Variations of quantum electronic pressure under the external compression in crystals with halogen bonds assembled in Cl3-, Br3-, I3-synthons

The inner-crystal quantum electronic pressure was estimated for unstrained C6Cl6, C6Br6, and C6I6 crystals and for those under external compression simulated from 1 to 20 GPa. The changes in its distribution were analyzed for the main structural elements in considered crystals: for triangles of the typical halogen bonds assembled in Hal3-synthons, where Hal = Cl, Br, I; for Hal...Hal stacking interactions, as well as for covalent bonds. Under simulated external compression, the quantum electronic pressure in the intermolecular space reduces as the electron density increases, indicating spatial areas of relatively less crystal resistance to external compression. The most compliant C6Cl6 crystal shows the largest changes of quantum electronic pressure in the centre of Cl3-synthon while the deformation of rigid I3-synthon under external compression depends only on the features of I...I halogen bonds.

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"ANTI-HALOGEN" BONDS AS A FACTOR DETERMINING THE TETRAHEDRAL STRUCTURE OF COPPER IN ITS COMPLEXES WITH (5Z, 5'Z)-2,2'- (ETHANE-1,2-DIYLDISULFANYLDIYL)BIS(5-(2-PYRIDYLMETHYLENE)-3-ALLYL-3,5-DIHYDRO- 4H-IMIDAZOLE-4-ONE)

National Association of Scientists ◽

10.31618/nas.2413-5291.2021.2.74.522 ◽

2021 ◽

Vol 2 (74) ◽

pp. 38-41

Author(s):

A. Al-Khazraji ◽

I. Dudkin ◽

E. Ofitserov ◽

A. Finko ◽

E. Beloglazkina

Keyword(s):

Electron Density ◽

Copper Atom ◽

Halogen Bond ◽

Halogen Bonds ◽

Tetrahedral Structure ◽

Angle Of Rotation

Analysis of the valence angles of the Si and carbon atoms of the C-S bond in the obtained complexes of CiVg2 c (5Z, 5'Z)-2,2’-(ethane-1,2-diyldisulfanyldiyl)bis(5-(2-pyridylmethylene)-3-allyl-3,5-dihydro-4Нimidazole-4-one) unambiguously indicates the determinant effect of the non-valent interactions of the electron density centroids of the NEP of bromine atoms and sulfur atoms, leading to a change in the plane structure of Cu(II) towards tetrahedral with a likely change in the magnetochemical properties of the copper atom, and the angle of rotation of the planes is almost 900. This interaction is the opposite of what is commonly called a halogen bond. In this case, it is an "anti-halogen" bond.

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On the transfer of theoretical multipole parameters for restoring static electron density and revealing and treating atomic anharmonic motion. Features of chemical bonding in crystals of an isocyanuric acid derivative

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520621009690 ◽

2021 ◽

Vol 77 (6) ◽

Author(s):

Sergey A. Shteingolts ◽

Julia K. Voronina ◽

Liliya F. Saifina ◽

Marina M. Shulaeva ◽

Vyacheslav E. Semenov ◽

...

Keyword(s):

Electron Density ◽

Acid Derivative ◽

Noncovalent Interactions ◽

Initial Guess ◽

Atomic Motion ◽

Total Probability ◽

Electronic Temperature ◽

Covalent Bonds ◽

Isocyanuric Acid ◽

Static Electron

The crystal and electronic structure of an isocyanuric acid derivative was studied by high-resolution single-crystal X-ray diffraction within the Hansen–Coppens multipole formalism. The observed deformation electron density shows signs of thermal smearing. The experimental picture meaningfully assigned to the consequences of unmodelled anharmonic atomic motion. Straightforward simultaneous refinement of all parameters, including Gram–Charlier coefficients, resulted in more significant distortion of apparent static electron density, even though the residual density became significantly flatter and more featureless. Further, the method of transferring multipole parameters from the model refined against theoretical structure factors as an initial guess was employed, followed by the subsequent block refinement of Gram–Charlier coefficients and the other parameters. This procedure allowed us to appropriately distinguish static electron density from the contaminant smearing effects of insufficiently accounted atomic motion. In particular, some covalent bonds and the weak π...π interaction between isocyanurate moieties were studied via the mutual penetration of atomic-like kinetic and electrostatic potential φ-basins with complementary atomic ρ-basins. Further, local electronic temperature was applied as an advanced descriptor for both covalent bonds and noncovalent interactions. Total probability density function (PDF) of nuclear displacement showed virtually no negative regions close to and around the atomic nuclei. The distribution of anharmonic PDF to a certain extent matched the residual electron density from the multipole model before anharmonic refinement. No signs of disordering of the sulfonyl group hidden in the modelled anharmonic motion were found in the PDF.

