DFT Studies of Graphene-Functionalised Derivatives of Capecitabine

AbstractCancer is one of the major problems for so many people around the world; therefore, dedicating efforts to explore efficient therapeutic methodologies is very important for researchers of life sciences. In this case, nanostructures are expected to be carriers of medicinal compounds for targeted drug design and delivery purposes. Within this work, the graphene (Gr)-functionalised derivatives of capecitabine (CAP), as a representative anticancer, have been studied based on density functional theory calculations. Two different sizes of Gr molecular models have been used for the functionalisation of CAP counterparts, CAP-Gr3 and CAP-Gr5, to explore the effects of Gr-functionalisation on the original properties of CAP. All singular and functionalised molecular models have been optimised and the molecular and atomic scale properties have been evaluated for the optimised structures. Higher formation favourability has been obtained for CAP-Gr5 in comparison with CAP-Gr3 and better structural stability has been obtained in the water-solvated system than the isolated gas-phase system for all models. The CAP-Gr5 model could play a better role of electron transferring in comparison with the CAP-Gr3 model. As a concluding remark, the molecular properties of CAP changed from singular to functionalised models whereas the atomic properties remained almost unchanged, which is expected for a carrier not to use significant perturbations to the original properties of the carried counterpart.

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The Role of SiH3 Diffusion in Determining the Surface Smoothness of Plasma-Deposited Amorphous Si Thin Films: An Atomic-Scale Analysis

MRS Proceedings ◽

10.1557/proc-862-a3.2 ◽

2005 ◽

Vol 862 ◽

Author(s):

Mayur S. Valipa ◽

Tamas Bakos ◽

Eray S. Aydil ◽

Dimitrios Maroudas

Keyword(s):

Thin Films ◽

Density Functional ◽

Activation Barrier ◽

Density Functional Theory Calculations ◽

Atomic Scale ◽

Functional Theory ◽

Weak Adsorption ◽

Dynamics Simulations ◽

Hydrogenated Amorphous

AbstractDevice-quality hydrogenated amorphous silicon (a-Si:H) thin films grown under conditions where the SiH3 radical is the dominant deposition precursor are remarkably smooth, as the SiH3 radical is very mobile and fills surface valleys during its diffusion on the a-Si:H surface. In this paper, we analyze atomic-scale mechanisms of SiH3 diffusion on a-Si:H surfaces based on molecular-dynamics simulations of SiH3 radical impingement on surfaces of a-Si:H films. The computed average activation barrier for radical diffusion on a-Si:H is 0.16 eV. This low barrier is due to the weak adsorption of the radical onto the a-Si:H surface and its migration predominantly through overcoordination defects; this is consistent with our density functional theory calculations on crystalline Si surfaces. The diffusing SiH3 radical incorporates preferentially into valleys on the a-Si:H surface when it transfers an H atom and forms a Si-Si backbond, even in the absence of dangling bonds.

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Coadsorption of NRR and HER intermediates determines the performance of Ru-N4 towards electrocatalytic N2 reduction

10.26434/chemrxiv-2021-38gkc ◽

2021 ◽

Author(s):

Tongwei Wu ◽

Marko Melander ◽

Karoliina Honkala

Keyword(s):

Density Functional ◽

Density Functional Theory Calculations ◽

Reduction Reaction ◽

Atomic Scale ◽

Potential Density ◽

Functional Theory ◽

Proton Donors ◽

Constant Potential ◽

Insight Into

Efficiency of the electrochemical N2 reduction reaction (NRR) to ammonia is seriously limited by the competing hydrogen evolution reaction (HER) but our current atomic-scale insight on the factors controlling HER/NRR competition are unknown. Herein we unveil the elementary mechanism, thermodynamics, and kinetics determining the HER/NRR selectivity on the state-of-the-art NRR electrocatalyst, Ru-N4 using constant potential density functional theory calculations (DFT). The calculations show that NRR and HER intermediates coadsorb on the catalyst where HER is greatly suppressed by the NRR intermediates. The first reaction step leading to either *NNH or *H determines the selectivity towards NRR or HER. Our results also demonstrate that an explicitly potential-dependent treatment of reaction kinetics is needed to understand NRR selectivity. We provide crucial insight into the complex NRR/HER competition and the role of non-innocent adsorbates, show the necessity of constant potential DFT calculations, and suggest that interfacial proton donors will improve NRR selectivity.

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Role of Chemistry and Crystal Structure on the Electronic Defect States in Cs-Based Halide Perovskites

Materials ◽

10.3390/ma14041032 ◽

2021 ◽

Vol 14 (4) ◽

pp. 1032

Author(s):

Anirban Naskar ◽

Rabi Khanal ◽

Samrat Choudhury

Keyword(s):

Crystal Structure ◽

Density Functional ◽

Covalent Bond ◽

Density Functional Theory Calculations ◽

Antisite Defect ◽

Defect States ◽

Functional Theory ◽

Electronic Defect ◽

Constituent Elements

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

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Atomic-Scale Understanding of Structure and Properties of Complex Pyrophosphate Crystals by First-Principles Calculations

Applied Sciences ◽

10.3390/app9050840 ◽

2019 ◽

Vol 9 (5) ◽

pp. 840 ◽

Cited By ~ 1

Author(s):

Redouane Khaoulaf ◽

Puja Adhikari ◽

Mohamed Harcharras ◽

Khalid Brouzi ◽

Hamid Ez-Zahraouy ◽

...

