Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes

Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs

The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.

Ionization spectroscopies and theoretical calculations of cis and trans 3-fluoro-N-methylaniline-Arn(n=1,2) van der Waals clusters: Structures and binding energies

The ab initio and dispersion-corrected density functional theory (DFT) calculations of the van der Waals (vdW) clusters of cis and trans 3-fluoro-N-methylaniline-Ar_n (3FNMA-Ar_n) (n=1,2) predict that, for cis and trans 3FNMA-Ar₁ clusters, the π-bound geometry with the Ar atom sitting over the ring is the global minimum in both neutral and cationic states, while for cis and trans 3FNMA-Ar₂ clusters, the [π|π]-bound sandwich structure with two Ar ligands occupying nearly equivalent π-bound positions above and below the ring plane is the global minimum. The vibronic spectra of cis and trans 3FNMA-Ar₁ clusters in the S₁ state were recorded by using one-color and two-color resonant two-photon ionization (R2PI) techniques, the comparison of which yields an estimate of the binding energy of cluster in the S₁ state. It is found that the linear correlation between the redshift of the S₁←S₀ electronic transition energy (E₁) of cluster and the E₁ of the monomer also holds for the Ar clusters of hetero-di-substituted aromatics. By recording the photoionization efficiency (PIE) curves and mass-analyzed threshold ionization (MATI) dissociation spectra of cis and trans 3FNMA-Ar₁ clusters, the ionization energies (IE) and binding energies of clusters in the D₀ state are obtained. The MATI spectra of the cis and trans 3FNMA-Ar₁ cations exhibit significant progressions of the vdW bending mode (b_x), indicating the structural changes of the clusters in the bending coordinate upon ionization. The combination of the three kinds of spectroscopic methods provides the binding energies of cis and trans 3FNMA-Ar₁ clusters in the S₀, S₁ and D₀ states with good accuracy, and the values estimated by dispersion-corrected DFT calculations compare well with the experimental results. From our studies, the ωB97X-D and TD-ωB97X-D methods using high quality basis set are recommended for studying the intermolecular interaction of such vdW clusters in the ground and excited states.

A comparative interplay between small heterorings and hypofluorous acids

Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out strong contacts and stable interactions in these complexes, and the relationships between the frequency shifts on the H-F and H-O bonds as well as O-F σ-holes with the interaction strength are the benchmarks of this current work. The computations of charge transfer amounts in light of the ChelpG and NBO approaches revealed a separation of charge density on the O-F σ-holes, whose statement is reinforced by the QTAIM descriptors. Despite that O∙∙∙H and N∙∙∙H H-bonds have been characterized as closed-shell interactions, qualitatively the appearance of a partial covalent profile also was unveiled by the QTAIM protocol.

DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.

Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

We present a set of 40 noncovalent complexes of organic halides, halohydrides, and halogen molecules where the halogens participate in a variety of interaction types. The set, named X40, covers electrostatic interactions, London dispersion, hydrogen bonds, halogen bonding, halogen-π interactions, and stacking of halogenated aromatic molecules. Interaction energies at equilibrium geometries were calculated using a composite CCSD(T)/CBS scheme where the CCSD(T) contribution is calculated using triple-ζ basis sets with diffuse functions on all atoms but hydrogen. For each complex, we also provide 10 points along the dissociation curve calculated at the CCSD(T)/CBS level. We use this accurate reference to assess the accuracy of selected post-HF methods.