Journal articles: 'KS-DFT'

1

Li, Hong Zhi, Lin Li, Zi Yan Zhong, Yi Han, LiHong Hu, and Ying Hua Lu. "An Accurate and Efficient Method to Predict Y-NO Bond Homolysis Bond Dissociation Energies." Mathematical Problems in Engineering 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/860357.

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The paper suggests a new method that combines the Kennard and Stone algorithm (Kenstone, KS), hierarchical clustering (HC), and ant colony optimization (ACO)-based extreme learning machine (ELM) (KS-HC/ACO-ELM) with the density functional theory (DFT) B3LYP/6-31G(d) method to improve the accuracy of DFT calculations for the Y-NO homolysis bond dissociation energies (BDE). In this method, Kenstone divides the whole data set into two parts, the training set and the test set; HC and ACO are used to perform the cluster analysis on molecular descriptors; correlation analysis is applied for selecting the most correlated molecular descriptors in the classes, and ELM is the nonlinear model for establishing the relationship between DFT calculations and homolysis BDE experimental values. The results show that the standard deviation of homolysis BDE in the molecular test set is reduced from 4.03 kcal mol−1calculated by the DFT B3LYP/6-31G(d) method to 0.30, 0.28, 0.29, and 0.32 kcal mol−1by the KS-ELM, KS-HC-ELM, and KS-ACO-ELM methods and the artificial neural network (ANN) combined with KS-HC, respectively. This method predicts accurate values with much higher efficiency when compared to the larger basis set DFT calculation and may also achieve similarly accurate calculation results for larger molecules.

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Fu, Zhiqiang, Lili Yang, Dongru Sun, Zexing Qu, Yufen Zhao, Jiali Gao, and Yong Wang. "Coupled electron and proton transfer in the piperidine drug metabolism pathway by the active species of cytochromes P450." Dalton Transactions 49, no. 32 (2020): 11099–107. http://dx.doi.org/10.1039/c9dt03056e.

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Ranasinghe, Duminda S., Ajith Perera, and Rodney J. Bartlett. "A note on the accuracy of KS-DFT densities." Journal of Chemical Physics 147, no. 20 (November 28, 2017): 204103. http://dx.doi.org/10.1063/1.5001939.

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Zhao, Yifen, Decong Li, and Zuming Liu. "A DFT study of pressure-induced phase transitions, structural and electronic properties of Cu2ZnSnS4." Modern Physics Letters B 30, no. 16 (June 20, 2016): 1650176. http://dx.doi.org/10.1142/s0217984916501761.

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The structural properties, phase transitions, and electronic structures of Cu2ZnSnS4 (CZTS) in the three structures have been researched using the first-principles density functional theory (DFT). The results indicate that the energies of stannite (ST) and pre-mixed Cu–Au (PMCA) CZTS are higher than those of kesterite (KS) CZTS, indicating that the KS CZTS is more stable. We found the phase transition pressure between the KS and ST structures of CZTS is about 32 GPa. Moreover, for KS- and PMCA-CZTS, there exists in the mischcrystal phase between 52 GPa and 65 GPa. The band structures show that the KS- and ST-CZTS are direct band gap semiconductors. The band gaps of three-type CZTS increase with increasing pressure, and the maximum band gap of KS and ST structures for CZTS occurs at 50 GPa. However, PMCA CZTS possesses metal property. Furthermore, the PMCA CZTS translates from metal to the indirect semiconductor with increasing pressure. The results play an important role in future experimental and theoretical work for CZTS materials.

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Mostafanejad, Mohammad, Jessica Haney, and A. Eugene DePrince. "Kinetic-energy-based error quantification in Kohn–Sham density functional theory." Physical Chemistry Chemical Physics 21, no. 48 (2019): 26492–501. http://dx.doi.org/10.1039/c9cp04595c.

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Yepes, Diana, Joel Valenzuela, Jorge I. Martínez-Araya, Patricia Pérez, and Pablo Jaque. "Effect of the exchange–correlation functional on the synchronicity/nonsynchronicity in bond formation in Diels–Alder reactions: a reaction force constant analysis." Physical Chemistry Chemical Physics 21, no. 14 (2019): 7412–28. http://dx.doi.org/10.1039/c8cp02284d.

