London Dispersion Helps Refine Steric A-Values: Dispersion Energy Donor Scales

2021 ◽  
Author(s):  
Ephrath Solel ◽  
Marcel Ruth ◽  
Peter R. Schreiner
Keyword(s):  
Dispersion Energy ◽  
Energy Donor ◽  
London Dispersion

scholarly journals Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds – an experimental and theoretical study

2018 ◽  
Vol 14 ◽  
pp. 2125-2145 ◽  
Author(s):  
Ana-Maria Preda ◽  
Małgorzata Krasowska ◽  
Lydia Wrobel ◽  
Philipp Kitschke ◽  
Phil C Andrews ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Van Der Waals ◽  
Structural Features ◽  
Van Der Waals Interactions ◽  
Model Systems ◽  
Bismuth Atom ◽  
Dispersion Energy ◽  
Space Group ◽  
Intermolecular Contacts ◽  
London Dispersion

The dispersion type Bi···π arene interaction is one of the important structural features in the assembly process of arylbismuth compounds. Several triarylbismuth compounds and polymorphs are discussed and compared based on the analysis of single crystal X-ray diffraction data and computational studies. First, the crystal structures of polymorphs of Ph3Bi (1) are described emphasizing on the description of London dispersion type bismuth···π arene interactions and other van der Waals interactions in the solid state and the effect of it on polymorphism. For comparison we have chosen the substituted arylbismuth compounds (C6H4-CH═CH2-4)3Bi (2), (C6H4-OMe-4)3Bi (3), (C6H3-t-Bu2-3,5)3Bi (4) and (C6H3-t-Bu2-3,5)2BiCl (5). The structural analyses revealed that only two of them show London dispersion type bismuth···π arene interactions. One of them is the styryl derivative 2, for which two polymorphs were isolated. Polymorph 2a crystallizes in the orthorhombic space group P212121, while polymorph 2b exhibits the monoclinic space group P21/c. The general structure of 2a is similar to the monoclinic C2/c modification of Ph3Bi (1a), which leads to the formation of zig-zag Bi–arenecentroid ribbons formed as a result of bismuth···π arene interactions and π···π intermolecular contacts. In the crystal structures of the polymorph 2b as well as for 4 bismuth···π arene interactions are not observed, but both compounds revealed C–HPh···π intermolecular contacts, as likewise observed in all of the three described polymorphs of Ph3Bi. For compound 3 intermolecular contacts as a result of coordination of the methoxy group to neighboring bismuth atoms are observed overruling Bi···π arene contacts. Compound 5 shows a combination of donor acceptor Bi···Cl and Bi···π arene interactions, resulting in an intermolecular pincer-type coordination at the bismuth atom. A detailed analysis of three polymorphs of Ph3Bi (1), which were chosen as model systems, at the DFT-D level of theory supported by DLPNO-CCSD(T) calculations reveals how van der Waals interactions between different structural features balance in order to stabilize molecular arrangements present in the crystal structure. Furthermore, the computational results allow to group this class of compounds into the range of heavy main group element compounds which have been characterized as dispersion energy donors in previous work.

scholarly journals Evaluation of bismuth-based dispersion energy donors – synthesis, structure and theoretical study of 2-biphenylbismuth(iii) derivatives

2020 ◽  
Vol 22 (18) ◽  
pp. 10189-10211
Author(s):  
Ana-Maria Fritzsche ◽  
Sebastian Scholz ◽  
Małgorzata Krasowska ◽  
Kalishankar Bhattacharyya ◽  
Ana Maria Toma ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Dispersion Interactions ◽  
Dispersion Energy ◽  
London Dispersion

Intramolecular Bi⋯π arene London dispersion interactions in (biphenyl)3−xBiXx amount to ca. 20 kJ mol−1 with distances of 3.8–4.0 Å.

QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE

2008 ◽  
Vol 07 (03) ◽  
pp. 317-329 ◽  
Author(s):  
SIAVASH RIAHI ◽  
MOHAMMAD REZA GANJALI ◽  
PARVIZ NOROUZI
Keyword(s):  
Base Pair ◽  
Dft Method ◽  
Base Pairs ◽  
Dispersion Energy ◽  
Charge Delocalization ◽  
Dna Base ◽  
Quantum Mechanical Description ◽  
London Dispersion ◽  
Dna Base Pair ◽  
The Stability

Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.

scholarly journals The effect of electronic excitation on London dispersion

2018 ◽  
Vol 96 (7) ◽  
pp. 730-737 ◽  
Author(s):  
Xibo Feng ◽  
Alberto Otero-de-la-Roza ◽  
Erin R. Johnson
Keyword(s):  
Density Functional ◽  
Electronic Excitation ◽  
Organic Dyes ◽  
Dispersion Model ◽  
Dispersion Energy ◽  
Dispersion Coefficients ◽  
Light Emitting ◽  
Molecular Dispersion ◽  
London Dispersion

Atomic and molecular dispersion coefficients can now be calculated routinely using density-functional theory. In this work, we present the first determination of how electronic excitation affects molecular C6 London dispersion coefficients from the exchange-hole dipole moment (XDM) dispersion model. Excited states are typically found to have larger dispersion coefficients than the corresponding ground states, due to their more diffuse electron densities. A particular focus is both intramolecular and intermolecular charge-transfer excitations, which have high absorbance intensities and are important in organic dyes, light-emitting diodes, and photovoltaics. In these classes of molecules, the increase in C6 for the electron-accepting moiety is largely offset by a decrease in C6 for the electron-donating moiety. As a result, the change in dispersion energy for a chromophore interacting with neighbouring molecules in the condensed phase is minimal.

scholarly journals A Generally Applicable Atomic-Charge Dependent London Dispersion Correction Scheme

2018 ◽  
Author(s):  
Eike Caldeweyher ◽  
Sebastian Ehlert ◽  
Andreas Hansen ◽  
Hagen Neugebauer ◽  
Sebastian Spicher ◽  
...  
Keyword(s):  
Density Functional ◽  
Dispersion Model ◽  
Atomic Charge ◽  
Body Part ◽  
Dispersion Interactions ◽  
Dispersion Energy ◽  
Dispersion Coefficients ◽  
Charge Dependence ◽  
London Dispersion ◽  
Dynamic Polarizabilities

<div>The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modelling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are pre-computed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole, as well as dipole-quadrupole interactions. For a benchmark set of 1225 molecular dipole-dipole dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.9% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested and an energy correction based on D4 polarizabilities is found to be advantageous for larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common density functionals. For various standard energy benchmark sets DFT-D4 slightly but consistently outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence of the dispersion coefficients improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as other low-cost approaches like force-fields or semi-empirical models.</div>

scholarly journals Extension and Evaluation of the D4 London Dispersion Model for Periodic Systems

2019 ◽  
Author(s):  
Eike Caldeweyher ◽  
Jan-Michael Mewes ◽  
Sebastian Ehlert ◽  
Stefan Grimme
Keyword(s):  
Materials Science ◽  
Dispersion Model ◽  
Low Cost ◽  
Chem Phys ◽  
Periodic Systems ◽  
Computationally Efficient ◽  
Dispersion Energy ◽  
Alkaline Metals ◽  
Standard Application ◽  
London Dispersion

<div>London-dispersion effects are of great relevance to many aspects of materials science and for various condensed matter problems. In this work we present an adaptation and implementation of the DFT-D4 model [Caldeweyher et al., J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredient are better computed reference polarizabilities for high coordination numbers (including alkaline metals, earth alkaline metals, and d-metals of group 3-5), which are consistently derived from periodic electrostatically embedded cluster calculations. Some technical extensions have been added concerning the coordination number, the partial charges, and the dispersion energy expression. To demonstrate the performance of the improved scheme, several test cases are considered, for which we compare D4 results to those of its predecessor D3(BJ) as well as to several other dispersion corrected methods. The largest improvements are observed for solid state polarizabilities of 16 inorganic salts, where the new D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides high accuracy similar to MBD/HI or uncorrected DFT/SCAN approaches. These results suggest the standard application of the proposed periodic D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.</div>

scholarly journals Extension and Evaluation of the D4 London Dispersion Model for Periodic Systems

2019 ◽  
Author(s):  
Eike Caldeweyher ◽  
Jan-Michael Mewes ◽  
Sebastian Ehlert ◽  
Stefan Grimme
Keyword(s):  
Materials Science ◽  
Dispersion Model ◽  
Low Cost ◽  
Chem Phys ◽  
Periodic Systems ◽  
Computationally Efficient ◽  
Dispersion Energy ◽  
Alkaline Metals ◽  
Standard Application ◽  
London Dispersion

