Nucleobase–Fluorobenzene Interactions: Hydrogen Bonding Wins over π Stacking

Catalysis of Free C-C Bond Rotation: C-F---H-X H-Bonds Find a Catalytic Role

There are few dynamic processes in organic chemistry that are more central to the molecular structure than C-C bond rotation. It is notable, however, that there exist few (if any) cases in which its hindered variants can actually be catalyzed. In this communication, we report a unique model system for the clear documentation of the catalysis of 360° C-C bond rotation that employs a transient but key N-H---F-C hydrogen bond as a linchpin and secondary "dual" charge-induced n → π* interactions and ion pairing effects that bolster catalysis.

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br−) is front > top. The stability order for the different microhydrates is following T-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-2Br−-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr− complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.

Dipole moment enhanced π-π stacking in fluorophenylacetylenes is carried over from gas-phase dimers to crystal structures propagated through liquid like clusters

The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra in the acetylenic and aromatic C-H stretching regions suggests that, unlike the parent non-fluorinated phenylacetylene, the substitution of a F atom on the phenyl ring increases the dipole moment, leading to robustness in the formation of a ππ stacked dimer, which propagates incorporating C-Hπ_{Ar/Ac} and C-HF interactions involving both acetylenic and aromatic C-H groups. The structural evolution of fluorophenylacetylene aggregates in the gas phase shows marginal effects due to fluorine atom position on the phenyl ring, with substitution in the para-position tending towards phenylacetylene. The present study signifies that the ππ stacked dimers act as a nucleus for the growth of higher clusters to which other molecular units are added predominantly via the {Ar}_C-Hπ_{Ar} type of interaction and the dominant interactions present in the crystal structures gradually emerge with increasing cluster size. Based on these features, gas-phase clusters of fluorophenylacetylene are hypothesized as "liquid-like clusters" acting as intermediates in the generation of various polymorphic forms starting from a ππ stacked dimer as the core molecular unit.

A theoretical investigation into the cooperativity effect on the TNT melting point under external electric field

External electric field has been regarded as an effective tool to induce the variation of melting points of molecular crystals. The melting point of 2,4,6-trinitrotoluene (TNT) was calculated by molecular dynamics simulations under external electric field, and the electric field effects on the cooperativity effects of the ternary (TNT)₃ were investigated at the M06-2X/6-311+G(d) and ωB97X-D/6-311++G(2d,p) levels. The results show that the melting points are decreased while the intermolecular interactions are strengthened under the external electric fields, suggesting that the intermolecular interactions cannot be used to explain the decreased melting points. A deduction based on the cooperativity effect is put forward: the enhanced cooperativity effects create the more serious defects in the melting process of the molecular crystal under the external electric fields, and simultaneously the local order parameters are decreased, leading to the decreased melting point. Thus, the cooperativity effect stemmed from the intermolecular C-H∙∙∙O H-bonding interactions controls the change of TNT melting point under the external electric field. Employing the information-theoretic approach (ITA), the origin of the cooperativity effects on the melting points of molecular crystal is revealed. This study opens a new way to challenge the problems involving the melting points for the molecular crystal under the external electric fields. However, note that above deduction needs to be improved; after all, the simple (TNT)₃ model cannot replace the crystal structure.

Dipole Moment Propels π-Stacking of Heterodimers of Fluorophenylacetylenes

Electronic and vibrational spectroscopic investigations in combination with quantum chemical calculations were carried out to probe the formation of four sets of heterodimers of phenylacetylene with 2-fluorohenylacetylene, 3-fluorophenylacetylene, 4-fluorophenylacetylene, and 2,6-difluorophenylacetylene. The interaction of phenylacetylene with fluorophenylacetylenes leads to marginal (2-9 cm^-1) red-shifts in the acetylenic C-H stretching frequencies of fluorophenylacetylenes, which suggests that constituent monomers are minimally perturbed in the heterodimer. On the other hand, the density-functional-theory-based calculations indicate that π-stacked structures outweigh other structures incorporating C-H···π and C-H···F interactions by about 8 kJ mol^-1 or more. The IR spectra in the acetylenic C-H stretching region were interpreted based on the perturbed dipole model, which suggests formation of predominantly antiparallel π-stacked structures, propelled by dipole moment. However, the energy decomposition analysis suggests that among stabilizing components dispersion dominates, while electrostatics plays a pivotal role in the formation of the π-stacked structures. Interestingly, the ability of 2-fluorophenylacetylene and 2,6-difluorophenylacetylene to π-stack differs significantly, even though both of them have almost identical dipole moments and the dipole moment propels the formation of π-stack structures. These results suggest π-stacking transcends the classical electrostatic description in terms of dipole moment.

