scholarly journals C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

2020 ◽  
Vol 21 (8) ◽  
pp. 2882 ◽  
Author(s):  
Grazyna Leszczynska ◽  
Marek Cypryk ◽  
Bartlomiej Gostynski ◽  
Klaudia Sadowska ◽  
Paulina Herman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Density Functional ◽  
Negative Charge ◽  
Positive Charge ◽  
Dominant Role ◽  
Regulation Of Gene Expression ◽  
Side Chain ◽  
Functional Theory ◽  
Physiological Conditions ◽  
Synonymous Codons

5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1–3 were assessed to be significantly lower compared to their 2-thio- and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called “new wobble base pair”, which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5′-NNG-3′ synonymous codons, unlike their 2-thio- and 2-oxo-precursors, which preferentially read the 5′-NNA-3′ codons. Thus, the interplay between the levels of U-, S2U- and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3′-A- and 3′-G-ending codons.

Iron-Water Interface under Electrochemical Condition

2016 ◽  
Vol 879 ◽  
pp. 1399-1403
Author(s):  
Norio Nunomura ◽  
Satoshi Sunada
Keyword(s):  
Density Functional ◽  
Negative Charge ◽  
Positive Charge ◽  
Density Functional Theory Calculations ◽  
Energy Shift ◽  
Contact Layer ◽  
Water Molecules ◽  
Functional Theory ◽  
Electrochemical Condition ◽  
Spin Polarized

Spin polarized density functional theory calculations have been performed to characterize the structure of water molecules on iron surface under applied charges. It is found that water molecules of the contact layer take H-down configuration under the negative charge, on the other hand, under the positive charge, they adsorbed on a top site of iron atom, as the applied charge increases, the dissociation of water molecules proceed. In addition, we found that the energy shift of the Fermi level varies linearly in the range from-e to +e, while beyond this range it tends to saturate.

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>

scholarly journals Citrullination – small change with a great consequence

2013 ◽  
Vol 9 ◽  
pp. 17-25 ◽  
Author(s):  
Mariusz Gogól
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Multiple Sclerosis ◽  
Positive Charge ◽  
Regulation Of Gene Expression ◽  
Slight Modification ◽  
Post Translational Modifications ◽  
Myelin Sheaths ◽  
Physiological Processes ◽  
Small Change

Citrullination is one of the possible post-translational modifications of proteins. It is based on a conversion of L-arginine residue (L-Arg) to L-citrulline residue (L-Cit). The reaction is catalyzed by peptidylarginine deiminases (PAD). The change of L-Arg imino moiety results in a loss of a positive charge. This slight modification can contribute to significant changes in physicochemical properties of proteins, which may also cause a change of their functions. Citrullination is the modification observed in physiological processes such as epidermal keratinization, regulation of gene expression and the reorganization of myelin sheaths. The changes in the efficacy of citrullination may contribute to the pathogenesis of many different diseases including: psoriasis, multiple sclerosis, rheumatoid arthritis and cancer.

scholarly journals Possible Mechanisms of Fullerene C60Antioxidant Action

2013 ◽  
Vol 2013 ◽  
pp. 1-4 ◽  
Author(s):  
V. A. Chistyakov ◽  
Yu. O. Smirnova ◽  
E. V. Prazdnova ◽  
A. V. Soldatov
Keyword(s):  
Reactive Oxygen Species ◽  
Density Functional Theory ◽  
Antioxidant Activity ◽  
Mitochondrial Respiration ◽  
Density Functional ◽  
Positive Charge ◽  
Ros Production ◽  
Oxygen Species ◽  
Functional Theory ◽  
Mild Uncoupling

Novel mechanism of antioxidant activity of buckminsterfullerene C60based on protons absorbing and mild uncoupling of mitochondrial respiration and phosphorylation was postulated. In the present study we confirm this hypothesis using computer modeling based on Density Functional Theory. Fullerene's geroprotective activity is sufficiently higher than those of the most powerful reactive oxygen species scavengers. We propose here that C60has an ability to acquire positive charge by absorbing inside several protons and this complex could penetrate into mitochondria. Such a process allows for mild uncoupling of respiration and phosphorylation. This, in turn, leads to the decrease in ROS production.

Diffusion of Fluorine-Silicon Interstitial Complex in Crystalline Silicon

2005 ◽  
Vol 864 ◽  
Author(s):  
Scott A. Harrison ◽  
Thomas F. Edgar ◽  
Gyeong S. Hwang
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Charge State ◽  
First Principles ◽  
Density Functional ◽  
Positive Charge ◽  
Crystalline Silicon ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
And Diffusion

AbstractBased on first principles density functional theory calculations, we identify the structure and diffusion pathway for a fluorine-silicon interstitial complex (F-Sii). We find the F-Sii complex to be most stable in the singly positive charge state at all Fermi leVels. At mid-gap, the complex is found to have a binding energy of 1.08 eV relative to bond-centered F+ and (110)-split Sii. We find the F-Sii complex has an overall migration barrier of 0.76 eV, which suggests that this complex may play an important role in fluorine diffusion. Our results should lead to more accurate models that describe the behavior of fluorine co-implants crystalline silicon.

