Collision dynamics of cytosine under proton irradiation

2021 ◽  
pp. 2150242
Author(s):  
Chaoyi Qian ◽  
Zhiping Wang ◽  
Xuefen Xu ◽  
Yanbiao Wang ◽  
Fengshou Zhang
Keyword(s):  
Kinetic Energy ◽  
Incident Energy ◽  
Density Functional ◽  
Collision Dynamics ◽  
Electronic Density ◽  
Functional Theory ◽  
Scattering Angle ◽  
Valence Electrons ◽  
Damage Process ◽  
Incident Kinetic Energy

In the framework of the time-dependent density-functional theory, applied to valence electrons, coupled non-adiabatically to molecular dynamics of ions, the collision dynamics of cytosine impacted by proton is studied. We especially focus on the effect of the collision orientations on the damage of cytosine by choosing two collision orientations taking the oxygen atom on the double bond CO as the collision site with the incident energy of proton ranging from 150 eV to 1000 eV. First, two collision dynamical processes are explored by analyzing the molecular ionization, the ionic position and the kinetic energy, the energy loss of proton and the electronic density evolution. The results show that the damage process of cytosine induced by proton impact is mainly the capture of electrons by proton, the departments of ions and groups as well as the opening of ring. It is found that the orientation has little effect on the loss of the kinetic energy of proton, which is about 21.5[Formula: see text] of the incident energy of proton. Although the scattering angle [Formula: see text] has a polynomial relationship with [Formula: see text] in both cases, it is greatly affected by the orientation. When [Formula: see text] eV, the scattering angle of proton colliding with O along the x-axis is greater than that of proton colliding with O along the y-axis. The orientation also has a great effect on the mass distribution of the fragments and the fragmentation route. When proton moves along the x-axis, the fragmentation route is that O leaves the cytosine and the rest keeps on vibration, while products are not only related to the incident kinetic energy, but also show diversity when proton moves along the y-axis.

scholarly journals Intercalated architecture of MA2Z4 family layered van der Waals materials with emerging topological, magnetic and superconducting properties

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lei Wang ◽  
Yongpeng Shi ◽  
Mingfeng Liu ◽  
Ao Zhang ◽  
Yi-Lun Hong ◽  
...  
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Layer Structure ◽  
Atomic Layer ◽  
Type I ◽  
Hybrid Functional ◽  
Functional Theory ◽  
Valence Electrons ◽  
Nonmagnetic Metals ◽  
Standard Density

AbstractThe search for new two-dimensional monolayers with diverse electronic properties has attracted growing interest in recent years. Here, we present an approach to construct MA2Z4 monolayers with a septuple-atomic-layer structure, that is, intercalating a MoS2-type monolayer MZ2 into an InSe-type monolayer A2Z2. We illustrate this unique strategy by means of first-principles calculations, which not only reproduce the structures of MoSi2N4 and MnBi2Te4 that were already experimentally synthesized, but also predict 72 compounds that are thermodynamically and dynamically stable. Such an intercalated architecture significantly reconstructs the band structures of the constituents MZ2 and A2Z2, leading to diverse electronic properties for MA2Z4, which can be classified according to the total number of valence electrons. The systems with 32 and 34 valence electrons are mostly semiconductors. Whereas, those with 33 valence electrons can be nonmagnetic metals or ferromagnetic semiconductors. In particular, we find that, among the predicted compounds, (Ca,Sr)Ga2Te4 are topologically nontrivial by both the standard density functional theory and hybrid functional calculations. While VSi2P4 is a ferromagnetic semiconductor and TaSi2N4 is a type-I Ising superconductor. Moreover, WSi2P4 is a direct gap semiconductor with peculiar spin-valley properties, which are robust against interlayer interactions. Our study thus provides an effective way of designing septuple-atomic-layer MA2Z4 with unusual electronic properties to draw immediate experimental interest.

