Efficient Modeling of Large Molecules: Geometry Optimization Dynamics and Correlation Energy

2003 ◽  
Author(s):  
Peter Pulay ◽  
Jon Baker
Keyword(s):  
Correlation Energy ◽  
Geometry Optimization ◽  
Large Molecules ◽  
Efficient Modeling

CLB18: A New Structural Database with Unusual Carbon–Carbon Long Bonds

2020 ◽  
Author(s):  
Pierpaolo Morgante ◽  
Roberto Peverati
Keyword(s):  
Transition Metal Complexes ◽  
Low Cost ◽  
Geometry Optimization ◽  
Structure Calculation ◽  
Unique Property ◽  
Spin States ◽  
Calculation Methods ◽  
Large Molecules ◽  
Barrier Heights ◽  
Structural Database

<div><div><div><p>In this Letter, we introduce a new database called carbon long bond 18 (CLB18), composed of 18 structures with one long C–C bond. We use this new database to evaluate the performance of several low-cost methods commonly used for geometry optimization of medium and large molecules. We found that the long bonds in CLB18 are electronically different from those found in barrier heights databases. We also report the unexpected correlation between the results of CLB18 and those of the energetics of spin states in transition-metal complexes. Given this unique property, CLB18 can be a useful tool for assessing existing electronic structure calculation methods and developing new ones.</p></div></div></div>

scholarly journals BEYOND DENSITY FUNCTIONAL THEORY: THE DOMESTICATION OF NONLOCAL POTENTIALS

2004 ◽  
Vol 18 (02n03) ◽  
pp. 73-82 ◽  
Author(s):  
ROBERT K. NESBET
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Correlation Energy ◽  
Mean Field Theory ◽  
Mean Field ◽  
Energy Functional ◽  
Functional Theory ◽  
Large Molecules ◽  
Cellular Method ◽  
Nonlocal Potentials

Due to efficient scaling with electron number N, density functional theory (DFT) is widely used for studies of large molecules and solids. Restriction of an exact mean-field theory to local potential functions has recently been questioned. This review summarizes motivation for extending current DFT to include nonlocal one-electron potentials, and proposes methodology for implementation of the theory. The theoretical model, orbital functional theory (OFT), is shown to be exact in principle for the general N-electron problem. In practice it must depend on a parametrized correlation energy functional. Functionals are proposed suitable for short-range Coulomb-cusp correlation and for long-range polarization response correlation. A linearized variational cellular method (LVCM) is proposed as a common formalism for molecules and solids. Implementation of nonlocal potentials is reduced to independent calculations for each inequivalent atomic cell.

scholarly journals The experimental and theoretical QTAIMC study of the atomic and molecular interactions in dinitrogen tetroxide

2009 ◽  
Vol 65 (5) ◽  
pp. 647-658 ◽  
Author(s):  
Vladimir G. Tsirelson ◽  
Anastasia V. Shishkina ◽  
Adam I. Stash ◽  
Simon Parsons
Keyword(s):  
Energy Density ◽  
Potential Energy ◽  
Electron Density ◽  
Molecular Interactions ◽  
Electrostatic Potential ◽  
Correlation Energy ◽  
Three Dimensional ◽  
Geometry Optimization ◽  
Intermolecular Bond ◽  
Experimental Electron Density