Keyword(s):

First Principles ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Atomic Scale ◽

Functional Theory ◽

Local Structures ◽

Cationic Group ◽

Metallic Cations ◽

Bonding And Bridging ◽

Open Question

The electronic structure and mechanical and optical properties of five pyrophosphate crystals with very complex structures are studied by first principles density functional theory calculations. The results show the complex interplay of the minor differences in specific local structures and compositions can result in large differences in reactivity and interaction that are rare in other classes of inorganic crystals. These are discussed by dividing the pyrophosphate crystals into three structural units. H2P2O7 is the most important and dominating unit in pyrophosphates. The other two are the influential cationic group with metals and water molecules. The strongest P-O bond in P2O5 is the strongest bond for crystal cohesion, but O-H and N-H bonds also play an important part. Different type of bonding between O and H atoms such as O-H, hydrogen bonding, and bridging bonds are present. Metallic cations such as Mg, Zn, and Cu form octahedral bonding with O. The water molecule provides the unique H∙∙∙O bonds, and metallic elements can influence the structure and bonding to a certain extent. The two Cu-containing phosphates show the presence of narrow metallic bands near the valence band edge. All this complex bonding affects their physical properties, indicating that fundamental understanding remains an open question.

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Subsurface cation vacancy stabilization of the magnetite (001) surface

Science ◽

10.1126/science.1260556 ◽

2014 ◽

Vol 346 (6214) ◽

pp. 1215-1218 ◽

Cited By ~ 133

Author(s):

R. Bliem ◽

E. McDermott ◽

P. Ferstl ◽

M. Setvin ◽

O. Gamba ◽

...

Keyword(s):

Iron Oxides ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Atomic Scale ◽

Scanning Tunneling ◽

Tunneling Microscopy ◽

Material Interface ◽

Functional Theory ◽

Ordered Array ◽

Low Energy Electron

Iron oxides play an increasingly prominent role in heterogeneous catalysis, hydrogen production, spintronics, and drug delivery. The surface or material interface can be performance-limiting in these applications, so it is vital to determine accurate atomic-scale structures for iron oxides and understand why they form. Using a combination of quantitative low-energy electron diffraction, scanning tunneling microscopy, and density functional theory calculations, we show that an ordered array of subsurface iron vacancies and interstitials underlies the well-known (2×2)R45° reconstruction of Fe3O4(001). This hitherto unobserved stabilization mechanism occurs because the iron oxides prefer to redistribute cations in the lattice in response to oxidizing or reducing environments. Many other metal oxides also achieve stoichiometry variation in this way, so such surface structures are likely commonplace.

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Theoretical Insights into the Role of Water Molecule in The Aqueous/Cu(111) Interface during Corrosion Pathway

Journal of New Materials for Electrochemical Systems ◽

10.14447/jnmes.v19i4.275 ◽

2014 ◽

Vol 19 (4) ◽

pp. 235-240

Author(s):

Jun Hu ◽

Xiao-yong Fan ◽

Chao-Ming Wang

Keyword(s):

Water Molecule ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Adsorbed Water ◽

Dipole Interaction ◽

Hydrogen Atoms ◽

Functional Theory ◽

Adsorbed Water Molecule ◽

The One

The absorption and possible reaction paths during corrosion have been systematically identified at the molecular level by us-ing density functional theory calculations. The results show that the co-adsorbed water molecule has a two-fold impact on the corrosive kinetics process. The one is the solvation effect, where water molecule affects the various reactions through ion dipole interaction, without bond fracture and formation. Another is the H-transfer mediator, where the bond of co-adsorbed water molecule breaks and regenerates in order to transfer hydrogen atoms.

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Density functional theory calculations on the active site of biotin synthase: mechanism of S transfer from the Fe2S2 cluster and the role of 1st and 2nd sphere residues

JBIC Journal of Biological Inorganic Chemistry ◽

10.1007/s00775-015-1296-9 ◽

2015 ◽

Vol 20 (7) ◽

pp. 1147-1162 ◽

Cited By ~ 4

Author(s):

Atanu Rana ◽

Subal Dey ◽

Amita Agrawal ◽

Abhishek Dey

Keyword(s):

Density Functional Theory ◽

Active Site ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Biotin Synthase ◽

Functional Theory

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Polarity and structure of derivatives of bis(2-phenylethyl)selenophosphinic acid

Pure and Applied Chemistry ◽

10.1515/pac-2016-0802 ◽

2017 ◽

Vol 89 (3) ◽

pp. 393-401 ◽

Cited By ~ 2

Author(s):

Yana Vereshchagina ◽

Rezeda Khanafieva ◽

Denis Chachkov ◽

Eleonora Ishmaeva ◽

Svetlana Malysheva ◽

...

Keyword(s):

Density Functional Theory ◽

Conformational Analysis ◽

Density Functional ◽

Conformational Equilibrium ◽

Dipole Moments ◽

Density Functional Theory Calculations ◽

Functional Theory ◽

Derivatives Of

AbstractConformational analysis of derivatives of bis(2-phenylethyl)selenophosphinic acid was carried out by the method of dipole moments and density functional theory calculations. The conformations of the examined compounds fit into the overall conformational picture for the PIV compounds: these derivatives exist as conformational equilibrium of non-eclipsed gauche and trans forms with propeller arrangement of the substituents relative to the P=Se bond. We stipulate that the eclipsed cis orientation of substituent may be caused by the formation of H-contact.

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