Investigation, using density function theory, of coverage of the kaolinite (001) surface during hydrogen adsorption

Clay Minerals ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 393-402 ◽  
Author(s):  
Jian Zhao ◽  
Wei Gao ◽  
Zhi-Gang Tao ◽  
Hong-Yun Guo ◽  
Man-Chao He
Keyword(s):  
Density Functional ◽  
Hydrogen Adsorption ◽  
Function Theory ◽  
Lattice Relaxation ◽  
Electronic Density ◽  
Functional Theory ◽  
Adsorption Sites ◽  
Coverage Dependence ◽  
Hydrogen Molecules ◽  
Wide Range

ABSTRACTKaolinite can be used for many applications, including the underground storage of gases. Density functional theory was employed to investigate the adsorption of hydrogen molecules on the kaolinite (001) surface. The coverage dependence of the adsorption sites and energetics was studied systematically for a wide range of coverage, Θ (from 1/16 to 1 monolayer). The three-fold hollow site is the most stable, followed by the bridge, top-z and top sites. The adsorption energy of H2 decreased with increasing coverage, thus indicating the lower stability of surface adsorption due to the repulsion of neighbouring H2 molecules. The coverage has obvious effects on hydrogen adsorption. Other properties of the H2/kaolinite (001) system, including the lattice relaxation and changes of electronic density of states, were also studied and are discussed in detail.

scholarly journals Towards a density functional theory of molecular fragments. What is the shape of atoms in molecules?

2020 ◽  
Vol 44 (170) ◽  
pp. 269-279
Author(s):  
Victor H. Chávez ◽  
Adam Wasserman
Keyword(s):  
Density Functional Theory ◽  
Schrödinger Equation ◽  
Schrodinger Equation ◽  
Density Functional ◽  
Computational Cost ◽  
Atoms In Molecules ◽  
Electronic Density ◽  
Functional Theory ◽  
New Methods ◽  
The Cost

In some sense, quantum mechanics solves all the problems in chemistry: The only thing one has to do is solve the Schrödinger equation for the molecules of interest. Unfortunately, the computational cost of solving this equation grows exponentially with the number of electrons and for more than ~100 electrons, it is impossible to solve it with chemical accuracy (~ 2 kcal/mol). The Kohn-Sham (KS) equations of density functional theory (DFT) allow us to reformulate the Schrödinger equation using the electronic probability density as the central variable without having to calculate the Schrödinger wave functions. The cost of solving the Kohn-Sham equations grows only as N3, where N is the number of electrons, which has led to the immense popularity of DFT in chemistry. Despite this popularity, even the most sophisticated approximations in KS-DFT result in errors that limit the use of methods based exclusively on the electronic density. By using fragment densities (as opposed to total densities) as the main variables, we discuss here how new methods can be developed that scale linearly with N while providing an appealing answer to the subtitle of the article: What is the shape of atoms in molecules?

Structural, Elastic and Electronic Properties of γ˝ Phase Precipitate in Mg-Gd-Zn Alloy

2019 ◽  
Vol 41 (6) ◽  
pp. 932-932
Author(s):  
Mengmeng Wu Mengmeng Wu ◽  
Rongkai Pan Rongkai Pan ◽  
Jilei Liang Jilei Liang ◽  
Guohai Zhou Guohai Zhou ◽  
Li Ma and Chunyu Zhang Li Ma and Chunyu Zhang
Keyword(s):  
Density Functional ◽  
Elastic Anisotropy ◽  
Poisson Ratio ◽  
Covalent Bond ◽  
Generalized Gradient ◽  
Electronic Density ◽  
Functional Theory ◽  
Full Relaxation ◽  
Principle Density Functional Theory ◽  
Zn Alloy

The γ˝ phase (Mg4GdZn) precipitate in Mg-Gd-Zn alloy was calculated via first-principle density functional theory within the generalized gradient approximation. Through structure optimization of full relaxation, the lattice parameters were theoretically obtained, and the calculated Mg4GdZn is the most energetically stable in view of the formation energy. Independent elastic constants were also calculated, illustrating the calculated Mg4GdZn is mechanically stable. The shear modulus, polycrystalline bulk modulus, Poisson ratio, and Young’s modulus of Mg4GdZn were calculated via the Voigt-Reuss-Hill approximation. Elastic anisotropy and ductility were analyzed in details. Seen from their charge density distribution and electronic density of states, both metallic bond and covalent bond were found in Mg4GdZn.

