Identification of noncovalent interactions driving the folding of cylindrin-like structures using theoretical calculations

AbstractThis study is focused on the adsorption of hexavalent chromium ions Cr(vi) using graphene oxide (GO). The GO was prepared by chemical oxidation (Hummers method) of graphite particles. The synthesized GO adsorbent was characterized by Fourier transform infrared spectroscopy and UV-Vis spectroscopy. It was used for the adsorption of Cr(vi) ions. The theoretical calculations based on density functional theory and Monte Carlo calculations were used to explore the preferable adsorption site, interaction type, and adsorption energy of GO toward the Cr(vi) ions. Moreover, the most stable adsorption sites were used to calculate and plot noncovalent interactions. The obtained results are important as they give molecular insights regarding the nature of the interaction between GO surface and the adsorbent Cr(vi) ions. The found adsorption energy of −143.80 kcal/mol is indicative of the high adsorptive tendency of this material. The adsorption capacity value of GO toward these ions is q = 240.361 mg/g.

Download Full-text

Solid State NMR for Nonexperts: An Overview of Simple but General Practical Methods

Solids ◽

10.3390/solids2020009 ◽

2021 ◽

Vol 2 (2) ◽

pp. 139-154

Author(s):

Ilya G. Shenderovich ◽

Hans-Heinrich Limbach

Keyword(s):

Noncovalent Interactions ◽

Theoretical Calculations ◽

Heterogeneous Systems ◽

Organometallic Compounds ◽

Ease Of Use ◽

Specific System ◽

Main Research ◽

Specialized Equipment ◽

Technical Simplicity ◽

Analytical Tools

There are varieties of methods available for the exploration of solids using nuclear magnetic resonance (NMR) spectroscopy. Some of these methods are quite sophisticated, others require specialized equipment. This review is addressed to those for whom NMR is not the main research method. It discusses simple methods that can be applied to solids with little or no adaptation to a specific system. Despite their technical simplicity and ease of use, these methods are powerful analytical tools that provide unique insights into the structure, dynamics, and noncovalent interactions in homo- and heterogeneous systems. Particular attention is paid to the characterization of porous materials and solids containing phosphorus. 31P NMR of organometallic compounds has been used as an example of how theoretical calculations can help in deeper analysis of experimental data.

Download Full-text

Methyl groups as widespread Lewis bases in noncovalent interactions

Nature Communications ◽

10.1038/s41467-021-25314-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Oliver Loveday ◽

Jorge Echeverría

Keyword(s):

Electron Density ◽

Lewis Acids ◽

Alkaline Earth ◽

Noncovalent Interactions ◽

Theoretical Calculations ◽

Methyl Groups ◽

Halogen Bonds ◽

Common Pattern ◽

Lewis Bases ◽

Significant Strength

AbstractIt is well known that, under certain conditions, C(sp3) atoms behave, via their σ-hole, as Lewis acids in tetrel bonding. Here, we show that methyl groups, when bound to atoms less electronegative than carbon, can counterintuitively participate in noncovalent interactions as electron density donors. Thousands of experimental structures are found in which methyl groups behave as Lewis bases to establish alkaline, alkaline earth, triel, tetrel, pnictogen, chalcogen and halogen bonds. Theoretical calculations confirm the high directionality and significant strength of the interactions that arise from a common pattern based on the electron density holes model. Moreover, despite the absence of lone pairs, methyl groups are able to transfer charge from σ bonding orbitals into empty orbitals of the electrophile to reinforce the attractive interaction.

Download Full-text

Benchmark Experimental Gas-Phase Intermolecular Dissociation Energies by the SEP-R2PI Method

Annual Review of Physical Chemistry ◽

10.1146/annurev-physchem-050317-014224 ◽

2020 ◽

Vol 71 (1) ◽

pp. 189-211 ◽

Cited By ~ 1

Author(s):

Richard Knochenmuss ◽

Rajeev K. Sinha ◽

Samuel Leutwyler

Keyword(s):

Gas Phase ◽

Vibrational Energy ◽

Noncovalent Interactions ◽

Theoretical Calculations ◽

Interaction Strength ◽

Closed Shell ◽

Stimulated Emission ◽

Laser Method ◽

Experimental Database ◽

Dissociation Energies

The gas-phase ground-state dissociation energy D0( S0) of an isolated and cold bimolecular complex is a fundamental measure of the intermolecular interaction strength between its constituents. Accurate D0 values are important for the understanding of intermolecular bonding, for benchmarking high-level theoretical calculations, and for the parameterization of dispersion-corrected density functionals or force-field models that are used in fields ranging from crystallography to biochemistry. We review experimental measurements of the gas-phase D0( S0) and D0( S1) values of 55 different M⋅S complexes, where M is a (hetero)aromatic molecule and S is a closed-shell solvent atom or molecule. The experiments employ the triply resonant SEP-R2PI laser method, which involves M-centered ( S0 → S1) electronic excitation, followed by S1 → S0 stimulated emission spanning a range of S0 state vibrational levels. At sufficiently high vibrational energy, vibrational predissociation of the M⋅S complex occurs. A total of 49 dissociation energies were bracketed to within ≤1.0 kJ/mol, providing a large experimental database of accurate noncovalent interactions.

