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Journal articles on the topic 'DFT. DFTB'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

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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2

Lee, Ka Hung, Van Quan Vuong, Victor Fung, De-en Jiang, and Stephan Irle. "Density-Functional Tight-Binding for Platinum Clusters and Bulk: Electronic vs Repulsive Parameters." MRS Advances 4, no. 33-34 (2019): 1821–32. http://dx.doi.org/10.1557/adv.2019.284.

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ABSTRACTWe present a general purpose Pt-Pt density-functional tight-binding (DFTB) parameter for Pt clusters as well as bulk, using a genetic algorithm (GA) to automatize the parameterization effort. First we quantify the improvement possible by only optimizing the repulsive potential alone, and second we investigate the effect of improving the electronic parameter as well. During both parameterization efforts we employed our own training set and test sets, with one set containing ∼20,000 spin-polarized DFT structures. We analyze the performance of our two DFTB Pt-Pt parameter sets against density functional theory (DFT) as well as an earlier DFTB Pt-Pt parameters. Our study sheds light on the role of both repulsive and electronic parameters with regards to DFTB performance.

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3

Aktürk, Abdurrahman, and Ali Sebetci. "BH-DFTB/DFT calculations for iron clusters." AIP Advances 6, no. 5 (May 2016): 055103. http://dx.doi.org/10.1063/1.4948752.

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4

Jahangiri, Soran, and Nicholas J. Mosey. "Effects of reduced dimensionality on the properties of magnesium hydroxide and calcium hydroxide nanostructures." Physical Chemistry Chemical Physics 19, no. 3 (2017): 1963–74. http://dx.doi.org/10.1039/c6cp07968g.

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5

Pal, Amrita, Lai Kai Wen, Chia Yao Jun, Il Jeon, Yutaka Matsuo, and Sergei Manzhos. "Comparative density functional theory–density functional tight binding study of fullerene derivatives: effects due to fullerene size, addends, and crystallinity on band structure, charge transport and optical properties." Phys. Chem. Chem. Phys. 19, no. 41 (2017): 28330–43. http://dx.doi.org/10.1039/c7cp05290a.

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6

Dominguez-Flores, Fabiola, Elizabeth Santos, Wolfgang Schmickler, and Fernanda Juarez. "Interaction between chloride ions mediated by carbon nanotubes: a chemical attraction." Journal of Solid State Electrochemistry 24, no. 11-12 (September 15, 2020): 3207–14. http://dx.doi.org/10.1007/s10008-020-04802-z.

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Abstract The interaction between two Cl− ions separated by the wall of a narrow carbon nanotube has been investigated by density functional theory (DFT) and by DFT-based tight binding (DFTB+). The direct Coulomb interaction between the ions is screened by the nanotube, no matter if the latter is conducting or semiconducting. The presence of the ions induces changes in the electronic density of states of the nanotube, which results in an effective attraction between the ions of the order of 0.2–0.3 eV. The interaction of the outside ions with the tube has a covalent component, when the two ions are near there is even a direct chemical attraction between the ions. In contrast to the effective attraction between two Li+ ions reported before (Juarez et al., Phys Chem Chem Phys 22:10,603, 2020), the effect cannot be explained in terms of physical concepts alone. DFTB+ performs well when compared with DFT, and lends itself to fast calculations for large systems.

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Guo, Lei, Chengwei Qi, Xingwen Zheng, Renhui Zhang, Xun Shen, and Savaş Kaya. "Toward understanding the adsorption mechanism of large size organic corrosion inhibitors on an Fe(110) surface using the DFTB method." RSC Advances 7, no. 46 (2017): 29042–50. http://dx.doi.org/10.1039/c7ra04120a.

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8

Li, Wenxuan, Konstantinos Kotsis, and Sergei Manzhos. "Comparative density functional theory and density functional tight binding study of arginine and arginine-rich cell penetrating peptide TAT adsorption on anatase TiO2." Physical Chemistry Chemical Physics 18, no. 29 (2016): 19902–17. http://dx.doi.org/10.1039/c6cp02671k.

