A practical scheme for ab initio determination of a crystal structure based on the Dirac equation

An applicable formulation of ab initio crystal structure determination based on the Dirac equation is presented. For this purpose, Dirac equation without regard to electron correlation effects is reduced to its spin-free one-component form by means of regular approximations, and then, connected to crystallographic notions. Thus, a relativistically valid structural description of a crystal structure is made possible by using single crystal X-ray diffraction data. The relativistic scheme was tested with a previously reported crystal structure containing heavy elements, and the results show that accuracy of the phase assignment process increases as the order of regular approximation is raised

pi-Cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds?

The results from absolutely localized molecular orbital (ALMO)-energy decomposition analysis (EDA) and ALMO-charge transfer analysis (CTA) at M06-2X/cc-pVTZ level reveal that double-proton transfer (DPT) reactions through base pairing H-bonds have nonignorable effects on the stacking energies of dinucleotide steps, which introduces us to a novel stabilization (or destabilization) factor in the DNA duplex. Thus, intra-and inter-strand base stacking interactions are coalesced with each other mediated by H-bridged quasirings between base pairs. Changes in stacking energies of dinucleotide steps depending on the positions of H atoms are due to variations in local aromaticities of individual nucleobases, manifesting pi-cooperativity effects. CT analyses show that dispersion forces in dinucleotide steps can lead to radical changes in the redox properties of nucleobases, in particular those of adenine and guanine stacked dimers in a strand. Besides Watson-Crick rules, novel base pairing rules were propounded by considering CT results. According to these, additional base pairing through pi-stacks of nucleobases in dinucleotide steps does not cause any intrinsic oxidative damage to the associated nucleobases throughout DPT

Geometry dependence of electron donating or accepting abilities of amine groups in 4,4'-disulfanediylbis(methylene)dithiazol-2-amine: Pyramidal versus planar

The molecular and crystal structure of the title compound in which two thiazole-2-amine rings are linked to each other by disulfide bridge (-C-S-S-C-) were studied by single-crystal X-ray diffraction, FT-IR, NMR spectroscopy, quantum chemical calculations and topological analyses on the electron density. A novel synthesis route for the compounds having symmetrical disulfide bridge is reported. The most important result regarding the compound is about electron donating or accepting properties of the terminal amine groups. Planar amine group acts as an electron-donating group, while pyramidal amine behaves as electron-accepting group. This inference was confirmed by scrutiny of crystallographic geometry and quantum chemical studies. To ascertain underlying reasons for this fact, intermolecular interactions (N-H center dot center dot center dot N type H-bonds and C-H center dot center dot center dot pi interactions) were studied. These interactions involving aromatic thiazole rings are verified by topological electron density and Hirshfeld surface analyses. Intermolecular interactions do not have an effect on the differentiation in electron donating or accepting ability of amine groups, because both amine groups are involved in N-H center dot center dot center dot N type H-bonds. In methodological sense, it has been understood that Ehrenfest forces acting on electron density are useful theoretical probe to analyze intra-molecular charge transfer processes. 2017 Elsevier B.V. All rights reserved

Supramolecular aromaticity

We report experimental and theoretical evidences for supramolecular aromaticity as a new concept to be widely used in researches about molecular crystals. CSD survey regarding frequently encountered resonance-assisted H-bonds (RAHBs) in formic acid, formamide, formimidamide, formic acid-formamide, and formamide-formimidamide dimers shows that supramolecular quasirings formed by RAHBs have remarkable electronic delocalization within themselves, which is reminiscent of aromaticity at supramolecular level. This study criticizes and reevaluates the validity of conventional judgment which states that ring systems formed by intermolecular H-bonds cannot be aromatic. Thus, the term aromaticity can be extended to supramolecular systems formed by RAHBs. Supramolecular aromaticity has a multi-fold nature involving both sigma- and pi-delocalization, and sigma-delocalization through RAHBs takes on a task of compensating a-deficiency within quasirings. Atomic composition in donor-acceptor set of the dimers is descriptive for supramolecular aromaticity. We revised bond-valence parameters for RAHBs and they suggest that hypervalent character of H atoms is more pronounced than their hypovalent character in RAHBs. The sigma-delocalized bonding within H-bonded quasirings necessitates hypervalent character of H atoms. Quantum chemical calculations based on adiabatic Hydrogen Atom Transfer (HAT) between the monomers reveal that topological parameters at ring critical points (RCPs) of the quasirings correlate well with Shannon's entropic aromaticity index. The presence of additional LP orbital on 0 atoms implying more diffused LP-orbitals in donor-acceptor set leads to the formation of resonance-disabling states reducing supramolecular aromaticity of a quasiring and energetic cost of the electron transfer between the monomers. There is a nonignorable electron transfer between the monomers even in the cases where H atoms are close to donor or acceptor atom. NBO analyses have revealed that formally vacant LP* orbitals on H-atoms in TS geometries mediate intermolecular electron transfer as a result of the hyperconjugative stereoelectronic interactions. (C) 2014 Elsevier B.V. All rights reserved

