Polarization energies of molecular crystals

1970 ◽  
Vol 23 (12) ◽  
pp. 2397 ◽  
Author(s):  
M Batley ◽  
LJ Johnston ◽  
LE Lyons
Keyword(s):  
Electrostatic Interaction ◽  
Molecular Crystals ◽  
Organic Crystals ◽  
Interaction Energies ◽  
Free Molecule ◽  
Emission Data ◽  
Large Molecules ◽  
Photoelectric Emission ◽  
Electrostatic Polarization ◽  
Made In

The electrostatic polarization energies have been calculated for 17 molecular crystals, including some of two-components. Comparison with photoelectric emission data confirms that the energies of ionized states in organic crystals can be described in terms of properties of the free molecule and classical electrostatic interaction energies. The calculations were made in more detail and for a greater number of compounds than has been attempted previously; contributions from terms formerly neglected are significant especially for large molecules like pentacene.

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

Electrostatic interaction energies with overlap effects from a localized approach

2007 ◽  
Vol 445 (4-6) ◽  
pp. 315-320 ◽  
Author(s):  
Fazle Rob ◽  
Rafał Podeszwa ◽  
Krzysztof Szalewicz
Keyword(s):  
Electrostatic Interaction ◽  
Interaction Energies

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

2020 ◽  
Vol 76 (6) ◽  
pp. 630-651
Author(s):  
Daniel Nguyen ◽  
Piero Macchi ◽  
Anatoliy Volkov
Keyword(s):  
Interaction Energy ◽  
Crystal Structures ◽  
Electron Density ◽  
Small Molecule ◽  
Electrostatic Interaction ◽  
Multipole Moment ◽  
Interaction Energies ◽  
Acta Cryst ◽  
Löwdin Α Function ◽  
Direct Summation

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170–175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536; Nguyen & Volkov (2019). Acta Cryst. A75, 448–464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283–4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10−5 kJ mol−1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28–64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

Matrix Elements for Many-Electron Atoms: Electrostatic Interaction Energies for One-Open-Shell Configurations

1974 ◽  
Vol 52 (3) ◽  
pp. 238-240
Author(s):  
J. Karwowski ◽  
S. Fraga
Keyword(s):  
Electrostatic Interaction ◽  
Open Shell ◽  
Numerical Results ◽  
Interaction Energies ◽  
Matrix Elements ◽  
The Matrix ◽  
Racah Parameters

The matrix elements of the electrostatic interaction have been determined and tabulated, in terms of Slater–Condon integrals or Racah parameters, for the states arising from pN, dN, fN, and gN configurations; in particular, the results for gN configurations have never been determined before. The effect of the interaction between states of the same symmetry and multiplicity, arising from a given configuration, is exemplified with numerical results for Pr, 4f36s2.

scholarly journals Modeling of the optical properties of molecular crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C384-C384
Author(s):  
Tomasz Seidler ◽  
Marlena Gryl ◽  
Benoît Champagne ◽  
Katarzyna Stadnicka
Keyword(s):  
Good Accuracy ◽  
Molecular Crystals ◽  
Electronic Structure Calculations ◽  
Organic Crystals ◽  
Susceptibility Tensor ◽  
Uniform Embedding ◽  
Two Component ◽  
Interaction Scheme ◽  
Electric Susceptibility ◽  
Structure Calculations

In this contribution we present our current findings in the calculations of the linear and second-order nonlinear electric susceptibility tensor components of organic crystals. The methodology used for this purpose is based on a combination of the electrostatic interaction scheme developed by Hurst and Munn (Hurst & Munn, 1986) with electronic structure calculations for the isolated molecules. Our modification of the method consists in i) running periodic boundary condition (PBC) calculations for an adequate chromophore geometry (either experimental or optimized) to obtain atomic charges and in ii) performing the calculations of the molecular properties within a non-uniform embedding field generated by point charges located spherically around the reference molecule. Using this approach good accuracy is achieved on the electric susceptibility tensor components in comparison with the uniform dipole electric field (Seidler et al., 2013). We extend here the application of this method to other molecular crystals as well as we present the first attempt to predict the chi(1) and chi(2) components of two-component organic crystals (Gryl et al., 2014).

scholarly journals New Ligands and New Insights for Vitamin D Receptor from Charge Density

2014 ◽  
Vol 70 (a1) ◽  
pp. C966-C966
Author(s):  
Maura Malińska ◽  
Andrzej Kutner ◽  
Krzysztof Woźniak
Keyword(s):  
Vitamin D ◽  
Hydrogen Bonds ◽  
Charge Density ◽  
Interaction Energy ◽  
Vitamin D Receptor ◽  
Electrostatic Interaction ◽  
Interaction Energies ◽  
Average Strength ◽  
Vitamin D Analogs ◽  
Wide Range