A density functional theory study of the hydration of calcium ions confined in the interlayer space of montmorillonites

2014 ◽  
Vol 13 (04) ◽  
pp. 1450028 ◽  
Author(s):  
Zhaoyang Lou ◽  
Houbin Liu ◽  
Yao Zhang ◽  
Yingfeng Meng ◽  
Qun Zeng ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Interlayer Space ◽  
Negative Charge ◽  
Internal Surface ◽  
Water Molecules ◽  
Surrounding Water ◽  
Functional Theory ◽  
Internal Surfaces

The structures of Ca2+hydrates in the interlayer space of montmorillonites (MMT) were studied by periodic density functional theory (DFT) calculations under the GGA/PBE approximation. Affected by the internal surfaces, which are rich of negative charge, the Ca2+hydration exhibits different behaviors from that in gas phase. The Ca2+is located at the six-oxygen-ring (SOR) on the internal surface in dry MMT, while the incoming water molecules bind with the Ca2+, the O atoms on surface, and/or with each other. The water molecules have a tendency of forming a hydrogen bond (HB) network that connects the upper and lower surfaces. Attracted by surrounding water molecules, the Ca2+gradually moves outward with increasing number of water molecules. Moreover, the hydration energy (EH) of Ca2+is determined not only by the interaction between Ca2+and H2O , but also by that among Ca2+, H2O and the surfaces. As a result, the EHhas only small changes for additional incoming water molecules, in contrast to the great and monotonic decrease in gas phase.

scholarly journals Crystal structure, Hirshfeld surface analysis and DFT studies of 6-bromo-3-(12-bromododecyl)-2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine

2020 ◽  
Vol 76 (5) ◽  
pp. 677-682 ◽  
Author(s):  
Zainab Jabri ◽  
Karim Jarmoni ◽  
Tuncer Hökelek ◽  
Joel T. Mague ◽  
Safia Sabir ◽  
...  
Keyword(s):  
Surface Analysis ◽  
Density Functional ◽  
Energy Gap ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Side Chain ◽  
Functional Theory ◽  
Compound C ◽  
Homo Lumo

The title compound, C24H30Br2N4O2, consists of a 2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine entity with a 12-bromododecyl substituent attached to the pyridine N atom. The middle eight-carbon portion of the side chain is planar to within 0.09 (1) Å and makes a dihedral angle of 21.9 (8)° with the mean plane of the imidazolopyridine moiety, giving the molecule a V-shape. In the crystal, the imidazolopyridine units are associated through slipped π–π stacking interactions together with weak C—HPyr...ONtr and C—HBrmdcyl...ONtr (Pyr = pyridine, Ntr = nitro and Brmdcyl = bromododecyl) hydrogen bonds. The 12-bromododecyl chains overlap with each other between the stacks. The terminal –CH2Br group of the side chain shows disorder over two resolved sites in a 0.902 (3):0.098 (3) ratio. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H...H (48.1%), H...Br/Br...H (15.0%) and H...O/O...H (12.8%) interactions. The optimized molecular structure, using density functional theory at the B3LYP/ 6–311 G(d,p) level, is compared with the experimentally determined structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.

Structural analysis of an iron-assisted carbon monolayer for delivery of 2-thiouracil

2021 ◽  
pp. 1-9
Author(s):  
Azar Asgari Pari ◽  
Mohammad Yousefi ◽  
Susan Samadi ◽  
Mohammad Reza Allahgholi Ghasri ◽  
Maryam Bikhof Torbati
Keyword(s):  
Drug Delivery ◽  
Molecular Orbital ◽  
Density Functional ◽  
Dominant Role ◽  
Structural Features ◽  
Coupling Constants ◽  
Functional Theory ◽  
Quadrupole Coupling ◽  
Atomic Descriptors

An idea of employing an iron-assisted carbon (FeC) monolayer for delivery of 2-thiouracil (2TU) was examined in this work by analyzing structural features for singular and bimolecular models. Density functional theory (DFT) calculations were performed for optimizing the structures and evaluating molecular and atomic descriptors for analyzing the models systems. Two bimolecular models were obtained assigning by S-FeC and O-FeC models, in which each of S and O atom of 2TU was relaxed towards the Fe region of FeC surface in the mentioned models, respectively. The results indicated that both models were achievable with slightly more favorability for formation of S-FeC model. The obtained molecular orbital properties revealed the dominant role of FeC monolayer for managing future interactions of attached 2TU, which is indeed a major role for employing nanomaterials for targeted drug delivery purposes. In addition to energies and molecular orbital features, atomic quadrupole coupling constants indicated the benefit of employing FeC monolayer for drug delivery of 2TU.

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