Influence of Intermolecular Hydrogen Bonds on the Tautomerism of Pyridine Derivatives

The effect of the dimerization, by hydrogen-bond (HB) complexation, on the tautomerism of 2-hydroxypyridine and a series 2-aminopyridines has been carried using ab initio methods. The results obtained for 2-hydroxypyridine fit satisfactorily with the experimental data and show that the 2-pyridone/2-pyridone homodimer complex is the most stable. For 2-aminopyridines, the effect of the substituent on the amino group has been investigated. For the monomers studied, the most favorable tautomer is the 2H; however, with electronegative substituents, the 1H/1H homodimers are more stable than the corresponding 2H/2H ones. The atom in molecule methodology has been used to characterize the HBs formed. Exponential relationships have been found between the electron density and its laplacian at the HB critical point vs the HB distance

Self-Discrimination of Enantiomers in Hydrogen-Bonded Dimers

The homochiral and heterochiral hydrogen-bonded (HB) dimers of a set of small model molecules (α-amino alcohols) have been studied by means of ab initio methods. The gas-phase calculations have been carried out with the hybrid HF/DFT B3LYP method and the 6-311++G** basis set. The electron density of the complexes has been analyzed using the atoms in molecules (AIM) methodology, which allows characterization of the HB interactions and additional intermolecular contacts. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the ΔGsolv. The gas-phase results show that the heterochiral dimers are the most stable ones for each case studied, while in solution for several cases, the relative stability is reversed and the homochiral dimers become more stable. The AIM analysis shows the typical bond critical points characteristic of the HB and additional bond critical points denoting, in this case, destabilization of intermolecular interaction as CF3···F3C and CH3···H3C contacts

Interaction of Protein Backbone with Nucleic Acid Bases^†

A theoretical study of the hydrogen-bonded (HB) complexes between a protein model and nucleic acid bases (NAB) has been carried out. As protein models, N-formylglycinamide (For-Gly-NH2, 2-formylaminoacetamide), 1, in β- and γ-conformations and as NABs, the isolated ones, and the AU, GC dimers in the Watson−Crick (WC) disposition have been considered. Only those dispositions with a double HB between the protein model and the nucleic acid bases have been studied. The aromatic CH groups of the nucleic acids have been included as HB donor. The results indicate that the strongest HBs between the individual NAB and the protein models involve the atoms that participate in the formation of the WC dimers. In the trimeric complexes, no significant preference is obtained for the 1-AU trimers studied while in the 1-GC ones the complex where formylglycinamide interacts simultaneously with the carbonyl group of guanine and the amino of cytosine is favored. The electron density of the complexes has been analyzed using the atoms in molecules methodology, finding exponential relationships between the electron density and its Laplacian vs the bond distance. Finally, the effect in the nuclear chemical shielding due to the complexation has been explored. Exponential relationships have been found for the variation of the chemical shift of the 1H signal for the NH···O and NH···N interactions with the HB distance

Effect of Dimerization and Racemization Processes on the Electron Density and the Optical Rotatory Power of Hydrogen Peroxide Derivatives

The variation of the electron density properties and optical rotatory power of the monomers and dimers of seven monosubstituted hydrogen peroxide derivatives, HOOX (X = CCH, CH3, CF3, t-Bu, CN, F, Cl), upon racemization has been studied using DFT (B3LYP/6-31+G**) and MP2 (MP2/6-311+G**) methods. The geometrical results have been rationalized on the basis of natural bond orbital (NBO) analysis. The atomic partition of the electron density properties within the atoms in molecules (AIM) methodology has allowed investigating the energy and charge redistribution in the different structures considered. The calculated optical rotatory power (ORP) of the dimers are, in general, twice of the values obtained for the monomers

The Structure of Alkali Metal Derivatives of Azoles: N−σ versus π Structures

High level ab initio calculations have been used to study the relative stability of N−σ and π configurations of the neutral alkaline derivatives of azoles. The N−σ structure is the one normally expected for nonionized azolate salts. However, the results show that in the case of the pyrrole and imidazole the π configuration is more stable than the N−σ one. The preference of the N−σ vs π configurations is related to the presence or the absence of two contiguous nitrogen atoms in the azole ring. A search in the CSD shows that some pyrrolate and imidazolate salts exist in solid phase in the π configuration