Hydrogen-bridged chelate ring-assisted pi-stacking interactions

A salicylideneaniline (SA) derivative, (6Z)-6-({[2-(hydroxymethyl)phenyl]amino}methylidene)-3,5-dimethoxycyclohexa-2,4-dien-1-one monohydrate, has an increased aromaticity within its hydrogen-bridged chelate ring owing to its NH character. In the reported crystal structure, nonconventional pi-stacking interactions, which are referred to as hybrid pi-stacking interactions, are observed between a quasiaromatic chelate ring, formed as a result of the resonance-assisted intramolecular hydrogen bond and ordinary aromatic rings. Besides, pi-stacking interactions are also seen between two hydrogen-bridged quasiaromatic chelate rings, which are referred to as pure pi-stacking interactions. A CSD search has revealed that both kinds of interactions are frequently observed in molecular crystals of SA derivatives in fully or partially NH tautomeric form, and aromaticity levels of certain fragments of SA derivatives have dramatic effects on their stacking arrangements. These interactions are distinguished from the usual pi center dot center dot center dot pi interactions by their formation character, i.e. both sigma- and pi-deficient and sigma-deficient character of pure interactions is more pronounced than that of the hybrid ones

Changes in ligating abilities of the singlet and triplet states of normal, abnormal and remote N-heterocyclic carbenes depending on their aromaticities

Quantum chemical calculations at B3LYP/aug-cc-pVTZ level about singlet N-heterocyclic carbene (NHC) ligands, imidazol-2-ylidene, imidazol-4-ylidene, pyrazol-3-ylidene and pyrazol-4-ylidene, and their protonated analogues show that they are considerably aromatic except for pyrazol-3-ylidene. This result is experimentally verified by approximately five thousand NHC transition metal complexes retrieved from the Cambridge Structural Database (CSD). CSD search discloses that NHCs can participate in pi-stacking interactions, albeit scarce. Geometry-based HOMA and electronic aromaticity index FLU rather than NICS provide a satisfactory description of the bonding situations in NHC ligands. Singlet state of the normal NHC has electron-deficient aromaticity as compared to those of the abnormal and remote NHCs. Depending on the transition from the singlet to triplet state, NHCs become electron-deficient ligands except for remote NHC. Computational studies regarding electronic nature of free NHC ligands show that the pi-electronic population of the formally vacant p(pi) orbital on the carbene atoms in abnormal and remote NHC is occurred as a result of the aromaticity of NHCs, not as a result of the direct electron donation from LP-orbitals of N atoms to carbene atom according to putative push-pull effect used in understanding the electronic stabilization of normal NHC. Increase in the aromaticity raises sigma-donating ability of both imidazol-and pyrazol-based NHC ligands. Free abnormal and remote NHC ligands have higher sigma-donation ability than normal NHC ligands. The lack of sigma-donating ability of normal NHC is compensated by its relatively high pi-accepting ability, whereas pi-back donation abilities of abnormal and remote NHCs are prohibited by their almost fully occupied pi-orbitals. Aromaticities of the triplet NHC ligands are higher than that of the lowest-lying triplet state of benzene. Increase in the aromaticity of NHC ligands decreases van der Waals shortening in TM-NHC bonds mainly due to diminishing dative character of these bonds