Computational and Theoretical Chemistry最新文献

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Insights on formation of oxide layers, corrosion, and hydrogen embrittlement on the Ti2AlNb (1 1 0) surface: Density functional theory study

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-26 DOI: 10.1016/j.comptc.2024.115002

D.M. Tshwane , P.M. Maleka , R.S. Dima , L. Mogakane , T. Ngcobo , R.R. Maphanga

Ti₂AlNb alloys offer good mechanical qualities and promise for use in various applications, such as aero-engines and other industries. However, corrosion and hydrogen embrittlement remain important concerns and limitations for their use. In this work, first-principle density functional theory is used to investigate the adsorption of hydrogen, fluorine and oxygen on the surface of Ti₂AlNb (1 1 0). The effects of the considered adsorbates on the surface were compared by analysing the adsorption energy, charge density differences, density of states, and work function. The current findings revealed that the adsorption behaviour of all the adsorbates is exothermic and spontaneous due to the negative adsorption energy. More importantly, the effect of Van der Waals forces and dispersion correction was considered, it was found that for all adsorbates the dispersion correction approach exhibited the most stable adsorption energies (

E_{ads}^{DFT - D}

) than the standard density functional theory (

E_{ads}^{DFT}

). Thus, the standard DFT underestimates the adsorption energy. Furthermore, it was shown that the adsorption energy strength is dependent on the surface adsorption site, with the Ti-Nb and Al-Nb bridge sites being the most preferred sites for hydrogen, fluorine and oxygen adsorption. Subsequently, it was discovered that oxygen adsorption on the surface of Ti₂AlNb (1 1 0) was more thermodynamically stable than hydrogen and fluorine. This suggests that the Ti₂AlNb surface will likely suffer from oxidation rather than corrosion and hydrogen embrittlement. In addition, surface atoms showed electron-charge depletion, while adsorbates showed charge accumulation. The adsorption caused charge density redistribution and altered the surface work function.

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引用次数: 0

Geometrical features, stability and hydrogen positions in (Al2Cu)n clusters

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-26 DOI: 10.1016/j.comptc.2024.114999

Xi Wang , Yule Yan , Qiman Liu

The phase equilibria of the Al-Cu alloys have been well-established, with the Al₂Cu being a crucial component of the phase diagram. Constructing an atomic model with a 2:1 stoichiometric ratio of Al and Cu holds significance for further investigating the local structures of the alloy phases. Here, we employ the GA-DFT method to explore the structural potential energy surfaces of (Al₂Cu)_n clusters (n = 1–6). The results reveal that the (Al₂Cu)_n evolve from hollow cages to more densely packed configurations, with Al atoms relatively more concentrated and Cu atoms becoming more dispersed throughout the structures. The E_b and Δ₂E analyses show that the (Al₂Cu)₃ has a higher stability than that of its neighbors, and the AIMD simulations demonstrate that it can maintain the structural integrity at 700 K. The molecular orbitals reveal that 21 valence electrons of the (Al₂Cu)₃ fill superatomic orbits resulting in an electronic configuration of 1S²1P⁶1D¹⁰2S²1F¹, which is also confirmed by the density of states. The good stability of the (Al₂Cu)₃ allows the bonding of the H atom to it without causing significant deformation changes in the parent geometry, in which the H tends to preferentially locate at Al sites. The deformation of structures is particularly obvious when H is close to Cu atom.

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引用次数: 0

N-Boron-pyrrole: A negative charge stabilizing group

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-26 DOI: 10.1016/j.comptc.2024.115000

Younes Valadbeigi

We show that the N-boron-pyrrole (B-pyrrole) group stabilizes the negatively charged compounds, despite not being an electron withdrawing group (EWG). Density functional theory (DFT) calculations revealed that this distinctive property of the B-pyrrole group arises from enhanced π-electron delocalization within the pyrrole ring. The effect of B-pyrrole group on the Brønsted and Lewis acidity of various compound classes was examined and compared with common EWGs including F, Cl, Br, CN, NO₂. Substitution of pyrrole into the boracyclohexadiene derivatives enhances their acidity by about 1–6 kcal mol⁻¹ while the acidity enhancement due to pyrrole substitution into boric acid was about 17 kcal mol⁻¹. Interestingly, B(Pyrrole)₃ exhibited a fluoride affinity comparable to BF₃ (∼78 kcal mol⁻¹) and approximately 15 kcal mol⁻¹ higher than that of BH₃.

