Charge density of 4-methyl-3-[(tetrahydro-2H-pyran-2-yl)oxy]thiazole-2(3H)-thione. A comprehensive multipole refinement, maximum entropy method and density functional theory study

2020 ◽  
Vol 76 (3) ◽  
pp. 450-468
Author(s):  
Barbora Vénosová ◽  
Julia Koziskova ◽  
Jozef Kožíšek ◽  
Peter Herich ◽  
Karol Lušpai ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Charge Density ◽  
Maximum Entropy ◽  
Density Functional ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Experimental Results ◽  
Basis Set ◽  
Functional Theory ◽  
Radial Functions

The structure of 4-methyl-3-[(tetrahydro-2H-pyran-2-yl)oxy]thiazole-2(3H)-thione (MTTOTHP) was investigated using X-ray diffraction and computational chemistry methods for determining properties of the nitrogen—oxygen bond, which is the least stable entity upon photochemical excitation. Experimentally measured structure factors have been used to determine and characterize charge density via the multipole model (MM) and the maximum entropy method (MEM). Theoretical investigation of the electron density and the electronic structure has been performed in the finite basis set density functional theory (DFT) framework. Quantum Theory of Atoms In Molecules (QTAIM), deformation densities and Laplacians maps have been used to compare theoretical and experimental results. MM experimental results and predictions from theory differ with respect to the sign and/or magnitude of the Laplacian at the N—O bond critical point (BCP), depending on the treatment of n values of the MM radial functions. Such Laplacian differences in the N—O bond case are discussed with respect to a lack of flexibility in the MM radial functions also reported by Rykounov et al. [Acta Cryst. (2011), B67, 425–436]. BCP Hessian eigenvalues show qualitatively matching results between MM and DFT. In addition, the theoretical analysis used domain-averaged fermi holes (DAFH), natural bond orbital (NBO) analysis and localized (LOC) orbitals to characterize the N—O bond as a single σ bond with marginal π character. Hirshfeld atom refinement (HAR) has been employed to compare to the MM refinement results and/or neutron dataset C—H bond lengths and to crystal or single molecule geometry optimizations, including considerations of anisotropy of H atoms. Our findings help to understand properties of molecules like MTTOTHP as progenitors of free oxygen radicals.

Charge density study with the Maximum Entropy Method on model data of silicon. A search for non-nuclear attractors

1996 ◽  
Vol 74 (6) ◽  
pp. 1054-1058 ◽  
Author(s):  
R.Y. de Vries ◽  
W.J. Briels ◽  
D. Fell ◽  
G. te Velde ◽  
E.J. Baerends
Keyword(s):  
Charge Density ◽  
Maximum Entropy ◽  
Density Functional ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Structure Factors ◽  
The Density Functional Theory ◽  
Structure Calculations

In 1990 Sakata and Sato applied the maximum entropy method (MEM) to a set of structure factors measured earlier by Saka and Kato with the Pendellösung method. They found the presence of non-nuclear attractors, i.e., maxima in the density between two bonded atoms. We applied the MEM to a limited set of Fourier data calculated from a known electron density distribution (EDD) of silicon. The EDD of silicon was calculated with the program ADF-BAND. This program performs electronic structure calculations, including periodicity, based on the density functional theory of Hohenberg and Kohn. No non-nuclear attractor between two bonded silicon atoms was observed in this density. Structure factors were calculated from this density and the same set of structure factors that was measured by Saka and Kato was used in the MEM analysis. The EDD obtained with the MEM shows the same non-nuclear attractors that were later obtained by Sakata and Sato. This means that the non-nuclear attractors in silicon are really an artefact of the MEM. Key words: Maximum Entropy Method, non-nuclear attractors, charge density. X-ray diffraction.

scholarly journals Применение метода максимальной энтропии к временным рядам, получаемым в реальном времени в рамках нестационарной теории функционала плотности

2021 ◽  
pp. 64-73
Author(s):  
Y. Zempo ◽  
S.S. Kano
Keyword(s):  
Density Functional Theory ◽  
Spectral Analysis ◽  
Dipole Moment ◽  
Maximum Entropy ◽  
Density Functional ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Data Set ◽  
Functional Theory ◽  
Raw Data

The maximum entropy method is one of the key techniques for spectral analysis. The main feature is to describe spectra in low frequency with short timeseries data. We adopted the maximum entropy method to analyze the spectrum from the dipole moment obtained by the timedependent density functional theory calculation in real time, which is intensively studied and applied to computing optical properties. In the maximum entropy method analysis, we proposed that we use the concatenated data set made from severaltimes repeated raw data together with the phase. We have applied this technique to spectral analysis of the dynamic dipole moment obtained from timedependent density functional theory dipole moment of several molecules such as oligofluorene with n = 8. As a result, the higher resolution can be obtained without any peak shift due to the phase jump. The peak position is in good agreement to that of FT with just raw data. This paper presents the efficiency and characteristic features of this technique. Метод максимальной энтропии — один из основных в спектральном анализе. Его главная особенность — описание низкочастотных спектров короткими временными рядами данных. Авторы применили метод максимальной энтропии для анализа спектров дипольного момента, полученных расчетами в реальном времени по нестационарной теории функционала плотности. Данный вопрос интенсивно изучается и находит практическое применение при расчетах оптических свойств. При анализе методом максимальной энтропии предложено использовать объединенные наборы данных, включающие несколько повторяющихся последовательностей исходных данных с учетом фазы. Данный метод был применен при проведении спектрального анализа динамического дипольного момента, рассчитанного по нестационарной теории функционала плотности на основе дипольного момента нескольких молекул — в частности, молекул олигофлуорена при n = 8. В итоге удалось повысить разрешение без смещения максимумов из-за скачка фазы. Положение максимумов хорошо согласуется с результатами применения преобразования Фурье к необработанным исходным данным. В настоящей статье представлены особенности данного метода и показатели его эффективности.

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Absolute Error ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Framework Materials ◽  
Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

Dissociation of dinitrogen on iron clusters: A detailed study of the Fe16 + N2 case.

2020 ◽  
Author(s):  
Bole Chen ◽  
Gennady L. Gutsev ◽  
Weiguo Sun ◽  
Xiao-Yu Kuang ◽  
Cheng Lu ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Basis Set ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Iron Clusters ◽  
Generalized Gradient Approximation

The coalescence of two Fe8N as well as the structure of the Fe16N2 cluster were studied using density functional theory with the generalized gradient approximation and a basis set of...

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

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