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Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY–X···X–Z(B)m] Type (X = Cl, Br, I)

Molecules ◽

10.3390/molecules24152733 ◽

2019 ◽

Vol 24 (15) ◽

pp. 2733 ◽

Cited By ~ 6

Author(s):

Maxim L. Kuznetsov

Keyword(s):

Kinetic Energy ◽

Interaction Energy ◽

Electron Density ◽

Bond Critical Point ◽

Kinetic Energy Density ◽

Large Set ◽

Halogen Bonds ◽

Absolute Deviation ◽

The Individual ◽

Best Estimator

Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY–X···X–Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as −Eint = 0.128Gb2 − 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.

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Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides

Crystals ◽

10.3390/cryst9100506 ◽

2019 ◽

Vol 9 (10) ◽

pp. 506 ◽

Cited By ~ 6

Author(s):

Irina Yushina ◽

Natalya Tarasova ◽

Dmitry Kim ◽

Vladimir Sharutin ◽

Ekaterina Bartashevich

Keyword(s):

Electron Density ◽

Noncovalent Interactions ◽

Material Design ◽

Spectroscopic Properties ◽

Structural Features ◽

Halogen Bonds ◽

X Ray Diffraction ◽

Raman Spectroscopic ◽

Pairwise Interactions ◽

Noncovalent Bonds

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.

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Structure and electron density of oxysulfide Sm2Ti2S2O4.9, a visible-light-responsive photocatalyst

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768108007532 ◽

2008 ◽

Vol 64 (3) ◽

pp. 291-298 ◽

Cited By ~ 18

Author(s):

Masatomo Yashima ◽

Kiyonori Ogisu ◽

Kazunari Domen

Keyword(s):

Dft Calculations ◽

Visible Light ◽

Valence Band ◽

Electron Density ◽

Diffraction Data ◽

Density Functional ◽

Oxygen Deficiency ◽

Covalent Bonds ◽

Synchrotron Powder Diffraction ◽

Visible Wavelengths

We report the crystal structure and electron density of samarium titanium oxysulfide, Sm2Ti2S2O4.9, photocatalyst obtained through the Rietveld analysis, maximum-entropy method (MEM) and MEM-based pattern fitting of the high-resolution synchrotron powder diffraction data taken at 298.7 K. The Sm2Ti2S2O4.9 has a tetragonal structure with the space group I4/mmm. Refined occupancy factors at the `equatorial' O1 and `apical' O2 sites were 0.994 (3) and 0.944 (12), respectively, which strongly suggest oxygen deficiency at the O2 site. Electron-density analyses based on the synchrotron diffraction data of Sm2Ti2S2O4.9 in combination with density-functional theory (DFT) calculations of stoichiometric Sm2Ti2S2O5 reveal covalent bonds between Ti and O atoms, while the Sm and S atoms are more ionic. The presence of S 3p and O 2p orbitals results in increased dispersion of the valence band, raising the top of the valence band and making the material active at visible wavelengths. The present DFT calculations of stoichiometric Sm2Ti2S2O5 indicate the possibility of overall splitting of water, although Sm2Ti2S2O4.9 works as a visible-light-responsive photocatalyst in aqueous solutions only in the presence of sacrificial electron donors or acceptors. The oxygen deficiency and cocatalyst seem to be factors affecting the catalytic activity.

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6,8-Diiodo-4-oxo-4H-chromene-3-carbaldehyde

Acta Crystallographica Section E Structure Reports Online ◽

10.1107/s1600536814006904 ◽

2014 ◽

Vol 70 (5) ◽

pp. o536-o536

Author(s):

Yoshinobu Ishikawa

Keyword(s):

Least Squares ◽

Title Compound ◽

Three Dimensional ◽

Stacking Interactions ◽

Halogen Bonds ◽

Compound C ◽

Π Stacking ◽

Dimensional Network ◽

Centroid Distance

The title compound, C10H4I2O3, is an iodinated 3-formylchromone derivative, and the atoms are essentially coplanar [r.m.s. deviation = 0.049 Å, largest deviation from the least-squares plane = 0.111 (9) Å for the CH(=O) C atom]. In the crystal, molecules are linked into a three-dimensional network through halogen bonds [I...O = 3.352 (5) and 3.405 (7) Å, C—I...O = 144.2 (3) and 154.5 (3)°, and C=O...I = 134.9 (6) and 146.0 (6)°], and π–π stacking interactions [centroid–centroid distance = 3.527 (6) Å].