引用次数: 0

A quantum investigation of kinetic isotope effects in the Ne + HD+(v=0) → NeH+/NeD+ + D/H reaction Ne + HD+(v=0) → NeH+/NeD+ + D/H 反应中动力学同位素效应的量子研究

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-23 DOI: 10.1016/j.comptc.2024.114994

Hui Wu , Xiaohu He , Zhixin Duan

The exact quantum scattering calculations for the Ne + HD

^{+}

(v = 0, j = 0) reaction on its electronic ground state have been performed using the time-dependent wave packet method at the state-to-state level. The reaction mechanisms and intramolecular isotope effects have been investigated and analyzed in terms of integral reaction cross section, product internal state distributions and differential cross sections in the 0.4–1.2 eV collision energy interval. Results from the present calculations show that the products NeH

^{+}

and NeD

^{+}

are associated to different values of the total angular momentum, J. Competing reaction mechanisms that correlate with low and high J values show different preferences for products.

利用时变波包法在态对态水平上对 Ne + HD+（v = 0，j = 0）反应的电子基态进行了精确的量子散射计算。在 0.4-1.2 eV 的碰撞能量区间内，从积分反应截面、产物内部状态分布和微分截面的角度研究和分析了反应机理和分子内同位素效应。本计算的结果表明，产物 NeH+ 和 NeD+ 与总角动量 J 的不同值有关。

引用次数: 0

Molecular adsorption of chloromethane and vinyl chloride on square lattice net phosphorene – A first-principles study

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-22 DOI: 10.1016/j.comptc.2024.114996

V. Nagarajan, R. Bhuvaneswari, R. Chandiramouli

The advancement of two-dimensional (2D) materials after the discovery of graphene leads to the path of various 2D materials. One such 2D material is square lattice (sql) net phosphorene. Initially, the structural and dynamic stability of sql phosphorene is confirmed with regard to the formation energy and phonon-band-spectrum. The electronic properties of sql phosphorene are explored using band structure and projected density of states spectrum. Besides, the calculated band gap value of sql phosphorene is 3.174 eV which shows the semiconducting nature of the material. Owing to the structural firmness and semiconducting nature of sql phosphorene material, it is used as a sensing element for chloromethane and vinyl chloride molecules. Evidently, the adsorption of chloromethane and vinyl chloride on sql phosphorene leads to modulating the energy band gap, electron difference density, and charge transfer, which infers changes in the electronic properties of sql phosphorene. The adsorption energy range is recorded to be −0.152 eV to −0.608 eV which confirms that the chloromethane and vinyl chloride are physisorbed on sql phosphorene. The findings ensure that sql phosphorene is a proper sensing element for the detection of chloromethane and vinyl chloride molecules.

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引用次数: 0

Molecular dynamics insight of interaction between Artemisinin and its derivatives and the cancer cell membrane

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-21 DOI: 10.1016/j.comptc.2024.114997

Samaneh Boroomand , Delara Mohammad-Aghaie , Fatemeh Mohammadpour

In the present study, a molecular dynamics simulation approach has been utilized to investigate the effectiveness of four molecules, including Artemisinin, a natural product, and its derivatives Dihydroartemisinin, Artesunate, and Artemisone, on a membrane of a cancerous cell. Performed simulations predicted that Dihydroartemisinin and Artemisone form stronger hydrogen bonds with the cancer membrane, exhibit higher mobility, and have a longer lifetime at the water-membrane interface. Artemisone molecules could penetrate the hydrophobic part of the lipid’s tail, leading to higher fluidity of the cancer membrane. These two compounds exerted the greatest effect on the properties and characteristics of the membrane model while showing stronger anti-cancer effects than the other two compounds. The simulation outcomes and predictions were found to agree with the results of experimental studies. It is noticeable that Dihydroartemisinin and Artemisone enter the cancer cell membrane from their functional group side, while Artemisinin and Artesunate enter from their peroxide ring side.

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引用次数: 0

Computational investigation of magnetic field effect on thermal function of diatomic molecules with anharmonic oscillator potential 利用非谐波振荡器势计算研究磁场对双原子分子热函数的影响

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-19 DOI: 10.1016/j.comptc.2024.114991

Ahmad Ghanbari

In the present study, I have investigated the magnetic field contributions on thermal properties of diatomic molecules such as H₂, HCl and CO with isotropic oscillator plus inverse quadratic potential. To this end, I have solved the Schrödinger equation with the potential model in the presence of magnetic fields and have obtained bound states of the system via the Laplace transform approach. Applying the determined energy eigenvalues, I have computed the partition function and thermal function such as specific heat in constant pressure, Gibbs free energy and enthalpy in the presence of external magnetic field using Poisson summation formula. I have compared our results with experimental data and there is a good agreement between them. I have computed the average absolute deviations of specific heat in constant pressure, Gibbs free energy and enthalpy for diatomic molecules in the presence and absence of magnetic fields. All calculated average deviations are under 3 % that show our accuracy of computations. My results show that external magnetic fields have a significant influence on thermodynamic properties of diatomic molecules.

