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.

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 DFT and Plasmon-Coupling Models for Optical and Electronic Scattering Properties

2014 ◽  
Vol 70 (a1) ◽  
pp. C381-C381
Author(s):  
Jay Bourke ◽  
Christopher Chantler
Keyword(s):  
Density Functional Theory ◽  
Energy Loss ◽  
Electron Scattering ◽  
Density Functional ◽  
Low Energy ◽  
Scattering Data ◽  
Plasmon Coupling ◽  
Inelastic Electron ◽  
Functional Theory ◽  
X Ray

We present calculations and applications of optical energy loss data for use in studies of inelastic electron scattering in condensed matter systems. A new model of plasmon coupling and excitation broadening is implemented along with high-precision density functional theory to evaluate fundamental material properties critical to many areas of spectroscopic analysis. Recent developments in x-ray and electron spectroscopies have demonstrated critical dependence on low-energy electron scattering and optical loss properties, and significant discrepancies between theoretical and experimental scattering values [1]. Resolution of these discrepancies is required to validate experimental studies of material structures, and is particularly relevant to the characterization of small molecules and organometallic systems for which electron scattering data is often sparse or highly uncertain [2]. We have devised a new theoretical approach linking the optical dielectric function and energy loss spectrum of a material with its electron scattering properties and characteristic plasmon excitations. For the first time we present a model inclusive of plasmon coupling, allowing us to move beyond the longstanding statistical approximation and explicitly demonstrate the effects of band structure on the detailed behavior of bulk electron excitations in a solid or small molecule. This is a novel generalization of the optical response of the material, which we obtain using density functional theory [3]. We find that our developments improve agreement with experimental electron scattering results in the low-energy region (<~100 eV) where plasmon excitations are dominant; a region that is particularly crucial for structural investigations using x-ray absorption fine structure and electron diffraction. This work is further relevant to several commissions of the IUCr including the commissions on XAFS, International Tables, and Electron Crystallography.

Scattering-angle dependence of signal/background ratio of inner-shell electron excitation loss in EELS

1983 ◽  
Vol 41 ◽  
pp. 390-391
Author(s):  
T. Oikawa ◽  
M. Inoue ◽  
T. Honda ◽  
Y. Kokubo
Keyword(s):  
Energy Loss ◽  
Electron Excitation ◽  
Heavy Elements ◽  
Background Intensity ◽  
Light Elements ◽  
Energy Analyzer ◽  
High Background ◽  
Scattering Angle ◽  
Angle Dependence ◽  
Shell Electron

EELS allows us to make analysis of light elements such as hydrogen to heavy elements of microareas on the specimen. In energy loss spectra, however, elemental signals ride on a high background; therefore, the signal/background (S/B) ratio is very low in EELS. A technique which collects the center beam axial-symmetrically in the scattering angle is generally used to obtain high total intensity. However, the technique collects high background intensity together with elemental signals; therefore, the technique does not improve the S/B ratio. This report presents the experimental results of the S/B ratio measured as a function of the scattering angle and shows the possibility of the S/B ratio being improved in the high scattering angle range.Energy loss spectra have been measured using a JEM-200CX TEM with an energy analyzer ASEA3 at 200 kV.Fig.l shows a typical K-shell electron excitation edge riding on background in an energy loss spectrum.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

A New Phase of the Na+ Ion Conductor Na3PS4

2019 ◽  
Author(s):  
Theodosios Famprikis ◽  
James Dawson ◽  
François Fauth ◽  
Emmanuelle Suard ◽  
Benoit Fleutot ◽  
...  
Keyword(s):  
Solid Electrolytes ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Orthorhombic Crystal ◽  
Orthorhombic Crystal Structure ◽  
Ion Conductor ◽  
Solid State Batteries ◽  
Density Analysis ◽  
Two Phases ◽  
Dynamics Simulations

<div> <p>Solid electrolytes are crucial for next‑generation solid‑state batteries and Na<sub>3</sub>PS<sub>4</sub> is one of the most promising Na<sup>+</sup> conductors for such applications. At present, two phases of Na<sub>3</sub>PS<sub>4</sub> have been identified and it had been thought to melt above 500 °C. In contrast, we show that it remains solid above this temperature and transforms into a third polymorph, γ, exhibiting superionic behavior. We propose an orthorhombic crystal structure for γ‑Na<sub>3</sub>PS<sub>4</sub> based on scattering density analysis of diffraction data and density functional theory calculations. We show that the Na<sup>+</sup> superionic behavior is associated with rotational motion of the thiophosphate polyanions pointing to a rotor phase, based on <i>ab initio</i> molecular dynamics simulations and supported by high‑temperature synchrotron and neutron diffraction, thermal analysis and impedance spectroscopy. These findings are of importance for the development of new polyanion‑based solid electrolytes.</p> </div>