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The performance of 24 KS-DFT-based methods (GGA, MGGA, HGGA, HMGGA, and DHGGA) was assessed, finding that M11 and M06-2X (HMGGA) predicting reliable TS geometries, energetics, and (a)synchronicities in Diels–Alder reactions.

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Chávez, Victor H., and Adam Wasserman. "Towards a density functional theory of molecular fragments. What is the shape of atoms in molecules?" Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales 44, no. 170 (March 16, 2020): 269–79. http://dx.doi.org/10.18257/raccefyn.960.

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In some sense, quantum mechanics solves all the problems in chemistry: The only thing one has to do is solve the Schrödinger equation for the molecules of interest. Unfortunately, the computational cost of solving this equation grows exponentially with the number of electrons and for more than ~100 electrons, it is impossible to solve it with chemical accuracy (~ 2 kcal/mol). The Kohn-Sham (KS) equations of density functional theory (DFT) allow us to reformulate the Schrödinger equation using the electronic probability density as the central variable without having to calculate the Schrödinger wave functions. The cost of solving the Kohn-Sham equations grows only as N3, where N is the number of electrons, which has led to the immense popularity of DFT in chemistry. Despite this popularity, even the most sophisticated approximations in KS-DFT result in errors that limit the use of methods based exclusively on the electronic density. By using fragment densities (as opposed to total densities) as the main variables, we discuss here how new methods can be developed that scale linearly with N while providing an appealing answer to the subtitle of the article: What is the shape of atoms in molecules?

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Schäffer, Claus E., and Jesper Bendix. "Kohn–Sham DFT and ligand-field theory — Is there a synergy?" Canadian Journal of Chemistry 87, no. 10 (October 2009): 1302–12. http://dx.doi.org/10.1139/v09-061.

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In forming electronic states of the partially filled shell of transition-metal atomic and molecular systems, real, symmetry-based, fixed, Kohn–Sham eigenorbitals can be used to bridge KS-states with strong-field, ligand-field states. Thereby, DFT computations, restrained by the use of these frozen orbitals of the so-called average-of-configuration type, allow a central-field modeling of the partially filled shell whose Hamiltonian matrix consists of mutually orthogonal diagonal and non-diagonal parts, of which only the former can be computed. Mutually orthogonal operators of ligand-field theory are particularly suited to parameterize the energy “data” obtained from the bridges between molecular Kohn–Sham DFT states and ligand-field states. With the d2 configuration as the simplest example encompassing both ligand-field and interelectronic repulsion, each one-electron parameter, though defined by energy differences of perturbed d orbitals, is associated with a 45 × 45, diagonal, theoretical, strong-field-type coefficient matrix of the ligand field repulsion model (LFR), which is mapped in a one-to-one fashion onto a likewise diagonal KS-DFT computational energy matrix. For sets of mutually orthogonal operators, the mapping determines the value of any such ligand-field parameter as a scalar product between the DFT matrix and the coefficient matrix of the associated ligand-field operator. Each and every two-electron parameter of LFR is in the same strong-field function basis associated with a 45 × 45 coefficient matrix that includes a non-diagonal part. This matrix, nevertheless, by the formation of a scalar product with the appropriate diagonal, computational DFT matrix, provides the value of the two-electron parameter. In spite of the lacking non-diagonal DFT information, its non-diagonal elements of the two-electron interelectronic repulsion matrices are indirectly accessible through the parameterization based upon the computed diagonal DFT matrices combined with the mapping of the DFT energy results onto the parametric LFR. In this way, LFR delivers back to DFT a quantification of the deviation of the systems’ eigenbasis from the DFT-computed states, which are defined by having unit occupation numbers. This work focuses firstly on using the LFR model for forming a full DFT energy matrix and dissecting it into mutually orthogonal one- and two-electron parts and secondly on the use of the two-electron parts to obtain a complete ligand-field image of a nephelauxetic, molecular atom, intrinsic of the chemical system.