在本研究中，我研究了磁场对具有各向同性振荡器加反二次电动势的 H2、HCl 和 CO 等双原子分子热特性的影响。为此，我利用磁场存在时的势模型求解了薛定谔方程，并通过拉普拉斯变换方法获得了系统的束缚态。应用确定的能量特征值，我利用泊松求和公式计算了分割函数和热函数，如恒压下的比热、吉布斯自由能和存在外磁场时的焓。我将我们的结果与实验数据进行了比较，两者之间有很好的一致性。我计算了有磁场和无磁场条件下双原子分子的恒压比热、吉布斯自由能和焓的平均绝对偏差。所有计算出的平均偏差都小于 3%，这表明我们的计算是准确的。我的研究结果表明，外部磁场对双原子分子的热力学性质有重大影响。

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引用次数: 0

Dopamine interaction with DNA/RNA aptamers: Molecular dynamics simulation 多巴胺与 DNA/RNA 合体的相互作用：分子动力学模拟

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-19 DOI: 10.1016/j.comptc.2024.114990

Majid Sharifian, Tahereh Heidari, Mohammad Razmkhah, Fatemeh Moosavi

One method for detecting dopamine involves the use of RNA and DNA aptamers. Aptamers are single-stranded sequences of DNA or RNA that bind with high affinity to specific target molecules. Various aptamers have been developed to measure dopamine, making it crucial to identify which one exhibits the strongest interaction with it. This study, for the first time, examines the interaction between dopamine and aptamers using molecular dynamics simulations. The findings reveal that all three aptamers can interact with and detect dopamine. By calculating the binding Gibbs energy (ΔG_bind) between the aptamers and dopamine, it was determined that the DNA aptamer with 44 nucleotide residues is the most selective for dopamine. Additional analyses of the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radial distribution function (RDF), and radius of gyration (R_g) which assess structural stability and fluctuations further support that this aptamer has the most effective interaction with dopamine.

检测多巴胺的一种方法是使用 RNA 和 DNA 配合物。适配体是 DNA 或 RNA 的单链序列，能与特定目标分子产生高亲和力。目前已开发出多种用于测量多巴胺的适配体，因此确定哪种适配体与多巴胺的相互作用最强至关重要。这项研究首次利用分子动力学模拟研究了多巴胺与适配体之间的相互作用。研究结果表明，所有三种适配体都能与多巴胺相互作用并检测多巴胺。通过计算适配体与多巴胺之间的结合吉布斯能（ΔGbind），确定具有 44 个核苷酸残基的 DNA 适配体对多巴胺的选择性最强。评估结构稳定性和波动性的均方根偏差（RMSD）、均方根波动（RMSF）、径向分布函数（RDF）和回旋半径（Rg）等附加分析进一步证明了这种适配体与多巴胺的相互作用最为有效。

引用次数: 0

DFT insights into multifaceted properties of GaCaX3 (X = Cl, Br, I) inorganic cubic halide perovskites for advanced optoelectronic applications 用于先进光电应用的 GaCaX3（X = Cl、Br、I）无机立方卤化物包晶石多方面特性的 DFT 见解

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-19 DOI: 10.1016/j.comptc.2024.114993

Muhammad Riaz , Syed Mansoor Ali , N. Bano , Syed Danish Ali , Muhammad Asif Shakoori