The atomic and molecular interactions in a crystal of dinitrogen tetraoxide, α-N2O4, have been studied in terms of the quantum topological theory of molecular structure using high-resolution, low-temperature X-ray diffraction data. The experimental electron density and electrostatic potential have been reconstructed with the Hansen–Coppens multipole model. In addition, the three-dimensional periodic electron density of crystalline α-N2O4 has been calculated at the B3LYP/cc-pVDZ level of theory with and without the geometry optimization. The application of the quantum theory of atoms in molecules and crystals (QTAIMC) recovered the two types of intermolecular bond paths between O atoms in crystalline α-N2O4, one measuring 3.094, the other 3.116 Å. The three-dimensional distribution of the Laplacian of the electron density around the O atoms showed that the lumps in the negative Laplacian fit the holes on the O atoms in the adjacent molecules, both atoms being linked by the intermolecular bond paths. This shows that the Lewis-type molecular complementarity contributes significantly to intermolecular bonding in crystalline N2O4. Partial overlap of atomic-like basins created by zero-flux surfaces in both the electron density and the electrostatic potential show that attractive electrostatic interaction exists between O atoms even though they carry the same net formal charge. The exchange and correlation contributions to the potential energy density were also computed by means of the model functionals, which use the experimental electron density and its derivatives. It was found that the intermolecular interactions in α-N2O4 are accompanied by the correlation energy-density `bridges' lowering the local potential energy along the intermolecular O...O bond paths in the electron density, while the exchange energy density governs the shape of bounded molecules.

MOLECULAR TAILORING APPROACH: TOWARDS PC-BASED AB INITIO TREATMENT OF LARGE MOLECULES

2006 ◽  
Vol 05 (04) ◽  
pp. 835-855 ◽  
Author(s):  
SHRIDHAR R. GADRE ◽  
V. GANESH
Keyword(s):  
Ab Initio ◽  
Electron Density ◽  
Large Scale ◽  
Dipole Moments ◽  
Geometry Optimization ◽  
Parent Molecule ◽  
Large Molecules ◽  
Self Consistent Field ◽  
Moller Plesset ◽  
Molecular Tailoring

The development of a fragmentation-based scheme, viz. molecular tailoring approach (MTA) for ab initio computation of one-electron properties and geometry optimization is described. One-electron properties such as the molecular electrostatic potential (MESP), molecular electron density (MED), and dipole moments are computed by synthesizing the density matrix (DM) of the parent molecule from DMs of its small overlapping fragments. The electron density obtained via MTA was found to be typically within 0.5% of its actual counterpart, while maximum errors of about 2% were noticed in the case of the dipole moment and MESP distribution. An attempt is made to develop MTA-based geometry optimization that involves picking relevant energy gradients from fragment self-consistent field (SCF) calculations, bypassing the CPU and memory extensive SCF step of the complete molecule. This is based on the observation that the MTA gradients mimic the actual ones fairly well. As the calculations on individual fragments are mutually independent, this algorithm is amenable to large-scale parallelization and has been extended to a distributed setup of PCs. The code developed is put to test on γ-cyclodextrin, taxol, and a small albumin-binding protein (1prb) for one-electron properties. Further, molecules such as γ-cyclodextrin, taxol, a silicalite, and 1prb are subjected to MTA-based geometry optimization, on a PC cluster. The results indicate a favorable speedup of two to three times over the actual computations in the initial phase of optimization. Furthermore, it enables computations otherwise not possible on a PC. Preliminary results indicate similar savings with sustained accuracy even for large molecules at the level of Møller–Plesset second order perturbation (MP2) theory.

scholarly journals A simple fragment-based method for van der Waals corrections over density functional theory

2021 ◽  
Author(s):  
Prasanta Bandyopadhyay ◽  
Priya Priya ◽  
Mainak Sadhukhan
Keyword(s):  
Density Functional ◽  
Correlation Energy ◽  
Noncovalent Interactions ◽  
Low Cost ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Structure Theory ◽  
Large Molecules ◽  
Drude Oscillators ◽  
The Cost

Modelling intermolecular noncovalent interactions between large molecules remains a challenge for electron structure theory community. This is due to the high cost of calculating electron correlation energy. Fragment-based methods usually fare well in reducing the cost of computations in such systems while quantum Drude oscillators turn out to be a good model for van der Waals interactions. In this paper, we have developed a simple yet effective method based on oscillator methods for calculating van der Waals interactions between molecular fragments as a correction to low-cost DFT functional PBE. We have tested our method on S66X8 with significant success.

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