<div>London-dispersion effects are of great relevance to many aspects of materials science and for various condensed matter problems. In this work we present an adaptation and implementation of the DFT-D4 model [Caldeweyher et al., J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredient are better computed reference polarizabilities for high coordination numbers (including alkaline metals, earth alkaline metals, and d-metals of group 3-5), which are consistently derived from periodic electrostatically embedded cluster calculations. Some technical extensions have been added concerning the coordination number, the partial charges, and the dispersion energy expression. To demonstrate the performance of the improved scheme, several test cases are considered, for which we compare D4 results to those of its predecessor D3(BJ) as well as to several other dispersion corrected methods. The largest improvements are observed for solid state polarizabilities of 16 inorganic salts, where the new D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides high accuracy similar to MBD/HI or uncorrected DFT/SCAN approaches. These results suggest the standard application of the proposed periodic D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.</div>

INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY

2010 ◽  
Vol 09 (05) ◽  
pp. 875-888 ◽  
Author(s):  
SIAVASH RIAHI ◽  
SOLMAZ EYNOLLAHI ◽  
MOHAMMAD REZA GANJALI
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Rational Design ◽  
Dft Method ◽  
Physicochemical Interaction ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Face To Face ◽  
London Dispersion ◽  
Pharmaceutical Agents

In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.

On the change of the order od stability of DNA base pairs as a result of the methylation of guanine

1988 ◽  
Vol 53 (9) ◽  
pp. 1943-1945
Author(s):  
Pavel Hobza ◽  
Camille Sandorfy
Keyword(s):  
Ab Initio ◽  
Base Pairs ◽  
Dispersion Energy ◽  
Dna Base ◽  
Dna Base Pairs

The interaction of the 6-O methylguanine cation with cytosine and thymine was studied using the ab initio SCF method in combination with a London type expression for dispersion energy. The structure of the complex formed with cytosine differs from that found previously with guanine itself.

scholarly journals A Novel Index (RI) to Evaluate the Relative Stability of Soils Using Ultrasonic Agitation

2021 ◽  
Vol 13 (8) ◽  
pp. 4229
Author(s):  
Fakher Abbas ◽  
Fang Lin ◽  
Zhaolong Zhu ◽  
Shaoshan An
Keyword(s):  
Relative Stability ◽  
Characteristic Curve ◽  
Geometric Mean ◽  
Relative Strength ◽  
Soil Stability ◽  
Dispersion Energy ◽  
Ultrasonic Agitation ◽  
Mean Weight Diameter ◽  
Change In Mean ◽  
Wet Sieving

As soil stability is a complex phenomenon, various methods and indexes were introduced to assess the strength of soils. Because of the limitations of different stability methods and indexes (including wet sieving-based), we aimed to presents a relative stability index (RI) that was based on the estimated components of the soil overall disruptive characteristic curve (SODC): (1) soil disruption constant (Ki, that is based upon dispersion energy of soils); (2) resulting change in mean weight diameter (ΔMWD). To evaluate the effectiveness and limitations of RI as well as to compare it with classical soil stability indexes of mean weight diameter (MWD) and geometric mean diameter (GMD). Ultrasonic agitation (UA) along with a wet sieving method (followed by dry sieving) was applied against four different soils named on the basis of sample location, Qingling soil (QL), Guanzhong soil (GZ), Ansai soil (AS), and Jingbian soil (JB). To evaluate the relative strength of soils at different applied energies (increase in sonication duration usually resulted in increased input energy and temperature of soil–water suspension), soils were subjected to six sonication durations (0, 30, 60, 120, 210, and 300 s) with a fixed (and exact) initial amplitude and temperature. Output energy was calculated based on the amplitude and temperature of the suspension, vessel, and system. The most abrupt and maximum disruption of soil aggregates was observed at a dispersion energy level of 0–200 J g−1. The MWD value of surface and subsurface ranged between 0.58 to 0.15 mm and 0.37 to 0.17 mm, respectively, while GMD was ranged from 0.14 to 0.33 mm overall. The results for MWD and GMD showed a similar trend. MWD and GMD showed more strong associations with physicochemical characteristics of soil than RI. A non-significant correlation was found between RI and MWD/GMD. Contrary to MWD and GMD, RI was significantly positively correlated with sand content; this finding indicated the influential role of sand in assessing the soil’s relative strength. The results indicated that JB soil possessed the least MWD and GMD but proved to be relatively stable because of having the highest RI value.

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