1,3,5-Trifluoro-2,4,6-triiodobenzene–piperazine (2/1)

The single-crystal structure of the title compound, C4H10N2·2C6F3I3, features a moderately strong halogen bond between one of the three crystallographically distinct iodine atoms and the nitrogen atom. The iodine–nitrogen distance is 2.820 (3) Å, corresponding to 80% of the sum of their van der Waals radii. The C—I...N halogen bond angle is 178.0 (1)°, consistent with the linear interaction of nitrogen via a σ-hole opposite the carbon–iodine covalent bond. The other two iodine atoms do not engage in halogen bonding. Some weak C—H...F and —H...I interactions are also observed. The complete piperazine molecule is generated by symmetry.

Crystal Structure and Solid-State Packing of 4-Chloro-5H-1,2,3-dithiazol-5-one and 4-Chloro-5H-1,2,3-dithiazole-5-thione

The crystal structure and solid-state packing of 4-chloro-5H-1,2,3-dithiazol-5-one and two polymorphs of 4-chloro-5H-1,2,3-dithiazole-5-thione were analyzed and compared to structural data of similar systems. These five-membered S,N-rich heterocycles are planar with considerable bond localization. All three structures demonstrate tight solid-state packing without voids which is attributed to a rich network of short intermolecular electrostatic contacts. These include Sδ+…Nδ−, Sδ+…Oδ−, Sδ+…Clδ− and Sδ+…Sδ− interactions that are well within the sum of their van der Waals radii (∑VDW). B3LYP, BLYP, M06, mPW1PW, PBE and MP2 were employed to calculate their intramolecular geometrical parameters, the Fukui condensed functions to probe their reactivity, the bond order, Bird Index and NICS(1) to establish their aromaticity.

INTERCAAT: identifying interface residues between macromolecules

Summary The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure. First, INTERCAAT creates a Voronoi tessellation where each atom acts as a seed. Interactions are defined by atoms that share a hyperplane and whose distance is less than the sum of each atoms’ Van der Waals radii plus the diameter of a solvent molecule. Interacting atoms are then classified and interactions are filtered based on compatibility. INTERCAAT implements an adaptive atom classification method; therefore, it can explore interfaces between a variety macromolecules. Availability and implementation Source code is freely available at: https://gitlab.com/fiserlab.org/intercaat. Supplementary information Supplementary data are available at Bioinformatics online.

Crystalline Forms of Trazodone Dihydrates

In this study, treatment of anhydrous trazodone powder with ammonium carbamate in warm water crystallised two new polymorphs or dihydrates of trazodone after 5 h, whose structures were determined by X-ray single crystal diffraction. Each dihydrate contains infinite zigzag hydrogen-bonded chains of water molecules, which are stabilised by the N4 acceptor atom of the piperazine ring and the pendant carbonyl O1 atom of the triazole ring, as well as other water molecules. The strong dipole moment expected for the O1 atom makes it a good hydrogen bond acceptor for stabilising the chains of water molecules. Each molecule of trazodone has a similar conformation in both hydrates, except for the propyl chains, which adopt different conformations: anti-gauche in the β hydrate (triazole N-C-C-C and C-C-C-piperazine N) and anti-anti in the γ hydrate. Both piperazine rings adopt chair conformations, and the exocyclic N-C bonds are in equatorial orientations. The Hirshfeld surfaces and two-dimensional fingerprint plots for the polymorphs were calculated using CrystalExplorer17, which indicated contacts significantly shorter than the sum of the van der Waals radii in the vicinity of the piperazine N4 and triazole O1 atoms corresponding to the strong hydrogen bonds accepted by these atoms.