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9

Guo, Feng, Hong Zhang, Chao-Yang Zhang, Xin-Lu Cheng, and Hai-Quan Hu. "Effect of electronic excitation to intermolecular proton transfer in bulk nitromethane: Tuned parameter SCC-DFTB and first principles study." Journal of Theoretical and Computational Chemistry 14, no. 02 (March 2015): 1550013. http://dx.doi.org/10.1142/s0219633615500133.

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To understand the reaction mechanism involving hydrogen transfers through hydrogen-bond bridge, we carried out both Self-Consistent Charge Density Functional Tight-Binding (SCC-DFTB) calculations of bulk nitromethane and Density Functional Theory (DFT) calculations of singlet ground state/triplet excited state molecular nitromethane using B3LYP functional. Firstly, we tuned the repulsive parameters of the SCC-DFTB method for nitromethane with dataset calculated from DFT at B3LYP/6-311g level. The molecular dynamics simulations are carried out with tuned parameters to get the dynamical properties of the bulk nitromethane, and the static calculations are intended to give energy profile of the reaction process. These calculations indicate the excitation of nitromethane molecule making the proton transfer reactions possible, and lowering the reaction barrier.

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10

Arabnejad, Saeid, Koichi Yamashita, and Sergei Manzhos. "Defects in crystalline PVDF: a density functional theory-density functional tight binding study." Physical Chemistry Chemical Physics 19, no. 11 (2017): 7560–67. http://dx.doi.org/10.1039/c7cp00510e.

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We present a comparative density functional theory (DFT) and density functional tight binding (DFTB) study of structures, energetics, vibrational properties as well as electronic structures of the four crystalline phases of polyvinylidene fluoride (PVDF) with different types of defects.

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11

Polynski, Mikhail V., Mariia D. Sapova, and Valentine P. Ananikov. "Understanding the solubilization of Ca acetylide with a new computational model for ionic pairs." Chemical Science 11, no. 48 (2020): 13102–12. http://dx.doi.org/10.1039/d0sc04752j.

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Constructing the carbon framework from a carbon-neutral source: a new computational model for ionic pairs in solution based on DFTB MD and DFT helps to propose a strategy for sustainable organic transformations with solid CaC₂.

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12

Bold, Beatrix M., Monja Sokolov, Sayan Maity, Marius Wanko, Philipp M. Dohmen, Julian J. Kranz, Ulrich Kleinekathöfer, Sebastian Höfener, and Marcus Elstner. "Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes." Physical Chemistry Chemical Physics 22, no. 19 (2020): 10500–10518. http://dx.doi.org/10.1039/c9cp05753f.

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In the present work, we perform a benchmark study on both the isolated chromophores retinal and BChl a as well as on the biological systems, to determine the accuracy of LC-TD-DFT and LC-TD-DFTB for describing color-tuning effects.

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13

Rottmannová, Lenka, Kraiwan Punyain, Ján Rimarčík, Vladimír Lukeš, Erik Klein, and Anne-Marie Kelterer. "Theoretical study of 2-phenylpyrrole molecule using various quantum-chemical approaches." Acta Chimica Slovaca 5, no. 1 (April 1, 2012): 21–28. http://dx.doi.org/10.2478/v10188-012-0004-4.

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Theoretical study of 2-phenylpyrrole molecule using various quantum-chemical approaches A systematic theoretical study of 2-phenylpyrrole (PhPy) is presented for its neutral and monocharged states. The calculations were performed using the semiempirical Austin Model 1 (AM1) method, ab initio Møller-Plesset perturbation theory up to the second-order (MP2), density functional theory (DFT) and its tight-binding approximation (DFTB+). The comparison of the obtained equilibrium geometries showed that the C—C bond lengths in the phenylene ring are practically identical for the neutral state. Electric charging leads to significant changes in the geometry with respect to the neutral state. The C—N bonds in PhPy are elongated and the negative charging produces the out-of-plane distortion of N—H bond from the aromatic ring plane. The anionic state of the investigated molecule is connected with a higher perturbation of bond length alternation in both rings in comparison to the cationic state. The vibrationaly broadened absorption spectra, based on the on-the-fly molecular dynamics (MD) simulations, are also presented and compared with experimental spectra. Although the DFTB+ method has the tendency to planarize the investigated molecular structure, the agreement of simulated absorption spectra based on the MD DFTB+ geometries with TD-DFT calculations is acceptable.

