha-glycylglycine clusters

The aspects of N-H...O=CNH, N-H...O=CO and C-H...O=CNH interactions are analyzed by applying ab initio and DFT methods as well as Bader theory. We investigated geometry, binding energies, (17)O, (15)N chemical shift tensors, and Atoms in Molecules (AIM) properties of alpha-glycylglycine (alpha-glygly) clusters, via MP2, B3LYP and PW91(XC) methods. Dimer stabilization energies and equilibrium geometries are studied in various levels of theory. MP2 and DFT calculations reveal that for alpha-glygly clusters, stability of N-H...O and C-H...O hydrogen bonds are enhanced significantly as a result of cooperativity effects. Furthermore, a covalent nature is also detected for some hydrogen bondings. The n-dependent trend of (17)O and (15)N chemical shift tensors was reasonably correlated with cooperative effects in hydrogen-bond interactions. Regarding the various N-H...O=CNH, N-H...O=CO and C-H...O=CNH hydrogen bondings, capability of the alpha-glygly clusters for electron localization at the N-H...O and C-H...O bond critical points, depends on the cluster size. This leads to cooperative changes in the hydrogen-bond length and strength as well as (17)O and (15)N chemical shift tensors.

CLOPPA-IPPP analysis of cooperative effects in hydrogen-bonded molecular complexes. Application to intermolecular 2hJ(N,C) spin-spin coupling constants in linear (CNH)n complexes

The cooperative effects on NMR indirect nuclear coupling constants are analyzed by means of the IPPP-CLOPPA approach (where CLOPPA is the Contributions from Localized Orbitals within the Polarization Propagator Approach and IPPP is the Inner Projections of the Polarization Propagator). The decomposition of the J coupling allows one to classify these effects as those due to changes in the geometric structure and those that directly involve the transmission mechanisms. This latter contribution admits a further classification, taking into account its electronic origin. As an example, the cooperative effects on intermolecular 2hJ(N,C) couplings of the linear complexes (CNH)n (n = 2, 3, 4) are discussed.