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Elstner, Marcus, and Gotthard Seifert. "Density functional tight binding." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372, no. 2011 (March 13, 2014): 20120483. http://dx.doi.org/10.1098/rsta.2012.0483.

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This paper reviews the basic principles of the density-functional tight-binding (DFTB) method, which is based on density-functional theory as formulated by Hohenberg, Kohn and Sham (KS-DFT). DFTB consists of a series of models that are derived from a Taylor series expansion of the KS-DFT total energy. In the lowest order (DFTB1), densities and potentials are written as superpositions of atomic densities and potentials. The Kohn–Sham orbitals are then expanded to a set of localized atom-centred functions, which are obtained for spherical symmetric spin-unpolarized neutral atoms self-consistently. The whole Hamilton and overlap matrices contain one- and two-centre contributions only. Therefore, they can be calculated and tabulated in advance as functions of the distance between atomic pairs. The second contributions to DFTB1, the DFT double counting terms, are summarized together with nuclear repulsion energy terms and can be rewritten as the sum of pairwise repulsive terms. The second-order (DFTB2) and third-order (DFTB3) terms in the energy expansion correspond to a self-consistent representation, where the deviation of the ground-state density from the reference density is represented by charge monopoles only. This leads to a computationally efficient representation in terms of atomic charges (Mulliken), chemical hardness (Hubbard) parameters and scaled Coulomb laws. Therefore, no additional adjustable parameters enter the DFTB2 and DFTB3 formalism. The handling of parameters, the efficiency, the performance and extensions of DFTB are briefly discussed.

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Malvaldi, Marco, Samantha Bruzzone, Cinzia Chiappe, Sergey Gusarov, and Andriy Kovalenko. "Ab Initio Study of Ionic Liquids by KS-DFT/3D-RISM-KH Theory." Journal of Physical Chemistry B 113, no. 11 (March 19, 2009): 3536–42. http://dx.doi.org/10.1021/jp810887z.

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11

Kaplan, Ilya G. "Symmetry properties of the electron density and following from it limits on the KS-DFT applications." Molecular Physics 116, no. 5-6 (November 15, 2017): 658–65. http://dx.doi.org/10.1080/00268976.2017.1393573.

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12

Yau, Anthony D., Edward F. C. Byrd, and Betsy M. Rice. "An Investigation of KS-DFT Electron Densities used in Atoms-in-Molecules Studies of Energetic Molecules." Journal of Physical Chemistry A 113, no. 21 (May 28, 2009): 6166–71. http://dx.doi.org/10.1021/jp9010845.

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13

Casanova, David, Sergey Gusarov, Andriy Kovalenko, and Tom Ziegler. "Evaluation of the SCF Combination of KS-DFT and 3D-RISM-KH; Solvation Effect on Conformational Equilibria, Tautomerization Energies, and Activation Barriers." Journal of Chemical Theory and Computation 3, no. 2 (February 22, 2007): 458–76. http://dx.doi.org/10.1021/ct6001785.

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14

Kovalenko, Andriy. "Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials." Pure and Applied Chemistry 85, no. 1 (January 4, 2013): 159–99. http://dx.doi.org/10.1351/pac-con-12-06-03.