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14

Qi, Tingting, Charles W. Bauschlicher, John W. Lawson, Tapan G. Desai, Evan J. Reed, and Antonin Lenfant. "Addendum to “Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 1. Molecular Dynamics Simulations” and “Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 2. Elementary Reaction Paths”." Journal of Physical Chemistry A 118, no. 28 (July 2, 2014): 5355–57. http://dx.doi.org/10.1021/jp505594b.

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15

Qi, Tingting, Charles W. Bauschlicher, John W. Lawson, Tapan G. Desai, and Evan J. Reed. "Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 1. Molecular Dynamics Simulations." Journal of Physical Chemistry A 117, no. 44 (October 28, 2013): 11115–25. http://dx.doi.org/10.1021/jp4081096.

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16

Bauschlicher, Charles W., Tingting Qi, Evan J. Reed, Antonin Lenfant, John W. Lawson, and Tapan G. Desai. "Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 2. Elementary Reaction Paths." Journal of Physical Chemistry A 117, no. 44 (October 25, 2013): 11126–35. http://dx.doi.org/10.1021/jp408113w.

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17

Liu, Hongsheng, Gotthard Seifert, and Cristiana Di Valentin. "An efficient way to model complex magnetite: Assessment of SCC-DFTB against DFT." Journal of Chemical Physics 150, no. 9 (March 7, 2019): 094703. http://dx.doi.org/10.1063/1.5085190.

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18

Selli, Daniele, Gianluca Fazio, and Cristiana Di Valentin. "Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT." Journal of Chemical Physics 147, no. 16 (October 28, 2017): 164701. http://dx.doi.org/10.1063/1.4994165.

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19

Abdali, S., T. A. Niehaus, K. J. Jalkanen, X. Cao, L. A. Nafie, Th Frauenheim, S. Suhai, and H. Bohr. "Vibrational absorption spectra, DFT and SCC-DFTB conformational study and analysis of [Leu]enkephalin." Physical Chemistry Chemical Physics 5, no. 6 (February 7, 2003): 1295–300. http://dx.doi.org/10.1039/b210893c.

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20

Sakkaki, Babak, Hassan Rasooli Saghai, Ghafar Darvish, and Mehdi Khatir. "A new photodetector structure based on graphene nanomeshes: an ab initio study." Beilstein Journal of Nanotechnology 11 (July 15, 2020): 1036–44. http://dx.doi.org/10.3762/bjnano.11.88.

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Recent experiments suggest graphene-based materials as candidates in future electronic and optoelectronic devices. In this paper, we propose to investigate new photodetectors based on graphene nanomeshes (GNMs). Density functional theory (DFT) calculations are performed to gain insight into electronic and optical characteristics of various GNM structures. To investigate the device-level properties of GNMs, their current–voltage characteristics are explored by DFT-based tight-binding (DFTB) in combination with non-equilibrium Green’s function (NEGF) methods. Band structure analysis shows that GNMs have both metallic and semiconducting properties depending on the arrangements of perforations. Also, absorption spectrum analysis indicates attractive infrared peaks for GNMs with semiconducting characteristics, making them better photodetectors than graphene nanoribbon (GNR)-based alternatives. The results suggest that GNMs can be potentially used in mid-infrared detectors with specific detectivity values that are 100-fold that of graphene-based devices and 1000-fold that of GNR-based devices. Hence, the special properties of graphene combined with the quantum feathers of the perforation makes it suitable for optical devices.

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21

RIAHI, SIAVASH, MOHAMMAD REZA GANJALI, and PARVIZ NOROUZI. "QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE." Journal of Theoretical and Computational Chemistry 07, no. 03 (June 2008): 317–29. http://dx.doi.org/10.1142/s0219633608003770.