Download Full-text

XUV Absorption Spectra of Carbon Ions

International Astronomical Union Colloquium ◽

10.1017/s0252921100107444 ◽

1988 ◽

Vol 102 ◽

pp. 71-73

Author(s):

E. Jannitti ◽

P. Nicolosi ◽

G. Tondello

Keyword(s):

Absorption Spectra ◽

Cross Section ◽

Theoretical Calculations ◽

Photoionization Cross Section ◽

Carbon Ions

AbstractThe photoabsorption spectra of the carbon ions have been obtained by using two laser-produced plasmas. The photoionization cross-section of the CV has been absolutely measured and the value at threshold, σ=(4.7±0.5) × 10−19cm2, as well as its behaviour at higher energies agrees quite well with the theoretical calculations.

Download Full-text

Relative Intensities in ED Patterns From Thin Gold Films

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100096436 ◽

1972 ◽

Vol 30 ◽

pp. 636-637

Author(s):

R. H. Morriss ◽

J. D. C. Peng ◽

C. D. Melvin

Keyword(s):

Theoretical Calculations ◽

Diffraction Theory ◽

Gold Films ◽

Reasonable Accuracy ◽

Experimental Conditions ◽

Crystal Perfection ◽

Heavy Atoms ◽

Fine Focus ◽

Convergent Beam ◽

Beam Diffraction

Although dynamical diffraction theory was modified for electrons by Bethe in 1928, relatively few calculations have been carried out because of computational difficulties. Even fewer attempts have been made to correlate experimental data with theoretical calculations. The experimental conditions are indeed stringent - not only is a knowledge of crystal perfection, morphology, and orientation necessary, but other factors such as specimen contamination are important and must be carefully controlled. The experimental method of fine-focus convergent-beam electron diffraction has been successfully applied by Goodman and Lehmpfuhl to single crystals of MgO containing light atoms and more recently by Lynch to single crystalline (111) gold films which contain heavy atoms. In both experiments intensity distributions were calculated using the multislice method of n-beam diffraction theory. In order to obtain reasonable accuracy Lynch found it necessary to include 139 beams in the calculations for gold with all but 43 corresponding to beams out of the [111] zone.

Download Full-text

Effects of Higher-Order Laue Zone reflections on structure images

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100148083 ◽

1993 ◽

Vol 51 ◽

pp. 450-451

Author(s):

H. S. Kim ◽

S. S. Sheinin

Keyword(s):

Wave Vector ◽

Theoretical Calculations ◽

Reciprocal Lattice ◽

Image Plane ◽

Bloch Wave ◽

Dynamical Theory ◽

Higher Order ◽

Lattice Image ◽

Lattice Vector ◽

Image Position

The importance of image simulation in interpreting experimental lattice images is well established. Normally, in carrying out the required theoretical calculations, only zero order Laue zone reflections are taken into account. In this paper we assess the conditions for which this procedure is valid and indicate circumstances in which higher order Laue zone reflections may be important. Our work is based on an analysis of the requirements for obtaining structure images i.e. images directly related to the projected potential. In the considerations to follow, the Bloch wave formulation of the dynamical theory has been used.The intensity in a lattice image can be obtained from the total wave function at the image plane is given by: where ϕg(z) is the diffracted beam amplitide given by In these equations,the z direction is perpendicular to the entrance surface, g is a reciprocal lattice vector, the Cg(i) are Fourier coefficients in the expression for a Bloch wave, b(i), X(i) is the Bloch wave excitation coefficient, ϒ(i)=k(i)-K, k(i) is a Bloch wave vector, K is the electron wave vector after correction for the mean inner potential of the crystal, T(q) and D(q) are the transfer function and damping function respectively, q is a scattering vector and the summation is over i=l,N where N is the number of beams taken into account.

Download Full-text

Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽

10.1039/d0ce01535k ◽

2021 ◽

Author(s):

Viktor N. Serezhkin ◽

Anton V. Savchenkov

Keyword(s):

Crystal Structures ◽

Molecular Crystal ◽

Noncovalent Interactions ◽

Organic Molecular Crystal ◽

Universal Approach ◽

Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

Download Full-text