Collision site effect on the radiation dynamics of cytosine induced by proton

2022 ◽  
Author(s):  
Xu Wang ◽  
Zhi-Ping Wang ◽  
Feng-Shou Zhang ◽  
Chao-Yi Qian
Keyword(s):  
Energy Loss ◽  
Incident Energy ◽  
Density Functional ◽  
Degrees Of Freedom ◽  
Site Effect ◽  
Low Energy ◽  
Microscopic Mechanism ◽  
Scattering Angle ◽  
Fragment Mass ◽  
Dynamics Simulations

Abstract By combing the time-dependent density functional calculations for electrons with molecular dynamics simulations for ions (TDDFT-MD) nonadiabatically in real time, we investigate the microscopic mechanism of collisions between cytosine and low-energy protons with incident energy ranging from 150 eV to 1000 eV. To explore the effects of the collision site and the proton incident energy on irradiation processes of cytosine, two collision sites are specially considered, which are N and O both acting as the proton receptors when forming hydrogen bonds with guanine. Not only the energy loss and the scattering angle of the projectile, but also the electronic and ionic degrees of freedom of the target are identified. It is found that the energy loss of proton increases linearly with the increase of the incident energy in both situations, which are 14.2% and 21.1% of the incident energy respectively. However, the scattering angles show different behaviors in these two situations when the incident kinetic energy increases. When proton collides with O, the scattering angle of proton is larger and the energy lost is more, while proton captures less electrons from O. The calculated fragment mass distribution shows the high counts of the fragment mass of 1, implying the production of H+ fragment ion from cytosine even for proton with the incident energy lower than keV. Furthermore, the calculated results show that N on cytosine is easier to be combined with low-energy protons to form NH bonds than O.

Density Functional Theory Study on the Absorption of CO2 by the Ionic Liquid of 1-butyl-3-methylimidazolium Acetate

2013 ◽  
Vol 807-809 ◽  
pp. 543-548 ◽  
Author(s):  
Yan Fei Chen ◽  
Yan Hong Cui ◽  
Dong Shun Deng ◽  
Ning Ai
Keyword(s):  
Density Functional Theory ◽  
Ionic Liquid ◽  
Ionic Liquids ◽  
Density Functional ◽  
Ion Pairs ◽  
Ion Pair ◽  
Frontier Molecular Orbitals ◽  
Density Functional Theory Study ◽  
Electronic Density ◽  
Functional Theory

The absorptions of CO2on the 1-butyl-3-methylimidazolium acetate ([Bmi [Ac]) with different substituents are calculated systematically at GGA/PW91 level. Three hydrogen bonds are formed between [A and cations of 1-n-[Bmi [A ([NBmi+) and 1-tert-[Bmi [A ([TBmi+). The interaction between CO2and the [NBmi [A by a C-O bond is much weaker than that with the [TBmi [A by forming a O...O...C...C four member-ring. The chemisorption of CO2on the ion pairs of [NBmi [A is much weaker than that on the [TBmi [A, resulted from the absorption energies analysis. The frontier molecular orbitals shows the electronic density overlap between absorbed CO2and the [A in CO2-[NBmi [A is much weaker than that in [TBmi [A. Therefore, the chemisorption of CO2on the ion pair of [NBmi [A is much weaker than that on the [TBmi [A. The ionic liquids based [NBmi+can be used repetitively, and the adsorbed CO2would be easier desorbed.

Theoretical study of NO3− interacting with carbon nanotube

Open Physics ◽  
2008 ◽  
Vol 6 (1) ◽  
Author(s):  
Silvete Guerini ◽  
David Azevedo ◽  
Maria Lima ◽  
Ivana Zanella ◽  
Josué Filho
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Quantum Mechanical ◽  
Mechanical Interaction ◽  
Electronic Density ◽  
Functional Theory ◽  
Consistent Field ◽  
The Density Functional Theory ◽  
Self Consistent Field ◽  
Field Form

AbstractThis paper deals with quantum mechanical interaction of no 3− with (5,5) and (8,0) swcnts. To perform this we have made an ab initio calculation based on the density functional theory. In these framework the electronic density plays a central role and it was obtained of a self-consistent field form. It was observed through binding energy that NO3− molecule interacts with each nanotube in a physisorption regime. We propose these swcnts as a potential filter device due to reasonable interaction with NO3− molecule. Besides this type of filter could be reusable, therefore after the filtering, the swcnts could be separated from NO3− molecule.

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