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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.

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22

Aldongarov, A. A., A. M. Assilbekova, I. S. Irgibaeva, and A. I. Mantel. "Comparison of calculated by DFTB electronic excitation energies of CdS nanosized clusters with DFT results." Eurasian Journal of Physics and Functional Materials 4, no. 3 (September 23, 2020): 255–60. http://dx.doi.org/10.29317/ejpfm.2020040308.

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23

Xu, Dingguo, Hua Guo, and Qiang Cui. "Antibiotic Binding to Dizinc β-Lactamase L1 fromStenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT Studies†." Journal of Physical Chemistry A 111, no. 26 (July 2007): 5630–36. http://dx.doi.org/10.1021/jp068746s.

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24

Szafraniec, Anna, Marcin Grajda, Hanna Jędrzejewska, Agnieszka Szumna, and Waldemar Iwanek. "Enaminone Substituted Resorcin[4]arene—Sealing of an Upper-Rim with a Directional System of Hydrogen-Bonds." International Journal of Molecular Sciences 21, no. 20 (October 11, 2020): 7494. http://dx.doi.org/10.3390/ijms21207494.

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The paper presents the synthesis of an enaminone resorcin[4]arene via a thermally activated o-quinomethide. The crystal structure indicates that in the solid state all enaminone units participate in a unidirectional seam of 12 intramolecular hydrogen bonds that are formed around the cavity. The molecule exhibits C2 symmetry, with two opposite-laying enaminone units directed inside the cavity (“in”), and the other two units outside the cavity (“out”). In the solution the enaminone resorcin[4]arene exists as a mixture of conformers with distribution controlled by temperature and solvent. The experimental data are compared with the results of theoretical calculations using DFT B3LYP/6-31G(d,p) and fast semi-empirical DFTB/GFN2-xTB method in various solvents.

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25

Sirirak, Jitnapa, Narin Lawan, Marc W. Van der Kamp, Jeremy N. Harvey, and Adrian J. Mulholland. "Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes." PeerJ Physical Chemistry 2 (May 20, 2020): e8. http://dx.doi.org/10.7717/peerj-pchem.8.

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To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.

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26

Lai, S. K., and Wafa Maftuhin. "An efficient optimization algorithm that hybridizes DFTB and DFT theories both operated within the modified basin hopping method." Computer Physics Communications 236 (March 2019): 164–75. http://dx.doi.org/10.1016/j.cpc.2018.10.027.

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27

Rasoolidanesh, Melahatsadat, Mohammad Astaraki, Mina Mostafavi, Mahyar Rezvani, and Masoud Darvish Ganji. "Toward efficient enantioseparation of ibuprofen isomers using chiral BNNTs: Dispersion corrected DFT calculations and DFTB molecular dynamic simulations." Diamond and Related Materials 119 (November 2021): 108561. http://dx.doi.org/10.1016/j.diamond.2021.108561.

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28

Fazio, Gianluca, Gotthard Seifert, Mathias Rapacioli, Nathalie Tarrat, and Jan-Ole Joswig. "Surface-Charge Dependent Orientation of Water at the Interface of a Gold Electrode: A Cluster Study." Zeitschrift für Physikalische Chemie 232, no. 9-11 (August 28, 2018): 1583–92. http://dx.doi.org/10.1515/zpch-2018-1136.

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Abstract A gold/water interface has been investigated with the DFT-based self-consistent-charge density-functional tight-binding (SCC-DFTB) method using a cluster model. Born–Oppenheimer molecular-dynamics simulations for mono-, bi-, and trilayers of water on the surface of a Au55 cluster have been computed. We have demonstrated the applicability of this method to the study of the structural and dynamical properties of the gold/water-multilayer interface. The results of the simulations clearly show the charge-dependent orientation and the corresponding polarization of the water sphere around the gold cluster. However, it was also shown that this polarization is restricted almost only to the first solvation shell. This illustrates the rather short-range screening behavior of water. The present study builds the basis for further investigations of metal/electrolyte interfaces on a reliable atomistic level, avoiding the problems of spurious artifacts in models using periodic boundary conditions.