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How Far Can One Push the Noble Gases Towards Bonding?: A Personal Account

Molecules ◽

10.3390/molecules24162933 ◽

2019 ◽

Vol 24 (16) ◽

pp. 2933 ◽

Cited By ~ 12

Author(s):

Ranajit Saha ◽

Gourhari Jana ◽

Sudip Pan ◽

Gabriel Merino ◽

Pratim Kumar Chattaraj

Keyword(s):

Electron Density ◽

High Pressures ◽

Noble Gases ◽

Activation Barrier ◽

Covalent Bond ◽

The Other ◽

Personal Account ◽

Covalent Bonds ◽

Other Hand ◽

Different Types

Noble gases (Ngs) are the least reactive elements in the periodic table towards chemical bond formation when compared with other elements because of their completely filled valence electronic configuration. Very often, extreme conditions like low temperatures, high pressures and very reactive reagents are required for them to form meaningful chemical bonds with other elements. In this personal account, we summarize our works to date on Ng complexes where we attempted to theoretically predict viable Ng complexes having strong bonding to synthesize them under close to ambient conditions. Our works cover three different types of Ng complexes, viz., non-insertion of NgXY type, insertion of XNgY type and Ng encapsulated cage complexes where X and Y can represent any atom or group of atoms. While the first category of Ng complexes can be thermochemically stable at a certain temperature depending on the strength of the Ng-X bond, the latter two categories are kinetically stable, and therefore, their viability and the corresponding conditions depend on the size of the activation barrier associated with the release of Ng atom(s). Our major focus was devoted to understand the bonding situation in these complexes by employing the available state-of-the-art theoretic tools like natural bond orbital, electron density, and energy decomposition analyses in combination with the natural orbital for chemical valence theory. Intriguingly, these three types of complexes represent three different types of bonding scenarios. In NgXY, the strength of the donor-acceptor Ng→XY interaction depends on the polarizing power of binding the X center to draw the rather rigid electron density of Ng towards itself, and sometimes involvement of such orbitals becomes large enough, particularly for heavier Ng elements, to consider them as covalent bonds. On the other hand, in most of the XNgY cases, Ng forms an electron-shared covalent bond with X while interacting electrostatically with Y representing itself as [XNg]+Y−. Nevertheless, in some of the rare cases like NCNgNSi, both the C-Ng and Ng-N bonds can be represented as electron-shared covalent bonds. On the other hand, a cage host is an excellent moiety to examine the limits that can be pushed to attain bonding between two Ng atoms (even for He) at high pressure. The confinement effect by a small cage-like B12N12 can even induce some covalent interaction within two He atoms in the He2@B12N12 complex.

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Noncovalent Interactions between 1,3,5-Trifluoro-2,4,6-triiodobenzene and a Series of 1,10-Phenanthroline Derivatives: A Combined Theoretical and Experimental Study

Crystals ◽

10.3390/cryst9030140 ◽

2019 ◽

Vol 9 (3) ◽

pp. 140 ◽

Cited By ~ 1

Author(s):

Yu Zhang ◽

Jian-Ge Wang ◽

Weizhou Wang

Keyword(s):

Crystal Structure ◽

Crystal Structures ◽

Quantum Chemical ◽

Halogen Bond ◽

Noncovalent Interactions ◽

Stacking Interactions ◽

Halogen Bonds ◽

Π Stacking ◽

Π Stacking Interaction ◽

Structural Competition

How many strong C−I⋯N halogen bonds can one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule form in a crystal structure? To answer this question, we investigated in detail the noncovalent interactions between 1,3,5-trifluoro-2,4,6-triiodobenzene and a series of 1,10-phenanthroline derivatives by employing a combined theoretical and experimental method. The results of the quantum chemical calculations and crystallographic experiments clearly show that there is a structural competition between a C−I⋯N halogen bond and π⋯π stacking interaction. For example, when there are much stronger π⋯π stacking interactions between two 1,10-phenanthroline derivative molecules or between two 1,3,5-trifluoro-2,4,6-triiodobenzene molecules in the crystal structures, then one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule forms only one C−I⋯N halogen bond with one 1,10-phenanthroline derivative molecule. Another example is when π⋯π stacking interactions in the crystal structures are not much stronger, one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule can form two C−I⋯N halogen bonds with two 1,10-phenanthroline derivative molecules.

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