Theoretical investigation into the cooperativity effect of 1,4-dimethoxy-D-glucosamine complex with Na+ and H2O

In order to explore the essence of the hydration process of chitin or chitosan in the presence of cation, the cooperativity effects between the H-bonding and Na⁺···molecule interactions in the 1,4-dimethoxy-D-glucosamine (DMGA) complexes with H₂O and Na⁺ were investigated at the B3LYP/6-311++G(d,p), M06-2X/6-311++G(2df,2p), and ωB97X-D/6-311++G(2df,2p) levels. The result shows that the complexes in which Na⁺ or H₂O is bonded simultaneously to the -NH and -OH groups connected to the C3 atom of DMGA are the most stable. The cooperativity and anti-cooperativity effects occur in DMGA···H₂O···DMGA and DMGA···Na⁺···H₂O, while only the cooperativities are confirmed in DMGA···Na⁺···DMGA. The cooperativity occurs in the DMGA···Na⁺···H₂O complexes without the hydration, while the anti-cooperativity occurs in those with the hydration. Furthermore, the cooperativity and anti-cooperativity in DMGA···Na⁺···H₂O are far stronger than those in DMGA···Na⁺···DMGA or DMGA···H₂O···DMGA. Therefore, a deduction is given that the cooperativity and anti-cooperativity effects play an important role in the hydration of chitin or chitosan in the presence of Na⁺. When only Na⁺ is linked with -OH and -NH groups of chitosan or chitin, due to the cooperativity effect, the hydration does not occur. When both Na⁺ and H₂O are linked with -OH and -NH groups, the anti-cooperativities are dominant in controlling of the aggregation process of Na⁺, H₂O, chitosan, and chitin, leading to the possible hydration. Atoms in molecules (AIM) analysis confirms the cooperativity and anti-cooperativity effects. Graphical abstract.

Hydration and swelling: a theoretical investigation on the cooperativity effect of H-bonding interactions between p-hydroxy hydroxymethyl calix[4]/[5]arene and H2O by many-body interaction and density functional reactivity theory

In order to explore the nature of the hydration and swelling of superabsorbent resin, a theoretical investigation into the cooperativity effect of the H-bonding interactions in the hydrates of four model compounds that can be regarded as the units of hydroquinone formaldehyde resin (HFR) (i.e., O-hydroxymethyl-1,4-dihydroxybenzene, methylene di-O-hydroxymethyl-1,4-dihydroxybenzene, p-hydroxy hydroxymethyl calix[4]arene and p-hydroxy hydroxymethyl calix[5]arene) was carried out by many-body interaction and density functional reactivity theory. The HFR···H₂O···H₂O complexes, in which the H₂O···H₂O moieties are bound with both the hydroxyl groups of HFR, are the most stable. For the HFR(H₂O)_n clusters, the interaction energy per building block is increased as the number of the size n increases, indicating the cooperativity effect. Therefore, a deduction is given that the cooperativity effects of the H-bonding interactions play an important role in the process of the hydration and swelling of HFR, and the swelling behavior is mainly attributed to the cooperativity effects which arised from the interactions between the H₂O molecules. The origin of the cooperativity effect was examined employing several information-theoretic quantities in the density functional reactivity theory. The degree of swelling of HFR was quantitated using a measure of volume. Graphical abstract.

Theoretical explanation for the pharmaceutical incompatibility through the cooperativity effect of the drug-drug intermolecular interactions in the phenobarbital∙∙∙paracetamol∙∙∙H2O complex

In order to reveal the essence of the pharmaceutical incompatibility, the cooperativity effects of the drug-drug intermolecular π∙∙∙π and H∙∙∙O H-bonding interactions involving hydration were evaluated in the phenobarbital∙∙∙paracetamol∙∙∙H₂O complex at the M06-2X/6-311++G** and MP2/6-311++G** levels. The thermodynamic cooperativity effects were also investigated by the statistical thermodynamic method. The results show that the π∙∙∙π stacking ternary complexes with the moderate anti-cooperativity effects are dominant in controling the aggregation process of phenobarbital, paracetamol, and H₂O, as is confirmed by the atoms-in-molecules (AIM) and reduced density gradient (RDG) analyses. Therefore, it can be inferred that the anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility, and thus a deduction on the formation process of the pharmaceutical incompatibility between phenobarbital and paracetamol, with the hydration effect, is given. Several valuable models that relate the features of molecular surface electrostatic potentials or their statistical parameters, such as the surface areas, average values ([Formula: see text]), variances ([Formula: see text], [Formula: see text] and [Formula: see text]), and product of [Formula: see text] and electrostatic balance parameter (ν) ([Formula: see text]ν), to the values of the cooperativity effects were predicted. The formation of the pharmaceutical incompatibility is a thermodynamic cooperativity process driven by the enthalpy change. Graphical abstract Anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility.

Cooperativity effect of the ππ interaction between drug and DNA on intercalative binding induced by H-bonds: a QM/QTAIM investigation of the curcuminadenineH2O model system

In order to reveal the nature of intercalative binding of drug to DNA, the cooperativity effect of the ππ interaction was investigated in the curcuminadenineH2O model system by applying a combined QM and QTAIM computational approach. The H-bonds between the electron-donating group of curcumin and adenine induce the formation of the ππ stacking. The introduction of H2O weakens the H-bonding and ππ interactions, leading to an anti-cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that the anti-cooperative effect is the main driving force for the intercalative binding of drug to DNA bases, which is in agreement with many experimental phenomena. Therefore, the designed DNA-targeted intercalating drugs should possess not only hydrophobic moieties, but also strong electron-donating groups bound to the DNA bases with H-bonds, which can slow the variation rates of the strengths of the H-bonding and ππ interactions between drug and DNA bases in the anti-cooperative process, leading to the intercalation formation. The enthalpy change is the major factor driving the positive thermodynamic cooperativity.