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29

Simon, A., M. Rapacioli, G. Rouaut, G. Trinquier, and F. X. Gadéa. "Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 375, no. 2092 (March 20, 2017): 20160195. http://dx.doi.org/10.1098/rsta.2016.0195.

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We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC–DFTB) level of theory. The SCC–DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C 2 H 2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C 2 H 2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

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30

Alkan, Fahri, and Christine M. Aikens. "TD-DFT and TD-DFTB Investigation of the Optical Properties and Electronic Structure of Silver Nanorods and Nanorod Dimers." Journal of Physical Chemistry C 122, no. 41 (June 2018): 23639–50. http://dx.doi.org/10.1021/acs.jpcc.8b05196.

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31

Bruschi, Maurizio, Luca Bertini, Vlasta Bonačić-Koutecký, Luca De Gioia, Roland Mitrić, Giuseppe Zampella, and Piercarlo Fantucci. "Speciation of Copper–Peptide Complexes in Water Solution Using DFTB and DFT Approaches: Case of the [Cu(HGGG)(Py)] Complex." Journal of Physical Chemistry B 116, no. 22 (May 23, 2012): 6250–60. http://dx.doi.org/10.1021/jp210409c.

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Lukose, Binit, Agnieszka Kuc, Johannes Frenzel, and Thomas Heine. "On the reticular construction concept of covalent organic frameworks." Beilstein Journal of Nanotechnology 1 (November 22, 2010): 60–70. http://dx.doi.org/10.3762/bjnano.1.8.

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The concept of reticular chemistry is investigated to explore the applicability of the formation of Covalent Organic Frameworks (COFs) from their defined individual building blocks. Thus, we have designed, optimized and investigated a set of reported and hypothetical 2D COFs using Density Functional Theory (DFT) and the related Density Functional based tight-binding (DFTB) method. Linear, trigonal and hexagonal building blocks have been selected for designing hexagonal COF layers. High-symmetry AA and AB stackings are considered, as well as low-symmetry serrated and inclined stackings of the layers. The latter ones are only slightly modified compared to the high-symmetry forms, but show higher energetic stability. Experimental XRD patterns found in literature also support stackings with highest formation energies. All stacking forms vary in their interlayer separations and band gaps; however, their electronic densities of states (DOS) are similar and not significantly different from that of a monolayer. The band gaps are found to be in the range of 1.7–4.0 eV. COFs built of building blocks with a greater number of aromatic rings have smaller band gaps.

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RIAHI, SIAVASH, SOLMAZ EYNOLLAHI, and MOHAMMAD REZA GANJALI. "INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY." Journal of Theoretical and Computational Chemistry 09, no. 05 (October 2010): 875–88. http://dx.doi.org/10.1142/s0219633610006055.

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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.

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Brandenburg, Jan Gerit, and Stefan Grimme. "Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 72, no. 4 (August 1, 2016): 502–13. http://dx.doi.org/10.1107/s2052520616007885.

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We analyze the energy landscape of the sixth crystal structure prediction blind test targets with variousfirst principlesandsemi-empiricalquantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko–Scheffler (TS) method, and the density-dependent dispersion correction dDsC. Recent methodological progress includes higher-order contributions in both the many-body and multipole expansions. We use the D3 correction with Axilrod–Teller–Muto type three-body contribution, the TS based many-body dispersion (MBD), and the nonlocal van der Waals density functional (vdW-DF2). The density functionals with D3 and MBD correction provide an energy ranking of the blind test polymorphs in excellent agreement with the experimentally found structures. As a computationally less demanding method, we test our recently presented minimal basis Hartree–Fock method (HF-3c) and a density functional tight-binding Hamiltonian (DFTB). Considering the speed-up of three to four orders of magnitudes, the energy ranking provided by the low-cost methods is very reasonable. We compare the computed geometries with the corresponding X-ray data where TPSS-D3 performs best. The importance of zero-point vibrational energy and thermal effects on crystal densities is highlighted.