Ratiometric Near-Infrared Fluorescent Probes Based on Hemicyanine Dyes Bearing Dithioacetal and Formal Residues for pH Detection in Mitochondria

Ratiometric near-infrared fluorescent probes (AH+ and BH+) have been prepared for pH determination in mitochondria by attaching dithioacetal and formal residues onto a hemicyanine dye. The reactive formyl group on probe BH+ allows for retention inside mitochondria as it can react with a protein primary amine residue to form an imine under slightly basic pH 8.0. Probes AH+ and BH+ display ratiometric fluorescent responses to pH changes through the protonation and deprotonaton of a hydroxy group in hemicyanine dyes with experimentally determined pKa values of 6.85 and 6.49, respectively. Calculated pKa values from a variety of theoretical methods indicated that the SMDBONDI method of accounting for solvent and van der Waals radii plus including a water molecule located near the site of protonation produced the closest overall agreement with the experimental values at 7.33 and 6.14 for AH+ and BH+ respectively.

Theoretical atomic radii of elements (H-Cm): A non-relativistic study with Gaussian basis set using HF, post-HF and DFT methods

We calculated the most probable radius of an atom for elements from H to Cm. The calculations were carried out by using non-relativistic, spin polarized, HF, MP2 and DFT methods with all electron Gaussian basis set. Periodicity of atomic radii was correlated with the experimental first ionization energies. This non-relativistic atomic radii were also compared with other theoretical atomic radii. With respect to the Dirac-Slater data, our values were in good agreement with the elements up to Sn. Relationship with van der Waals radii of noble gases was discussed. Anomalous properties of Gd and Pd were examined. Linearity of lanthanide contraction of elements with 4f electrons is illustrated. This linearity is found independent of the extent of electron correlation.

Theoretical Atomic Radii of Elements (H-Cm): A Non-Relativistic Study with Gaussian Basis Set Using HF, Post-HF and DFT Methods

<div><p>We calculated the most probable radius of an atom for elements from H to Cm. The calculations were carried out by using non-relativistic, spin polarized, HF, MP2 and DFT methods with all electron Gaussian basis set<i>. </i>Periodicity of atomic radii was correlated with the experimental first ionization energies. This non-relativistic atomic radii were also compared with other theoretical atomic radii. With respect to the Dirac-Slater data, our values were in good agreement with the elements up to Sn. Relationship with van der Waals radii of noble gases was discussed. Anomalous properties of Gd and Pd were examined. Linearity of lanthanide contraction of elements with <i>4f </i>electrons is illustrated. This linearity is found independent of the extent of electron correlation. S.I. give data of calculated radii and other correlated studies (with ionization energies, another theoretical radii etc.)</p></div>

Theoretical Atomic Radii of Elements (H-Cm): A Non-Relativistic Study with Gaussian Basis Set Using HF, Post-HF and DFT Methods

<div><p>We calculated the most probable radius of an atom for elements from H to Cm. The calculations were carried out by using non-relativistic, spin polarized, HF, MP2 and DFT methods with all electron Gaussian basis set<i>. </i>Periodicity of atomic radii was correlated with the experimental first ionization energies. This non-relativistic atomic radii were also compared with other theoretical atomic radii. With respect to the Dirac-Slater data, our values were in good agreement with the elements up to Sn. Relationship with van der Waals radii of noble gases was discussed. Anomalous properties of Gd and Pd were examined. Linearity of lanthanide contraction of elements with <i>4f </i>electrons is illustrated. This linearity is found independent of the extent of electron correlation. S.I. give data of calculated radii and other correlated studies (with ionization energies, another theoretical radii etc.)</p></div>

Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules

Diffusion is a spontaneous process and one of the physicochemical phenomena responsible for molecular transport, the rate of which is governed mainly by the diffusion coefficient; however, few coefficients are available because the measurement of diffusion rates is not straightforward. The translational diffusion coefficient is related by the Stokes–Einstein equation to the approximate radius of the diffusing molecule. Therefore, the stable conformations of small molecules were first calculated by molecular modeling. A simple radius rs and an effective radius re were then proposed and estimated using the stable conformers with the van der Waals radii of atoms. The diffusion coefficients were finally calculated with the Stokes–Einstein equation. The results showed that, for the molecules with strong hydration ability, the diffusion coefficients are best given by re and for other compounds, rs provided the best coefficients, with a reasonably small deviation of ~0.3 × 10−6 cm2/s from the experimental data. This demonstrates the effectiveness of the theoretical estimation approach, suggesting that diffusion coefficients have potential use as an additional molecular property in drug screening.