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

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.

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

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
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.

scholarly journals Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4′-Bipyridine Derivatives

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4409
Author(s):  
Carlo Gatti ◽  
Alessandro Dessì ◽  
Roberto Dallocchio ◽  
Victor Mamane ◽  
Sergio Cossu ◽  
...  
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Source Function ◽  
Noncovalent Interactions ◽  
Conformational Search ◽  
Atomic Group ◽  
Group Contributions ◽  
Conformational Freedom ◽  
Molecular Patterns ◽  
The Impact

Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader–Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4′-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C–Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.

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

2008 ◽  
Vol 64 (3) ◽  
pp. 291-298 ◽  
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.

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

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2933 ◽  
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.

scholarly journals Pillararenes Trimer for Self-Assembly

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 651 ◽  
Author(s):  
Huacheng Zhang ◽  
Zhaona Liu ◽  
Hui Fu
Keyword(s):  
Self Assembly ◽  
Driving Forces ◽  
Click Reaction ◽  
Noncovalent Interactions ◽  
Coupling Reaction ◽  
Covalent Bonds ◽  
Guest Molecules ◽  
Palladium Catalyzed ◽  
Noncovalent Bonds ◽  
External Stimuli

Pillararenes trimer with particularly designed structural geometry and excellent capacity of recognizing guest molecules is a very efficient and attractive building block for the fabrication of advanced self-assembled materials. Pillararenes trimers could be prepared via both covalent and noncovalent bonds. The classic organic synthesis reactions such as click reaction, palladium-catalyzed coupling reaction, amidation, esterification, and aminolysis are employed to build covalent bonds and integrate three pieces of pillararenes subunits together into the “star-shaped” trimers and linear foldamers. Alternatively, pillararenes trimers could also be assembled in the form of host-guest inclusions and mechanically interlocked molecules via noncovalent interactions, and during those procedures, pillararenes units contribute the cavity for recognizing guest molecules and act as a “wheel” subunit, respectively. By fully utilizing the driving forces such as host-guest interactions, charge transfer, hydrophobic, hydrogen bonding, and C–H…π and π–π stacking interactions, pillararenes trimers-based supramolecular self-assemblies provide a possibility in the construction of multi-dimensional materials such as vesicular and tubular aggregates, layered networks, as well as frameworks. Interestingly, those assembled materials exhibit interesting external stimuli responsiveness to e.g., variable concentrations, changed pH values, different temperature, as well as the addition/removal of competition guests and ions. Thus, they could further be used for diverse applications such as detection, sorption, and separation of significant multi-analytes including metal cations, anions, and amino acids.

scholarly journals A theoretical-electron-density databank using a model of real and virtual spherical atoms

2017 ◽  
Vol 73 (4) ◽  
pp. 610-625 ◽  
Author(s):  
Ayoub Nassour ◽  
Slawomir Domagala ◽  
Benoit Guillot ◽  
Theo Leduc ◽  
Claude Lecomte ◽  
...  
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Density Functional ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Ligand Complex ◽  
Urea Molecule ◽  
Covalent Bonds ◽  
Similar Chemical ◽  
Chemical Groups

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

scholarly journals The active site of hen egg-white lysozyme: flexibility and chemical bonding

2014 ◽  
Vol 70 (4) ◽  
pp. 1136-1146 ◽  
Author(s):  
Jeanette Held ◽  
Sander van Smaalen
Keyword(s):  
Quantum Theory ◽  
Electron Density ◽  
Active Site ◽  
Egg White ◽  
Hen Egg White Lysozyme ◽  
Acta Cryst ◽  
Covalent Bonds ◽  
Egg White Lysozyme ◽  
Hen Egg White ◽  
Hen Egg

Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM; Bader (1994),Atoms in Molecules: A Quantum Theory.Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wanget al.(2007),Acta Cryst.D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagalaet al.(2012),Acta Cryst.A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H...O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

scholarly journals Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures

1998 ◽  
Vol 54 (6) ◽  
pp. 1306-1318 ◽  
Author(s):  
Christian Jelsch ◽  
Virginie Pichon-Pesme ◽  
Claude Lecomte ◽  
André Aubry
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Diffraction Data ◽  
Protein Structures ◽  
Fourier Synthesis ◽  
Covalent Bonds ◽  
X Ray ◽  
Density Peaks ◽  
Deformation Electron Density ◽  
Temperature Factors

Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (\Delta B ≃ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 Å.

The Underlying Chemistry of Self-Healing Materials

MRS Bulletin ◽  
2008 ◽  
Vol 33 (8) ◽  
pp. 759-765 ◽  
Author(s):  
Kyle A. Williams ◽  
Daniel R. Dreyer ◽  
Christopher W. Bielawski
Keyword(s):  
Ring Opening ◽  
State Of The Art ◽  
Noncovalent Interactions ◽  
Self Healing ◽  
Covalent Bonds ◽  
The Past ◽  
Ring Opening Reactions ◽  
Ligand Interactions ◽  
Reversible Covalent ◽  
Metal Ligand

AbstractOver the past ten years, a broad range of self-healing materials, systems that can detect when they have been damaged and heal themselves either spontaneously or with the aid of a stimulus, has emerged. Although many unique compositions and components are used to create these materials, they all employ basic chemical reactions to facilitate repair processes. Kinetically controlled ring-opening reactions and reversible metal–ligand interactions have proven useful in autonomic self-healing materials, which require no stimulus (other than the formation of damage) for operation. In contrast, nonautonomic self-healing materials, which require some type of externally applied stimulus (such as heat or light) to enable healing functions, have capitalized on chemistries that utilize either reversible covalent bonds or various types of noncovalent interactions. This review describes the underlying chemistries used in state-of-the-art self-healing materials, as well as those currently in development.

Sign in / Sign up

Export Citation Format

Share Document