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35

He, C., G. Liu, W. X. Zhang, Z. Q. Shi, and S. L. Zhou. "Tuning the structures and electron transport properties of ultrathin Cu nanowires by size and bending stress using DFT and DFTB methods." RSC Advances 5, no. 29 (2015): 22463–70. http://dx.doi.org/10.1039/c4ra15051a.

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Electron transport properties of ultrathin Cu nanowires with diameters of 0.2–1.0 nm under different bending stresses are reported, using density functional theory and density-functional-based tight-binding approaches, for application in flexible displays and solar cells.

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Rogers, Ian L., and Kevin J. Naidoo. "Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction." Journal of Computational Chemistry 38, no. 20 (May 10, 2017): 1789–98. http://dx.doi.org/10.1002/jcc.24820.

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Zheng, Guishan, Stephan Irle, and Keiji Morokuma. "Performance of the DFTB method in comparison to DFT and semiempirical methods for geometries and energies of C20–C86 fullerene isomers." Chemical Physics Letters 412, no. 1-3 (August 2005): 210–16. http://dx.doi.org/10.1016/j.cplett.2005.06.105.

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Klusák, Vojtěch, Petr Dobeš, Jiří Černý, and Jiří Vondrášek. "How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins." Collection of Czechoslovak Chemical Communications 76, no. 5 (2011): 605–18. http://dx.doi.org/10.1135/cccc2011033.

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To determine reasonably which amino acid side chain contributes significantly to the stability of a protein or to the stability of a protein–ligand complex is not a straightforward task. We suggest a partial but systematic solution of the problem by a specific fragmentation of a protein chain into blocks of single amino acid side chains with their corresponding backbone part. For such systems of building blocks, we have calculated the stabilisation/interaction energies by means of correlated ab initio calculations. We have shown that a reasonable way to treat an amino-acid residue composing the protein is to break the homonuclear C–C bond between the Cα atom and the C(O) carboxyl carbon. The reference data obtained by the RI-MP2 method with the cc-pVDZ basis set were compared with RIDFT, RIDFT augmented by the dispersion term, SCC-DFTB-D and Hartree–Fock calculations. The results clearly show the failure of those methods lacking an appropriate treatment of the correlation energy. The DFT methods augmented by the empirical dispersion term on the other hand describe the interaction in good agreement with the reference method.

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Chen, Zhen, Yunguo Liu, Shuzhen Liao, Niannian Yi, and Qian Hu. "Treatment of adsorption of dioxane by using SiCNT toward efficient remediation of refractory organic contaminants from wastewater: DFT and DFTB-MD simulations." Journal of Molecular Liquids 316 (October 2020): 113869. http://dx.doi.org/10.1016/j.molliq.2020.113869.

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Ávila, Edward E., Asiloé J. Mora, Gerzon E. Delgado, Ricardo R. Contreras, Luis Rincón, Andrew N. Fitch, and Michela Brunelli. "Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculations." Acta Crystallographica Section B Structural Science 65, no. 5 (September 17, 2009): 639–46. http://dx.doi.org/10.1107/s0108768109027244.

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The molecular and crystalline structure of ethyl 1′,2′,3′,4′,4a′,5′,6′,7′-octahydrodispiro[cyclohexane-1,2′-quinazoline-4′,1′′-cyclohexane]-8′-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223–1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N—H...S and C—H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.

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Heydariyan, Shima, Mohammad Reza Nouri, Mojtaba Alaei, Zahed Allahyari, and Thomas A. Niehaus. "New candidates for the global minimum of medium-sized silicon clusters: A hybrid DFTB/DFT genetic algorithm applied to Sin, n = 8-80." Journal of Chemical Physics 149, no. 7 (August 21, 2018): 074313. http://dx.doi.org/10.1063/1.5037159.

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de Lima, Guilherme Ferreira, Hélio Anderson Duarte, and Josefredo R. Pliego. "Dynamical Discrete/Continuum Linear Response Shells Theory of Solvation: Convergence Test for NH4+and OH−Ions in Water Solution Using DFT and DFTB Methods." Journal of Physical Chemistry B 114, no. 48 (December 9, 2010): 15941–47. http://dx.doi.org/10.1021/jp110202e.