Computational Study on the Kinetics and Mechanisms of Unimolecular Reactions of (Z)-(Z)-N-(λ5-phosphanylidene) Formohydrazonic Formic Anhydride: Intramolecular aza-Wittig Reaction in Competition with Mumm Rearrangement

2020 ◽  
Vol 17 (11) ◽  
pp. 884-889
Author(s):  
Somayeh Mirdoraghi ◽  
Hamed Douroudgari ◽  
Farideh Piri ◽  
Morteza Vahedpour
Keyword(s):  
Rate Constants ◽  
Density Functional ◽  
Wittig Reaction ◽  
Computational Study ◽  
Single Step ◽  
Low Energy ◽  
Coupled Cluster ◽  
Unimolecular Reaction ◽  
Single Step Reaction ◽  
Good Agreement

For (Z)-(Z)-N-(λ5-phosphanylidene) formohydrazonic formic anhydride, Aza-Wittig reaction and Mumm rearrangement are studied using both density functional and coupled cluster theories. For this purpose, two different products starting from one substrate are considered that are competing with each other. The obtained products, P1 and P2, are thermodynamically favorable. The product of the aza-Wittig reaction, P1, is more stable than the product of Mumm rearrangement (P2). For the mentioned products, just one reliable pathway is separately proposed based on unimolecular reaction. Therefore, the rate constants based on RRKM theory in 300-600 K temperature range are calculated. Results show that the P1 generation pathway is a suitable path due to low energy barriers than the path P2. The first path has three steps with three transition states, TS1, TS2, and TS3. The P2 production path is a single-step reaction. In CCSD level, the computed barrier energies are 14.55, 2.196, and 10.67 kcal/mol for Aza-Wittig reaction and 42.41 kcal/mol for Mumm rearrangement in comparison with the corresponding complexes or reactants. For final products, the results of the computational study are in a good agreement with experimental predictions.

High-Performance and Low-Energy Loss Organic Solar Cells with Non-fused Ring Acceptor by Alkyl Chain Engineering

2021 ◽  
pp. 129768
Author(s):  
Dou Luo ◽  
Xue Lai ◽  
Nan Zheng ◽  
Chenghao Duan ◽  
Zhaojin Wang ◽  
...  
Keyword(s):  
Solar Cells ◽  
Energy Loss ◽  
Organic Solar Cells ◽  
High Performance ◽  
Alkyl Chain ◽  
Low Energy ◽  
Fused Ring

scholarly journals Complex magnetism of the two-dimensional antiferromagnetic Ge2F: from a Néel spin-texture to a potential antiferromagnetic skyrmion

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 8654-8663
Author(s):  
Fatima Zahra Ramadan ◽  
Flaviano José dos Santos ◽  
Lalla Btissam Drissi ◽  
Samir Lounis
Keyword(s):  
Density Functional Theory ◽  
Magnetic Properties ◽  
Density Functional ◽  
Low Energy ◽  
Two Dimensional ◽  
Functional Theory ◽  
2D Material ◽  
Energy Models ◽  
Spin Texture

Based on density functional theory combined with low-energy models, we explore the magnetic properties of a hybrid atomic-thick two-dimensional (2D) material made of germanene doped with fluorine atoms in a half-fluorinated configuration (Ge2F).

Realizing Stable High‐Performance and Low‐Energy‐Loss Ternary Photovoltaics through Judicious Selection of the Third Component

Solar RRL ◽  
2021 ◽  
pp. 2100450
Author(s):  
Bing-Huang Jiang ◽  
Yi-Peng Wang ◽  
Yu-Wei Su ◽  
Jia-Fu Chang ◽  
Chu-Chen Chueh ◽  
...  
Keyword(s):  
Energy Loss ◽  
High Performance ◽  
Low Energy ◽  
The Third ◽  
Selection Of

Graphene adlayer growth between nonepitaxial graphene and Ni(111) substrate: a promising theoretical scheme

2020 ◽  
Author(s):  
Lijuan Meng ◽  
Jinlian Lu ◽  
Yujie Bai ◽  
Lili Liu ◽  
Tang Jingyi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Chemical Vapor Deposition ◽  
Molecular Dynamics Simulations ◽  
Vapor Deposition ◽  
Density Functional ◽  
Chemical Vapor ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Dynamics Simulations

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...

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