Vitamin D protective effects result from its role as a nuclear transcription factor that regulates cell growth, differentiation, and a wide range of cellular mechanisms crucial to the development and progression of cancer.[1] Many academic investigators and pharmaceutical companies try to develop calcitriol analogs that exhibit equal or even increased anti-proliferative activity while exhibiting a reduced tendency to cause hypercalcemia. Analysis of 24 Vitamin D analogs bearing similar molecular structures with a complex of a Vitamin D Receptor (VDR) enabled the design of new agonists (TB1, TB2, TB3 and TB4). Undertaken approach was to minimize the electrostatic interaction energies available after the reconstruction of charge density with the aid of the pseudoatom databank (UBDB[2]). Comprehensive studies revealed 29 residues crucial for agonist binding. Trp286, which is specific to VDR among the representatives of the Nuclear Receptor Family, plays the crucial role of positioning the ligand forming dispersive interactions, mostly C-H...π, with an average strength of -4 kcal mol-1. The ligand binding pocket is primarily composed of hydrophobic residues, however there are 6 hydrogen bonds characteristic for all the ligands. They electrostatic interaction energies strongly contribute to the total interaction energy, with an average strength of -8, -19, -11 and -12 kcal mol-1 for hydrogen bonds to Ser237, Arg274, Ser278 and Tyr143. The aliphatic chain of the Vitamin D analogs adopt an extended conformation and the 25-hydroxyl group is hydrogen bonded to His305 and His397 with electrostatic interaction energies of -13 and -11 kcal mol-1. The geometries of complexes of the proposed ligand with VDR were obtained by the docking procedure implemented in Autodock4.3[3]. New agonsits form all mentioned before interactions with VDR. The final results of electrostatic interaction energy for TB1 and TB2 are -153 and -120 kcal mol-1, and this results are the smallest among all studied Vitamin D analogs.

scholarly journals Fast and accurate quantum Monte Carlo for molecular crystals

2018 ◽  
Vol 115 (8) ◽  
pp. 1724-1729 ◽  
Author(s):  
Andrea Zen ◽  
Jan Gerit Brandenburg ◽  
Jiří Klimeš ◽  
Alexandre Tkatchenko ◽  
Dario Alfè ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Quantum Monte Carlo ◽  
Materials Science ◽  
Computational Cost ◽  
Molecular Crystals ◽  
Intermolecular Forces ◽  
High Accuracy ◽  
Computational Approach ◽  
Large Molecules ◽  
Weak Intermolecular Forces

Computer simulation plays a central role in modern-day materials science. The utility of a given computational approach depends largely on the balance it provides between accuracy and computational cost. Molecular crystals are a class of materials of great technological importance which are challenging for even the most sophisticated ab initio electronic structure theories to accurately describe. This is partly because they are held together by a balance of weak intermolecular forces but also because the primitive cells of molecular crystals are often substantially larger than those of atomic solids. Here, we demonstrate that diffusion quantum Monte Carlo (DMC) delivers subchemical accuracy for a diverse set of molecular crystals at a surprisingly moderate computational cost. As such, we anticipate that DMC can play an important role in understanding and predicting the properties of a large number of molecular crystals, including those built from relatively large molecules which are far beyond reach of other high-accuracy methods.

Metal-like Ductility in Organic Plastic Crystals: Role of Molecular Shape and Dihydrogen Bonding Interactions in Aminoboranes

2020 ◽  
Author(s):  
Amit Mondal ◽  
Biswajit Bhattacharya ◽  
SUSOBHAN DAS ◽  
Surojit Bhunia ◽  
Rituparno Chowdhury ◽  
...  
Keyword(s):  
Molecular Crystals ◽  
Molecular Shape ◽  
High Symmetry ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
Plastic Crystals ◽  
Dihydrogen Bonding ◽  
Slip Planes

Ductility, which is a common phenomenon in most metals and metal-based alloys, is hard to achieve in molecular crystals. Organic crystals have been recently shown to deform plastically, but only on one or two faces, and fracture when stressed in any other arbitrary direction. Here, we report an exceptional metal-like ductility in crystals of two globular molecules, BH<sub>3</sub>NMe<sub>3</sub> and BF<sub>3</sub>NMe<sub>3</sub>, with characteristic stretching, necking and thinning with deformations as large as ~ 500%. Surprisingly, the mechanically deformed samples not only retained good long range order, but also allowed structure determination by single crystal X-ray diffraction. Molecules in these high symmetry crystals interact predominantly via electrostatic forces (B<sup>–</sup>–N<sup>+</sup>) and form columnar structures, thus forming multiple slip planes with weak dispersive forces among columns. While the former interactions hold molecules together, the latter facilitate exceptional malleability. On the other hand, the limited number of facile slip planes and strong dihydrogen bonding in BH<sub>3</sub>NHMe<sub>2</sub> negates ductility. We show the possibility to simultaneously achieve both exceptional ductility and crystallinity in solids of certain globular molecules, which may enable designing highly modular, easy-to-cast crystalline functional organics, for applications in barocalorimetry, ferroelectrics and soft-robotics.

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