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Kwon, Young Mi, Maximilian R. Stammnitz, Jinhong Wang, Kate Swift, Graeme W. Knowles, Ruth J. Pye, Alexandre Kreiss, et al. "Tasman-PCR: a genetic diagnostic assay for Tasmanian devil facial tumour diseases." Royal Society Open Science 5, no. 10 (October 2018): 180870. http://dx.doi.org/10.1098/rsos.180870.

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Tasmanian devils have spawned two transmissible cancer clones, known as devil facial tumour 1 (DFT1) and devil facial tumour 2 (DFT2). DFT1 and DFT2 are transmitted between animals by the transfer of allogeneic contagious cancer cells by biting, and both cause facial tumours. DFT1 and DFT2 tumours are grossly indistinguishable, but can be differentiated using histopathology, cytogenetics or genotyping of polymorphic markers. However, standard diagnostic methods require specialist skills and equipment and entail long processing times. Here, we describe Tasman-PCR: a simple polymerase chain reaction (PCR)-based diagnostic assay that identifies and distinguishes DFT1 and DFT2 by amplification of DNA spanning tumour-specific interchromosomal translocations. We demonstrate the high sensitivity and specificity of this assay by testing DNA from 546 tumours and 804 normal devils. A temporal–spatial screen confirmed the reported geographic ranges of DFT1 and DFT2 and did not provide evidence of additional DFT clones. DFT2 affects disproportionately more males than females, and devils can be co-infected with DFT1 and DFT2. Overall, we present a PCR-based assay that delivers rapid, accurate and high-throughput diagnosis of DFT1 and DFT2. This tool provides an additional resource for devil disease management and may assist with ongoing conservation efforts.

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Elstner, Marcus, Karl J. Jalkanen, Michaela Knapp-Mohammady, Thomas Frauenheim, and Sándor Suhai. "Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations." Chemical Physics 263, no. 2-3 (January 2001): 203–19. http://dx.doi.org/10.1016/s0301-0104(00)00375-x.

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Chopra, Siddheshwar. "Performance study of the electronic and optical parameters of thermally activated delayed fluorescence nanosized emitters (CCX-I and CCX-II) via DFT, SCC-DFTB and B97-3c approaches." Journal of Nanostructure in Chemistry 10, no. 2 (February 19, 2020): 115–24. http://dx.doi.org/10.1007/s40097-020-00334-0.

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Li, Dao Lin, and Hai Jun Li. "10-Point DFT and its Application in Power System Harmonic Analysis." Advanced Materials Research 433-440 (January 2012): 7458–64. http://dx.doi.org/10.4028/www.scientific.net/amr.433-440.7458.

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In this paper, an efficient algorithm for computing 10-point DFT, radix-10 FFT algorithm for computing10 Superscript textMSubscript text-point DFT and N=L×10 Superscript textMSubscript text-point DFT are presented. FFT is often employed in power systems harmonics analysis even though it is not accurate due to spectral leakage and barrier effect. When N=L×10Superscript textMSubscript text-point DFTs are used to analyze harmonics in power systems, comparing to N=2 Superscript textMSubscript text-point DFTs, very accurate harmonic parameters can be obtained. The simulation results in MATLAB show that the methods are feasible and effective to enhance analysis accuracy.

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Piskorz, Witold, Filip Zasada, Gabriela Wójtowicz, Antoni Morawski, Wojciech Macyk, and Zbigniew Sojka. "Attaching titania clusters of various size to reduced graphene oxide and its impact on the conceivable photocatalytic behavior of the junctions—a DFT/D + U and TD DFTB modeling." Journal of Physics: Condensed Matter 31, no. 40 (July 15, 2019): 404001. http://dx.doi.org/10.1088/1361-648x/ab2bc8.