Halide perovskites, known for their outstanding properties and flexible chemistry, gained considerable attention in diverse fields. This study explores the structural, optoelectronic, thermodynamic, and mechanical characteristics of the inorganic cubic halide perovskites, GaCaX₃ (X = Cl, Br and I) using DFT within the CASTEP framework. Electronic analysis determined band gaps of GaCaCl₃ (4.67 eV), GaCaBr₃ (3.89 eV), and GaCaI₃ (2.97 eV) respectively. Bond population analysis indicated that GaCaI₃ provides accurate electronic bond description with minimal charge loss (0.15 %). Optically, GaCaI₃ shows significant absorption, while GaCaCl₃ indicate strong plasmonic behavior, high refractive index and reflectivity. Mechanical stability confirmed through Born-stability condition through elastic constants (C₁₁, C₁₂, and C₄₄). Poisson’s ratio (n), Pugh’s ratio (B/G), and anisotropic factor further emphasize the ductility and anisotropic behavior for all materials. Also, bulk modulus (B), shear modulus (G), and Young’s modulus (E), follow the as GaCaCl₃ > GaCaBr₃ > GaCaI_3, respectively. From thermodynamic characteristics, GaCaCl₃ exhibits the maximum enthalpy, free energy, entropy, heat capacity, and Debye temperature indicating superior thermal stability. Confidently, these outstanding properties of GaCaX₃ (X = Cl, Br and I) halide perovskites hold significant potential for advanced optoelectronic devices.

卤化物类包晶石以其卓越的性能和灵活的化学性质而闻名，在多个领域受到广泛关注。本研究在 CASTEP 框架内采用 DFT 方法探讨了无机立方卤化物包晶 GaCaX3（X = Cl、Br 和 I）的结构、光电、热力学和机械特性。电子分析分别确定了 GaCaCl3（4.67 eV）、GaCaBr3（3.89 eV）和 GaCaI3（2.97 eV）的带隙。键群分析表明，GaCaI3 以最小的电荷损失（0.15%）提供了准确的电子键描述。从光学角度来看，GaCaI3 具有显著的吸收性，而 GaCaCl3 则具有很强的等离子特性、高折射率和反射率。通过弹性常数（C11、C12 和 C44）证实了博恩稳定条件下的机械稳定性。泊松比（n）、普氏比（B/G）和各向异性因子进一步强调了所有材料的延展性和各向异性。此外，体积模量（B）、剪切模量（G）和杨氏模量（E）分别与 GaCaCl3 > GaCaBr3 > GaCaI3 相同。从热力学特性来看，GaCaCl3 表现出最大的焓、自由能、熵、热容量和德拜温度，表明其具有优异的热稳定性。可以肯定的是，GaCaX3（X = Cl、Br 和 I）卤化物包晶的这些优异特性为先进光电器件的发展提供了巨大潜力。

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引用次数: 0

Investigating optical, electronic, and thermoelectric properties of X2ScIO6 (X = K, Rb, and Cs) double perovskite semiconductors for green energy applications 研究用于绿色能源应用的 X2ScIO6（X = K、Rb 和 Cs）双包晶半导体的光学、电子和热电特性

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL

Computational and Theoretical Chemistry

Pub Date : 2024-11-19 DOI: 10.1016/j.comptc.2024.114992

Saleh Hayat , Mansoor Ahmad Khan , Malak Azmat Ali , Afzal Khan , Razan A. Alshgari , Saikh Mohammad , Samah Al-Qaisi

We present our findings on the structural, optical, electronic, and thermoelectric characteristics of X₂ScIO₆ (X = K, Rb, and Cs) double perovskites using density functional theory (DFT) and post-DFT calculations. The calculated tolerance factor values exhibit the structural stability of these double perovskites, whereas negative values of the formation energy and Gibbs free energy verify their thermodynamic stability. Energy band structure calculations reveal the semiconducting nature of these perovskites with band gaps of 1.37, 1.03, and 0.55 eV for K₂ScIO₆, Rb₂ScIO_6, and Cs₂ScIO₆ respectively. These double perovskites could achieve higher optical absorption in the ultraviolet region beyond 5 eV. The Seebeck coefficient’s positive value indicates these compounds’ p-type nature. Their figure of merit values are greater than the other conventional double perovskites and therefore could be efficiently utilized in thermoelectric applications at elevated temperatures.

我们利用密度泛函理论（DFT）和后 DFT 计算，展示了 X2ScIO6（X = K、Rb 和 Cs）双包晶的结构、光学、电子和热电特性。计算得出的公差因子值显示了这些双包晶石的结构稳定性，而形成能和吉布斯自由能的负值则验证了它们的热力学稳定性。能带结构计算揭示了这些过氧化物的半导体性质，K2ScIO6、Rb2ScIO6 和 Cs2ScIO6 的能带隙分别为 1.37、1.03 和 0.55 eV。这些双包晶石可在 5 eV 以上的紫外区实现更高的光吸收。塞贝克系数的正值表明了这些化合物的 p 型性质。它们的优点值高于其他传统的双包晶石，因此可以在高温下有效地应用于热电领域。

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