Hydrogen bonds vs. π-stacking interactions in the p-aminophenolp-cresol dimer: an experimental and theoretical study

The gas phase structure and excited state lifetime of the p-aminophenolp-cresol heterodimer have been investigated by REMPI and LIF spectroscopy with nanosecond laser pulses and pump-probe experiments with picosecond laser pulses as a model system to study the competition between π-π and H-bonding interactions in aromatic dimers. The excitation is a broad and unstructured band. The excited state of the heterodimer is long lived (2.5 ± 0.5) ns with a very broad fluorescence spectrum red-shifted by 4000 cm^-1 with respect to the excitation spectrum. Calculations at the MP2/RI-CC2 and DFT-ωB97X-D levels indicate that hydrogen-bonded (HB) and π-stacked isomers are almost isoenergetic in the ground state while in the excited state only the π-stacked isomer exists. This suggests that the HB isomer cannot be excited due to negligible Franck-Condon factors and therefore the excitation spectrum is associated with the π-stacked isomer that reaches vibrationally excited states in the S₁ state upon vertical excitation. The excited state structure is an exciplex responsible for the fluorescence of the complex. Finally, a comparison was performed between the π-stacked structure observed for the p-aminophenolp-cresol heterodimer and the HB structure reported for the (p-cresol)₂ homodimer indicating that the differences are due to different optical properties (oscillator strengths and Franck-Condon factors) of the isomers of both dimers and not to the interactions involved in the ground state.

Theoretical insight into the solvent effect of H2O and formamide on the cooperativity effect in HMX complex

The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)∙∙∙HMX∙∙∙FA (formamide), HMX∙∙∙HMX∙∙∙H₂O and HMX∙∙∙HMX∙∙∙HMX complexes involving the chair and chair-chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6-31++G(d,p):PM3) and ONIOM2 (M06-2X/6-31++G(d,p):PM3) methods. The solvent effect of FA or H₂O on the cooperativity effect in HMX∙∙∙HMX∙∙∙HMX are evaluated by the integral equation formalism polarized continuum model. The results show that the cooperativity and anti-cooperativity effects are not notable in all the systems. Although the effect of solvation on the binding energy of ternary system HMX∙∙∙HMX∙∙∙HMX is not large, that on the cooperativity of H-bonds is notable, which leads to the mutually strengthened H-bonding interaction in solution. This is perhaps the reason for the formation of different conformation of HMX in different solvent. Surface electrostatic potential and reduced density gradient are used to reveal the nature of the solvent effect on cooperativity effect in HMX∙∙∙HMX∙∙∙HMX. Graphical abstract RDG isosurface and electrostatic potential surface of HMX∙∙∙HMX∙∙∙HMX.

Cooperative hydrogen bonding in glyco-oligoamides: DNA minor groove binders in aqueous media

A strategy to create cooperative hydrogen-bonding centers by using strong and directional intramolecular hydrogen-bonding motifs that can survive in aqueous media is presented. In particular, glyco-oligoamides, a family of DNA minor groove binders, with cooperative and non-cooperative hydrogen-bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β-D-Man-Py-γ-Py-Ind (1; Ind=indole, Man=mannose, Py=pyrrole) and β-D-Tal-Py-γ-Py-Ind (2; Tal=talose), were chosen according to our design. These sugar molecules should present one- or two-directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco-oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco-oligoamides with non-cooperative hydrogen-bonding centers, that is, β-D-Glc-Py-γ-Py-Ind (3; Glc=glucose), β-D-Gal-Py-γ-Py-Ind (4; Gal=galactose), and the model compounds β-D-Man-Py-NHAc (5) and β-D-Tal-Py-NHAc (6) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH-π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf-thymus DNA and poly(dA-dT)2 by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar-oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen-bonding and CH-π interactions are present.

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.

Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties

A correlation between 19F NMR isotropic chemical shift and close intermolecular F⋅⋅⋅H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F⋅⋅⋅X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F⋅⋅⋅H distance and F⋅⋅⋅H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target.

The MP2-F12 method in the Turbomole program package

A detailed description of the explicitly correlated second-order Møller-Plesset perturbation theory (MP2-F12) method, as implemented in the TURBOMOLE program package, is presented. The TURBOMOLE implementation makes use of density fitting, which greatly reduces the prefactor for integral evaluation. Methods are available for the treatment of ground states of open- and closed-shell species, using unrestricted as well as restricted (open-shell) Hartree-Fock reference determinants. Various methodological choices and approximations are discussed. The performance of the TURBOMOLE implementation is illustrated by example calculations of the molecules leflunomide, prednisone, methotrexate, ethylenedioxytetrafulvalene, and a cluster model for the adsorption of methanol on the zeolite H-ZSM-5. Various basis sets are used, including the correlation-consistent basis sets specially optimized for explicitly correlated calculations (cc-pVXZ-F12).