π-Systems as Simultaneous Hydride and Hydrogen Bond Acceptors

A theoretical study of the hydride bond complexes with tetrafluoro- and tetracyanoethylene, C2F4 and C2(CN)4, has been carried out by means of density functional theory (DFT) and ab initio methods, up to the MP2/aug-cc-pVTZ computational level. In addition, the ternary complexes formed by an additional standard hydrogen bond donor, such as hydrogen fluoride, have been explored. The results show that the hydride bond complexes are stable and an electron transfer took place from the hydride to the C2F4 and C2(CN)4 molecules. While these molecules are not able to form stable complexes between the π-electrons and hydrogen bond donors, the presence of the hydrides in the opposite face of the π-system of C2F4 stabilizes the ternary complexes showing cooperativity effects

Dihydrogen Bond Cooperativity in Aza-borane Derivatives

A theoretical study of the dihydrogen-bonded clusters of three aza-borane derivatives, H−N····B−H, has been carried out using DFT, M05-2X, computational methods. Clusters consisting of up to 10 monomers have been considered. The energetic results show an increment of the average interaction energy per monomer as the size of the cluster increases. Similarly, a shortening of the intermolecular distances up to 0.1 Å is observed. Among the electrostatic properties, an increment of the dipole moment and the absolute values of the molecular electrostatic potential at the interacting point of the cluster are observed. Finally, the orbital interaction responsible for the dihydrogen bond follows the same pattern observed for the bond distances. Thus, it can be concluded that these systems show behavior, with respect to cooperativity, similar to those observed in standard hydrogen bonds

Weakly Bound Complexes of N₂O: An ab Initio Theoretical Analysis Toward the Design of N₂O Receptors

Ab initio calculations at MP2/6-311++G(2d,2p) and MP2/6-311++G(3df,3pd) computational levels have been used to analyze the interactions between nitrous oxide and a series of small and large molecules that act simultaneously as hydrogen bond donors and electron donors. The basis set superposition error (BSSE) and zero point energy (ZPE) corrected binding energies of small N2O complexes (H2O, NH3, HOOH, HOO•, HONH2, HCO2H, H2CO, HCONH2, H2CNH, HC(NH)NH2, SH2, H2CS, HCSOH, HCSNH2) vary between −0.93 and −2.90 kcal/mol at MP2/6-311++G(3df,3pd) level, and for eight large complexes of N2O they vary between −2.98 and −3.37 kcal/mol at the MP2/6-311++G(2d,2p) level. The most strongly bound among small N2O complexes (HCSNH2−N2O) contains a NH··N bond, along with S → N interactions, and the most unstable (H2S−N2O) contains just S → N interactions. The electron density properties have been analyzed within the atoms in molecules (AIM) methodology. Results of the present study open a window into the nature of the interactions between N2O with other molecular moieties and open the possibility to design N2O abiotic receptors

An Attractive Interaction between the π-Cloud of C₆F₆ and Electron-Donor Atoms

A theoretical study of the possible interaction of the π-cloud of hexafluorobenzene (C6F6) with several small electron-donor molecules (FH, HLi, :CH2, NCH, and CNH) has been carried out. The calculations have been performed using HF, MP2, and hybrid HF/DFT methods (B3LYP) with the 6-31G** and 6-311++G** basis sets. The topology of the electron density of the complexes has been characterized using the AIM methodology. The characteristics of the electron density and molecular electrostatic potential maps of benzene and hexafluorobenzene have been compared. Finally, the results obtained from a search in the Cambridge Structural Database system of this kind of interaction are shown

Single Electron Pnicogen Bonded Complexes

A theoretical study of the complexes formed by monosubstituted phosphines (XH₂P) and the methyl radical (CH₃) has been carried out by means of MP2 and CCSD­(T) computational methods. Two minima configurations have been obtained for each XH₂P:CH₃ complex. The first one shows small P–C distances and, in general, large interaction energies. It is the most stable one except in the case of the H₃P:CH₃ complex. The second minimum where the P–C distance is large and resembles a typical weak pnicogen bond interaction shows interaction energies between −9.8 and −3.7 kJ mol^–1. A charge transfer from the unpaired electron of the methyl radical to the P–X σ* orbital is responsible for the interaction in the second minima complexes. The transition state (TS) structures that connect the two minima for each XH₂P:CH₃ complex have been localized and characterized