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Statistical–mechanical, 3D-RISM-KH molecular theory of solvation (3D reference interaction site model with the Kovalenko–Hirata closure) is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. 3D-RISM-KH explains the molecular mechanisms of self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), aggregation of prion proteins and β-sheet amyloid oligomers, protein-ligand binding, and function-related solvation properties of complexes as large as the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) and GroEL/ES chaperone. Molecular mechanics/Poisson–Boltzmann (generalized Born) surface area [MM/PB(GB)SA] post-processing of molecular dynamics (MD) trajectories involving SA empirical nonpolar terms is replaced with MM/3D-RISM-KH statistical–mechanical evaluation of the solvation thermodynamics. 3D-RISM-KH has been coupled with multiple time-step (MTS) MD of the solute biomolecule driven by effective solvation forces, which are obtained analytically by converging the 3D-RISM-KH integral equations at outer time-steps and are calculated in between by using solvation force coordinate extrapolation (SFCE) in the subspace of previous solutions to 3D-RISM-KH. The procedure is stabilized by the optimized isokinetic Nosé–Hoover (OIN) chain thermostatting, which enables gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties. The multiscale OIN/SFCE/3D-RISM-KH algorithm is implemented in the Amber package and illustrated on a fully flexible model of alanine dipeptide in aqueous solution, exhibiting the computational rate of solvent sampling 20 times faster than standard MD with explicit solvent. Further substantial acceleration can be achieved with 3D-RISM-KH efficiently sampling essential events with rare statistics such as exchange and localization of solvent, ions, and ligands at binding sites and pockets of the biomolecule. 3D-RISM-KH was coupled with ab initio complete active space self-consistent field (CASSCF) and orbital-free embedding (OFE) Kohn–Sham (KS) density functional theory (DFT) quantum chemistry methods in an SCF description of electronic structure, optimized geometry, and chemical reactions in solution. The (OFE)KS-DFT/3D-RISM-KH multi-scale method is implemented in the Amsterdam Density Functional (ADF) package and extensively validated against experiment for solvation thermochemistry, photochemistry, conformational equilibria, and activation barriers of various nanosystems in solvents and ionic liquids (ILs). Finally, the replica RISM-KH-VM molecular theory for the solvation structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous materials reveals the molecular mechanisms of sorption and supercapacitance in nanoporous carbon electrodes, which is drastically different from a planar electrical double layer.

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Chiappe, Cinzia, Marco Malvaldi, and Christian Silvio Pomelli. "Ab Initio Study of the Diels−Alder Reaction of Cyclopentadiene with Acrolein in a Ionic Liquid by KS-DFT/3D-RISM-KH Theory." Journal of Chemical Theory and Computation 6, no. 1 (October 29, 2009): 179–83. http://dx.doi.org/10.1021/ct900331e.

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16

Kathariya, Mitesh D., Prashant S. Viragi, KS Dwijendra, Kirti Chopra, Mahesh V. Dadpe, and HS Madhukar. "Dental Health and Treatment Needs Among Children in a Tribal Community." Journal of Contemporary Dental Practice 14, no. 4 (2013): 747–50. http://dx.doi.org/10.5005/jp-journals-10024-1395.

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ABSTRACT Objective To assess the dental health status and treatment needs among children of ‘Pardhi’ tribal community. Methods A total of 185 children were examined over a period of 2 months using WHO proforma. The statistical software namely SPSS version 15.0 and data was analyzed using Student's t-test and ANOVA test at p < 0.05. Results The mean score for dft and DMFT was 1.87 ± 1.073 and 2.04 ± 1.564 respectively with males subjects were having comparatively more scores. It was also found significant differences between age groups. Most of the children needed one surface filling, i.e. 29.40%, followed by pulp care and restoration (19.30%), two or more surface fillings (15.60%) and extraction (11.70%). Clinical significance The study subjects were characterized by a lack of dental care services, high prevalence of dental caries and treatment needs. Therefore, implementation of a basic oral health care program for this tribal population is a high priority How to cite this article Viragi PS, Dwijendra KS, Kathariya MD, Chopra K, Dadpe MV, Madhukar HS. Dental Health and Treatment Needs Among Children in a Tribal Community. J Contemp Dent Pract 2013;14(4):747-750.

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Calaminici, Patrizia, José M. Vásquez-Pérez, and Diego A. Espíndola Velasco. "A density functional study of Rh13." Canadian Journal of Chemistry 91, no. 7 (July 2013): 591–97. http://dx.doi.org/10.1139/cjc-2012-0493.

