scholarly journals Computational Insights in DNA Methylation: Catalytic and Mechanistic Elucidations

2021 ◽  
Author(s):  
Mansour H. Almatarneh ◽  
Ghada G. Kayed ◽  
Mohammednoor Altarawneh ◽  
Yuming Zhao ◽  
Amita Verma
Keyword(s):  
Density Functional ◽  
Cpg Island ◽  
Epigenetic Modification ◽  
Dna Methyltransferases ◽  
Functional Theory ◽  
Dft Modeling ◽  
Dna Strand ◽  
Target Activity ◽  
Insight Into ◽  
Shed Light

Methylation at C5 position of cytosine (5mC) is the most abundantly occurring methylation process at CpG island, which has been well-known as an epigenetic modification linked to many human’s diseases. Recently, another methylation approach has been discovered to show that DNA methyltransferases (DNMTs) promote the addition of methyl group at position 3 to yield 3mC. The existence of 3mC can cause severe damages to the DNA strand, such as blocking its replication, repair, and transcription, affecting its stability, and initiating a double-strand DNA break. To gain a deeper insight into the formation of 3mC, we have performed density functional theory (DFT) modeling studies at different levels of theory to clearly map out the mechanistic details for this new methylation approach. Our computed results are in harmony with pertinent experimental observations and shed light on a crucial off-target activity of DNMTs.

scholarly journals Ab Initio Study of Ferroelectric Critical Size of SnTe Low-Dimensional Nanostructures

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 732 ◽  
Author(s):  
Takahiro Shimada ◽  
Koichiro Minaguro ◽  
Tao Xu ◽  
Jie Wang ◽  
Takayuki Kitamura
Keyword(s):  
Density Functional ◽  
Critical Size ◽  
Density Functional Theory Calculations ◽  
Cell Width ◽  
Functional Theory ◽  
Unit Cells ◽  
Principle Density Functional Theory ◽  
Low Dimensional ◽  
Insight Into ◽  
Ferroelectric Perovskite

Beyond a ferroelectric critical thickness of several nanometers existed in conventional ferroelectric perovskite oxides, ferroelectricity in ultimately thin dimensions was recently discovered in SnTe monolayers. This discovery suggests the possibility that SnTe can sustain ferroelectricity during further low-dimensional miniaturization. Here, we investigate a ferroelectric critical size of low-dimensional SnTe nanostructures such as nanoribbons (1D) and nanoflakes (0D) using first-principle density-functional theory calculations. We demonstrate that the smallest (one-unit-cell width) SnTe nanoribbon can sustain ferroelectricity and there is no ferroelectric critical size in the SnTe nanoribbons. On the other hand, the SnTe nanoflakes form a vortex of polarization and lose their toroidal ferroelectricity below the surface area of 4 × 4 unit cells (about 25 Å on one side). We also reveal the atomic and electronic mechanism of the absence or presence of critical size in SnTe low-dimensional nanostructures. Our result provides an insight into intrinsic ferroelectric critical size for low-dimensional chalcogenide layered materials.

A density functional theory insight into the structure and reactivity of diphenyltin(IV) derivative of glycylphenylalanine

2016 ◽  
Vol 39 (3-4) ◽  
Author(s):  
Sandeep Pokharia ◽  
Rachana Joshi ◽  
Mamta Pokharia ◽  
Swatantra Kumar Yadav ◽  
Hirdyesh Mishra
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Functional Theory ◽  
Insight Into

AbstractThe quantum-chemical calculations based on density functional theory (DFT) have been performed on the diphenyltin(IV) derivative of glycyl-phenylalanine (H

How big is big? Separation by conventional methods, X-ray and electronic structures of positional isomers of bis-tert-butylisocyano adduct of 2(3),9(10),16(17),23(24)-tetrachloro-3(2),10(9),17(16),24(23)-tetra(2,6-di-iso-propylphenoxy)-phthalocyaninato iron(II) complex

2016 ◽  
Vol 20 (01n04) ◽  
pp. 337-351 ◽  
Author(s):  
Derrick R. Anderson ◽  
Pavlo V. Solntsev ◽  
Hannah M. Rhoda ◽  
Victor N. Nemykin
Keyword(s):  
Electronic Structures ◽  
Density Functional ◽  
Positional Isomers ◽  
Excitation Energies ◽  
Functional Theory ◽  
X Ray ◽  
Vertical Excitation ◽  
X Ray Crystallography ◽  
Tddft Calculations ◽  
Insight Into

A presence of bulky 2,6-di-iso-propylphenoxy groups in bis-tert-butylisocyano adduct of 2(3),9(10),16(17),23(24)-tetrachloro-3(2),10(9),17(16),24(23)-tetra(2,6-di-iso-propylphenoxy)-phthalocyaninato iron(II) complex allows separation of two individual positional isomers and a mixture of the remaining two isomers using conventional chromatography. X-ray structures of “[Formula: see text]” and “[Formula: see text]” isomers were confimed by X-ray crystallography. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations of each individual positional isomer allowed insight into their electronic structures and vertical excitation energies, which were correlated with the experimental UV-vis and MCD spectra.

scholarly journals A Computational Study of Direct CO2 Hydrogenation to Methanol on Pd Catalysts

2021 ◽  
Author(s):  
Igor Kowalec ◽  
Lara Kabalan ◽  
Richard Catlow ◽  
Andrew Logsdail
Keyword(s):  
Density Functional ◽  
Negative Charge ◽  
Computational Study ◽  
Adsorbed Species ◽  
Pd Catalysts ◽  
Functional Theory ◽  
Activation Barriers ◽  
Rate Determining Step ◽  
Adsorption Energies ◽  
Insight Into

<p>We investigate the mechanism of direct CO<sub>2</sub> hydrogenation to methanol on Pd (111), (100) and (110) surfaces using density functional theory (DFT), providing insight into the reactivity of CO<sub>2</sub> on Pd-based catalysts. The initial chemisorption of CO<sub>2</sub>, forming a partially charged CO<sub>2</sub><sup>δ-</sup>, is weakly endothermic on a Pd (111) surface, with an adsorption energy of 0.06 eV, and slightly exothermic on Pd (100) and (110) surfaces, with adsorption energies of -0.13 and -0.23 eV, respectively. Based on Mulliken analysis, we attribute the low stability of CO<sub>2</sub><sup>δ-</sup><sub> </sub>on the Pd (111) surface to a negative charge that accumulates on the surface Pd atoms interacting directly with the CO<sub>2</sub><sup>δ-</sup><sub> </sub>adsorbate. For the reaction of the adsorbed species on the Pd surface, HCOOH hydrogenation to H<sub>2</sub>COOH is predicted to be the rate determining step of the conversion to methanol in all cases, with activation barriers of 1.35, 1.26, and 0.92 eV on Pd (111), (100) and (110) surfaces, respectively.<br></p>

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