Are there specific sub-classes of halogen bonds? A statistical analysis of the interactions in crystal structures

Inferential Statistics

Structural competition between halogen bonds and lone-pair···π interactions in solution is studied using (13)C NMR combined with density functional theory calculations. Among the halogen bonds considered, only the iodine bonds and a few bromine bonds are strong enough to compete successfully with the lone-pair···π interactions.

A study was made of X-H...F-C interactions (X = N or O) in small-molecule crystal structures. It was primarily based on 6728 structures containing X-H and C-F and no atom heavier than chlorine. Of the 28 451 C-F moieties in these structures, 1051 interact with X-H groups. However, over three-quarters of these interactions are either the weaker components of bifurcated hydrogen bonds (so likely to be incidental contacts) or occur in structures where there is a clear insufficiency of good hydrogen-bond acceptors such as oxygen, nitrogen or halide. In structures where good acceptors are entirely absent, there is about a 2 in 3 chance that a given X-H group will donate to fluorine. Viable alternatives are X-H...π hydrogen bonds (especially to electron-rich aromatics) and dihydrogen bonds. The average H...F distances of X-H...F-C interactions are significantly shorter for CR3F (R = C or H) and Csp2-F acceptors than for CRF3. The X-H...F angle distribution is consistent with a weak energetic preference for linearity, but that of H...F-C suggests a flat energy profile in the range 100-180°. X-H...F-C interactions are more likely when the acceptor is Csp2-F or CR3F, and when the donor is C-NH2. They also occur significantly more often in structures containing tertiary alcohols or solvent molecules, or with Z' > 1, i.e. when there may be unusual packing problems. It is extremely rare to find X-H...F-C interactions in structures where there are several unused good acceptors. When it does happen, there is often a clear reason, e.g. awkwardly shaped molecules whose packing isolates a donor group from the good acceptors.

Editor's evaluation: Molecular basis of ligand-dependent Nurr1-RXRα activation

Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen-halogen contacts and hydrogen bonds (I⋯N, I⋯F, I⋯I, F⋯F, I⋯H and F⋯H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of -9.58kcalmol-1 and -7.10kcalmol-1 observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing. The electrostatic potential values calculated for all crystal structures have a positive σ-hole, which aids understanding of the nature of σ-hole bonds. The significance of the existence of halogen bonds in crystal packing environments was authenticated by replacing iodine atoms by bromine and chlorine atoms. Nucleus independent chemical shift analysis reported on the resonance contribution to the interaction energies of halogen bonds and halogen-halogen contacts. Hirshfeld surface analysis and topological analysis (atoms in molecules) were carried out to analyze the occurrence and strength of all non-covalent interactions. These analyses revealed that halogen bond interactions were more dominant than hydrogen bonding interactions in these crystal structures. Graphical Abstract Molecluar structure of 1,4-Di-iodotetrafluorobenzene bis(thianthrene 5-oxide) moelcule and its corresponding molecular electrostatic potential map for the view of σ-hole.

SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH · · · O) hydrogen bonds have been proposed to coordinate the methyl groups of AdoMet and methyllysine within the SET domain active site. However, the presence of these hydrogen bonds has only been inferred due to the uncertainty of hydrogen atom positions in x-ray crystal structures. To experimentally resolve the positions of the methyl hydrogen atoms, we used NMR (1)H chemical shift coupled with quantum mechanics calculations to examine the interactions of the AdoMet methyl group in the active site of the human KMT SET7/9. Our results indicated that at least two of the three hydrogens in the AdoMet methyl group engage in CH · · · O hydrogen bonding. These findings represent direct, quantitative evidence of CH · · · O hydrogen bond formation in the SET domain active site and suggest a role for these interactions in catalysis. Furthermore, thermodynamic analysis of AdoMet binding indicated that these interactions are important for cofactor binding across SET domain enzymes.

The CH-O interactions of pyridine with water molecules were studied by analysing the data in the Cambridge Structural Database (CSD) and by ab initio calculations. The analysis of the CH-O interactions in the crystal structures from the CSD indicates that pyridine C-H donors do not show preference for linear contacts. The results of the ab initio calculations are in accord with the CSD data and show that stabilization energy is larger for bifurcated interactions than for linear interactions. The calculated interaction energies at the MP2/cc-pVQZ level for linear CH-O interactions between water and pyridine ortho, meta, and para C-H groups are -1.24, -1.94 and -1.97 kcal mol(-1), respectively. The calculated energies for bifurcated ortho-meta and meta-para interactions are -1.96 and -2.16 kcal mol(-1). The data in the crystal structures from the CSD and ab initio calculations show a strong influence of simultaneous classical hydrogen bonds of pyridine on the CH-O interactions. The results show that simultaneous hydrogen bonds strengthen the CH-O interaction by about 20%. The calculated interaction energies for linear CH-O interactions between water and pyridine, with simultaneous hydrogen bonds, for ortho, meta, and para C-H groups are -1.64, -2.34, and -2.33 kcal mol(-1), respectively, while those for ortho-meta and meta-para bifurcated interactions are -2.44 and -2.58 kcal mol(-1). The energies of the meta-para bifurcated interactions calculated at the CCSD(T)(limit) level for pyridine without and with hydrogen bonds are -2.30 and -2.69 kcal mol(-1), respectively. The result that nonlinear interactions are energetically favoured can be very important for recognizing the CH-O interaction of heteroaromatic rings in the crystal structures and biomolecules.

Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono- and polysubstituted PH3 -NH3 complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self-assembly structures.

Synthesis, crystal structures and intermolecular interactions of two Mn(II) complexes with 4,4′-bipy and methyl benzoates

Low-dimensional hybrid lead-halide perovskites with broadband white-light emission upon near-UV excitation have attracted immense scientific interest due to their potential application for the next...

ABSTRACTIn the present work, the cooperativity between hydrogen bond‒hydrogen bond, halogen bond‒halogen bond and hydrogen bond‒halogen bond in ternary FX…diazine…XF (X = H and Cl) complexes is theoretically investigated. The sign of cooperative energy (Ecoop) obtained in all of the triads is positive which indicates that the ternary complex is less stable than the sum of the two isolated binary complexes. Moreover, our calculations show that Ecoop value in triads increases as FX…pyridazine…XF > FX…pyrimidine…XF > FX…pyrazine…XF. In agreement with energetic, geometrical and topological properties, electrostatic potentials and coupling constants across 15N…X−19F (X = 1H or 35Cl) hydrogen and halogen bonds indicate that hydrogen and halogen bonds are weakened in the considered complexes where two hydrogen and halogen bonds coexist. As compared to N…H hydrogen bond, it is also observed that cooperativity has greater effect on N…Cl halogen bond.

Cadmium complexes exhibit extensive potential applications in many fields, such as magnetism materials, biological active materials, optical device and catalysis materials [1]. The reported compound [Tetrakis(5-amino-3-carboxy-1H-1,2,4-triazol-4-ium) hexachloridocadmate (II) tetrahydrate (1) ] was prepared as part of our ongoing investigations of hydrogen-bonding interactions in the crystal structures of metal-protonated N-aromatic heterocyclic hybrid frameworks [2]. 5-Amino-1H-1,2,4-triazole-3-carboxylic acid arises as a promising ligand which can be employed in the preparation of coordination compounds as a consequence of its multiple buildings sites and its basic nitrogen capable of associating with a proton H+ in acid solution [3]. The single-crystal X-ray structure analysis revealed that (1) crystallizes in the monoclinic P-1 space group, the Cd(II) atom is located at a crystallographic inversion centre. The latter ion is octahedrally coordinated by six chloride anions, Due to the presence of a considerable number of proton donors and acceptors, the crystal structure is rich in hydrogen bonding interactions which led to the formation of discrete cation layers spaced by hexachloridocadmate anions. Examination of the cation-anion interactions reveals that N–H...Cl hydrogen bonding are the major packing interactions, It appears that the layered structure results from the octahedral [CdCl6]2- anions along with its ability to form hydrogen bonds in different directions, intermolecular hydrogen bonding interactions between the chloride atom and oxygen atoms of water molecules interconnect the layers into a three-dimensional framework.

Aims and Objectives : It is observed that negative studies published in medical journals are underpowered to detect the actual difference between the groups, but no data are available on the quality of the statistics reported in these studies. Therefore, this study was carried out with aim of evaluating negative studies published in Indian medical journals for adequacy of reporting of descriptive and inferential statistics. Materials and Methods : All the original articles published in 14 Pubmed-indexed Indian medical journals were analyzed to determine whether the study was negative or positive. All the negative studies were analyzed for correctness of the descriptive statistics and inferential statistics. The types of data and statistical methods were also noted down. Descriptive statistics was used and values were expressed as frequency, percentages and confidence interval. Results : Incorrect descriptive statistics was mentioned in 15 (28.8%, 95% CI 18.3-42.2%) studies. Information related to assumptions of statistical tests were mentioned in only two (3.8%, 95% CI 1.0-12.9%) articles. Inappropriate/incorrect statistical tests was used in 22 (42.3%, 95% CI 29.8-55.8%) studies. The most common reason for inappropriate reporting of descriptive statistics was use of mean and SD for description of ordinal data. The most common reason for incorrect statistical test was use of parametric test for ordinal data. The most common statistical test was the t-test. Conclusion : Negative studies published in prominent Indian medical journals are statistically weak, and readers critically analyze these studies before making any opinion based on them.

The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.

The crystal and molecular structure of quercetin: A biologically active and naturally occurring flavonoid