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A density functional study was performed for the Rh13 cluster using the linear combination of Gaussian-type orbitals density functional theory (LCGTO-DFT) approach. The calculations employed both the local density approximation (LDA) as well as the generalized gradient approximation (GGA) in combination with a quasi-relativistic effective core potential (QECP). Initial structures for the geometry optimization were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories. The BOMD trajectories were performed at different temperatures and considered different potential energy surfaces (PES). As a result, several hundred isomers of the Rh13 cluster in different spin multiplicities were optimized with the aim to determine the lowest energy structures. All geometry optimizations were performed without any symmetry restriction. A vibrational analysis was performed to characterize these isomers. Structural parameters, relative stability energy, harmonic frequencies, binding energy, and most relevant Kohn–Sham (KS) molecular orbitals are reported. The obtained results are compared with available data from the literature. This study predicts a low symmetry biplanarlike structure as the ground-state structure of Rh13 with 11 unpaired electrons. This isomer was first noticed by inspection of first-principle Born–Oppenheimer molecular dynamics (BOMD) simulations between 300 and 600 K. This represents the most extensive theoretical study on the ground-state structure of the Rh13 cluster and underlines the importance of BOMD simulations to fully explore the PES landscapes of complicated systems.

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Anzil, KSA, Eby Aluckal, Mathews Baby, Eldhose K. George, Sanju Lakshmanan, and Shilpa Chikkanna. "Association between Body Mass Index and Dental Caries among Anganwadi Children of Belgaum City, India." Journal of Contemporary Dental Practice 17, no. 10 (2016): 844–48. http://dx.doi.org/10.5005/jp-journals-10024-1941.

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ABSTRACT Introduction Body mass index (BMI) is an index that measures height for weight, which is commonly used to categorize underweight, overweight, and obese individuals. Deviation from normal weight results from an imbalance between caloric consumption and energy expenditure. Childhood obesity and childhood dental caries are coincidental in many populations, probably due to common confounding risk factors, such as intake frequency, cariogenic diet, and poor oral hygiene. So the aim of the present study was to assess the BMI status and to corelate between dental caries and BMI among the Anganwadi children of Belgaum city, Karnataka, India. Materials and methods Four hundred and thirty three children from 20 Anganwadi's belonging to the age group of 2 to 6 years of both sexes were measured for BMI and dental caries status. The caries index was measured as the number of decayed (d) and filled (f) teeth (t) (dft). The BMI in units of kg/m2 was determined and children were categorized according to ageand gender-specific criteria as underweight (<5th percentile), normal (5th–85th percentile), at risk for overweight (85th– 95th percentile), and overweight (>95th percentile). The data were subjected to statistical analysis using Student's t-test, analysis of variance (ANOVA), and Karl Pearson's correlation coefficient test with the help of Statistical Package for the Social Sciences (SPSS) version 18.0. Results The proportion of subjects in Centre for Disease Control (CDC) weight categories was: 5% underweight, 79% normal, 9% under the risk for overweight, and 6% overweight. Conclusion A significant association was found between children with normal BMI and those who were underweight, overweight, and under the risk for overweight. Children with overweight/obese or underweight/malnourished children had higher decayed and filled surfaces compared to children with normal weight. Clinical significance Nutritional status has a profound effect on dental caries. Both underweight/malnutrition and overweight/ obesity have significant adverse implications for health. Childhood obesity and childhood dental caries are coincidental in many populations. How to cite this article Aluckal E, Anzil KS A, Baby M, George EK, Lakshmanan S, Chikkanna S. Association between Body Mass Index and Dental Caries among Anganwadi Children of Belgaum City, India. J Contemp Dent Pract 2016;17(10):844-848.

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19

Ghosal, Abhisek, Tarun Gupta, Kishalay Mahato, and Amlan K. Roy. "Excitation energies through Becke’s exciton model within a Cartesian-grid KS DFT." Theoretical Chemistry Accounts 140, no. 1 (January 2021). http://dx.doi.org/10.1007/s00214-020-02699-5.

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Luo, Zhaolong, Xinming Qin, Lingyun Wan, Wei Hu, and Jinlong Yang. "Parallel Implementation of Large-Scale Linear Scaling Density Functional Theory Calculations With Numerical Atomic Orbitals in HONPAS." Frontiers in Chemistry 8 (November 26, 2020). http://dx.doi.org/10.3389/fchem.2020.589910.