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Korvel, Grazina, Bozena Kostek, and Olga Kurasova. "Comparative Analysis of Various Transformation Techniques for Voiceless Consonants Modeling." International Journal of Computers Communications & Control 13, no. 5 (September 29, 2018): 853–64. http://dx.doi.org/10.15837/ijccc.2018.5.3310.

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In this paper, a comparison of various transformation techniques, namely Discrete Fourier Transform (DFT), Discrete Cosine Transform (DCT) and Discrete Walsh Hadamard Transform (DWHT) is performed in the context of their application to voiceless consonant modeling. Speech features based on these transformation techniques are extracted. These features are mean and derivative values of cepstrum coefficients, derived from each transformation. Fea-ture extraction is performed on the speech signal divided into short-time seg-ments. The kNN and Naive Bayes methods are used for phoneme classification. Experiments show that DFT and DCT give better classification accuracy than DWHT. The result of DFT was not significantly different from DCT, but it was for DWHT. The same tendency was revealed for DCT. It was checked with the usage of the ANOVA test that the difference between results obtained by DCT and DWHT is significant.

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Duram, Leslie, and Amber Mead. "Exploring linkages between Consumer Food Co-operatives and Domestic Fair Trade in the United States." Renewable Agriculture and Food Systems 29, no. 2 (February 22, 2013): 151–60. http://dx.doi.org/10.1017/s1742170513000033.

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AbstractConsumer Food Co-operatives (co-ops) have provided consumers an alternative to corporate supermarkets and big-box stores since the 1960s. Producers seeking broader marketing opportunities often turn to co-ops. This study examines how, within alternative food networks (AFNs), co-ops play a role in the emergence of the Domestic Fair Trade (DFT) movement in the USA. The DFT movement is based on the idea that family farms and small- to mid-sized farms in the global north are facing many of the same pressures as producers in the global south. The Domestic Fair Trade Association (DFTA) in the USA is the umbrella organization for a variety of stakeholders. The DFTA seeks to ‘support family-scale farming, to reinforce farmer-led initiatives such as farmer co-operatives, and to bring these groups together with mission-based traders, retailers and concerned consumers to contribute to the movement for sustainable agriculture in North America’1. This study assessed five co-ops (through interviews and document analysis) to determine their experiences with integrating DFT into their business practices. The research reveals that DFT concepts are important to co-operative decision-makers, but they are faced with challenges when it comes to actually integrating DFT into their business model. Insight into stakeholder perceptions and professional-level DFT activities, indicates that co-ops will be a key factor in determining whether the DFT movement will succeed in the USA.

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Peng, Yaqiu, and Mingqi Li. "Discrete Fourier Transform-Based Block Faster-Than- Nyquist Transmission for 5G Wireless Communications." Applied Sciences 10, no. 4 (February 14, 2020): 1313. http://dx.doi.org/10.3390/app10041313.

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Faster-than-Nyquist (FTN) signaling is regarded as a potential candidate for improving data rate and spectral efficiency of 5G new radio (NR). However, complex detectors have to be utilized to eliminate the inter symbol interference (ISI) introduced by time-domain packing and the inter carrier interference (ICI) introduced by frequency-domain packing. Thus, the exploration of low complexity transceiver schemes and detectors is of great importance. In this paper, we consider a discrete Fourier transform (DFT) block transmission for multi-carrier FTN signaling, i.e., DBT-MC-FTN. With the aid of DFTs/IDFTs and frequency domain windowing, time- and frequency domain packing can be implemented flexibly and efficiently. At the receiver, the inherent ISI and ICI can be canceled via a soft successive interference cancellation (SIC) detector. The effectiveness of the detector is verified by the simulation over the additive white Gaussian noise channel and the fading channel. Furthermore, based on the characteristics of the efficient architecture of DFT-MC-FTN, two pilot-aided channel estimation schemes, i.e., time-division-multiplexing DBT-MC-FTN symbol-level pilot, and frequency-division-multiplexing subcarrier-level pilot within the DBT-MC-FTN symbol, respectively, are also derived. Numerical results show that the proposed channel estimation schemes can achieve high channel estimation accuracy.

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