scholarly journals Quantitative Assessment of Electrostatic Embedding in Density Functional Theory Calculations of Biomolecular Systems

2009 ◽  
Vol 5 (9) ◽  
pp. 2257-2264 ◽  
Author(s):  
J.-L. Fattebert ◽  
R. J. Law ◽  
B. Bennion ◽  
E. Y. Lau ◽  
E. Schwegler ◽  
...  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.


2019 ◽  
Author(s):  
Asmus Ougaard Dohn ◽  
Elvar Jónsson ◽  
Hannes Jonsson

The manuscript analyzes the accuracy of our recently developed reciprocal polarizable embedding scheme, where a density functional theory model of the QM region is coupled to a dipole- and quadrupole polarizable water potential of the MM region. We present calculations of water clusters and liquid water where we analyze the energy, atomic forces and total polarization to demonstrate that artifacts in energy and polarization introduced by the QM/MM coupling are small and well-behaved. Furthermore, our methodology improves the consistency of the structure of optimized water hexamer geometries when compared to results obtained with models that neglect polarization. Additionally, the manuscript provides evidence that our coupling scheme eliminates artifacts in the structure of liquid water obtained with simpler electrostatic embedding models.


2006 ◽  
Vol 71 (11-12) ◽  
pp. 1525-1531 ◽  
Author(s):  
Wojciech Grochala

The enthalpy of four polymorphs of CaN has been scrutinized at 0 and 100 GPa using density functional theory calculations. It is shown that structures of diamagnetic calcium diazenide (Ca2N2) are preferred over the cubic ferromagnetic polymorph (CaN) postulated before, both at 0 and 100 GPa.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Chih-Chuen Lin ◽  
Phani Motamarri ◽  
Vikram Gavini

AbstractWe present a tensor-structured algorithm for efficient large-scale density functional theory (DFT) calculations by constructing a Tucker tensor basis that is adapted to the Kohn–Sham Hamiltonian and localized in real-space. The proposed approach uses an additive separable approximation to the Kohn–Sham Hamiltonian and an L1 localization technique to generate the 1-D localized functions that constitute the Tucker tensor basis. Numerical results show that the resulting Tucker tensor basis exhibits exponential convergence in the ground-state energy with increasing Tucker rank. Further, the proposed tensor-structured algorithm demonstrated sub-quadratic scaling with system-size for both systems with and without a gap, and involving many thousands of atoms. This reduced-order scaling has also resulted in the proposed approach outperforming plane-wave DFT implementation for systems beyond 2000 electrons.


2021 ◽  
Vol 60 (8) ◽  
pp. 6016-6026
Author(s):  
Aydar Rakhmatullin ◽  
Maxim S. Molokeev ◽  
Graham King ◽  
Ilya B. Polovov ◽  
Konstantin V. Maksimtsev ◽  
...  

Author(s):  
Lijuan Meng ◽  
Jinlian Lu ◽  
Yujie Bai ◽  
Lili Liu ◽  
Tang Jingyi ◽  
...  

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...


2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Long Lin ◽  
Linwei Yao ◽  
Shaofei Li ◽  
Zhengguang Shi ◽  
Kun Xie ◽  
...  

AbstractFinding the active sites of suitable metal oxides is a key prerequisite for detecting CH$$_4$$ 4 . The purpose of the paper is to investigate the adsorption of CH$$_4$$ 4 on intrinsic and oxygen-vacancies CuO (111) and (110) surfaces using density functional theory calculations. The results show that CH$$_4$$ 4 has a strong adsorption energy of −0.370 to 0.391 eV at all site on the CuO (110) surface. The adsorption capacity of CH$$_4$$ 4 on CuO (111) surface is weak, ranging from −0.156 to −0.325 eV. In the surface containing oxygen vacancies, the adsorption capacity of CuO surface to CH$$_4$$ 4 is significantly stronger than that of intrinsic CuO surface. The results indicate that CuO (110) has strong adsorption and charge transfer capacity for CH$$_4$$ 4 , which may provide experimental guidance.


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