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Linear-scaling density functional theory (DFT) is an efficient method to describe the electronic structures of molecules, semiconductors, and insulators to avoid the high cubic-scaling cost in conventional DFT calculations. Here, we present a parallel implementation of linear-scaling density matrix trace correcting (TC) purification algorithm to solve the Kohn–Sham (KS) equations with the numerical atomic orbitals in the HONPAS package. Such a linear-scaling density matrix purification algorithm is based on the Kohn's nearsightedness principle, resulting in a sparse Hamiltonian matrix with localized basis sets in the DFT calculations. Therefore, sparse matrix multiplication is the most time-consuming step in the density matrix purification algorithm for linear-scaling DFT calculations. We propose to use the MPI_Allgather function for parallel programming to deal with the sparse matrix multiplication within the compressed sparse row (CSR) format, which can scale up to hundreds of processing cores on modern heterogeneous supercomputers. We demonstrate the computational accuracy and efficiency of this parallel density matrix purification algorithm by performing large-scale DFT calculations on boron nitrogen nanotubes containing tens of thousands of atoms.

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"Application of DFT-KS Orbitals in Predicting the Electrochemical and Spectral Properties of Porphyrin Supramolecular Donor-Acceptor Assemblies." ECS Meeting Abstracts, 2005. http://dx.doi.org/10.1149/ma2005-01/27/955.

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Weng, Zhichao, William P. Gillin, and Theo Kreouzis. "Fitting the magnetoresponses of the OLED using polaron pair model to obtain spin-pair dynamics and local hyperfine fields." Scientific Reports 10, no. 1 (October 8, 2020). http://dx.doi.org/10.1038/s41598-020-73953-w.

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Abstract Organic light-emitting diode (OLED) displays a sign reversal magnetic field effect (MFE) when the applied magnetic field range is reduced to the sub-milliTesla range and the Polaron Pair Model has been successful in explaining the ultra-small MFE. Here, we obtained high resolution (~ 1 µT) magnetoconductance (MC) and magnetoelectroluminescence (MEL) of a tris-(8-hydroxyquinoline)aluminium-based (Alq3) OLED within the magnetic field range of ± 500 µT with the earth magnetic field components cancelled. A clear “W” shaped MC with a dip position of ± 250 µT and a monotonic MEL were observed. We demonstrate a fitting technique using the polaron pair model to the experimentally obtained MC and MEL. The fitting process extracts physically significant parameters within a working OLED: the local hyperfine fields for electron and hole in Alq3: Bhf1 = (0.63 ± 0.01) mT (electron), Bhf2 = (0.24 ± 0.01) mT (hole); the separation rates for singlet and triplet polaron pairs: kS,s = (44.59 ± 0.01) MHz, kT,s = (43.97 ± 0.01) MHz, and the recombination rate for singlet polaron pair kS,r = (88 ± 6) MHz. The yielded parameters are highly reproducible across different OLEDs and are in broad agreement with density functional theory (DFT) calculations and reported experimental observations. This demonstrates the feasibility of this fitting technique to approach any working OLED for obtaining significant microscopic parameters.

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Williams-Young, David B., Wibe A. de Jong, Hubertus J. J. van Dam, and Chao Yang. "On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters." Frontiers in Chemistry 8 (December 10, 2020). http://dx.doi.org/10.3389/fchem.2020.581058.

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The predominance of Kohn–Sham density functional theory (KS-DFT) for the theoretical treatment of large experimentally relevant systems in molecular chemistry and materials science relies primarily on the existence of efficient software implementations which are capable of leveraging the latest advances in modern high-performance computing (HPC). With recent trends in HPC leading toward increasing reliance on heterogeneous accelerator-based architectures such as graphics processing units (GPU), existing code bases must embrace these architectural advances to maintain the high levels of performance that have come to be expected for these methods. In this work, we purpose a three-level parallelism scheme for the distributed numerical integration of the exchange-correlation (XC) potential in the Gaussian basis set discretization of the Kohn–Sham equations on large computing clusters consisting of multiple GPUs per compute node. In addition, we purpose and demonstrate the efficacy of the use of batched kernels, including batched level-3 BLAS operations, in achieving high levels of performance on the GPU. We demonstrate the performance and scalability of the implementation of the purposed method in the NWChemEx software package by comparing to the existing scalable CPU XC integration in NWChem.

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Journal articles on the topic 'KS-DFT'

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