Corona-García, C. A. Martínez-Olguín, A. C. Sánchez-Ochoa, Francisco Cocoletzi, Gregorio H.
Published in
Journal of Molecular Modeling
Structural, electronic, binding energies and magnetic properties of aluminum-doped and single vacancy blue phosphorene interacting with pollutant molecules are investigated using the density functional theory (DFT) with periodic boundary conditions. Acetylene, ozone, sulfur trioxide, hydrogen selenide, and sulfur dichloride molecules are considered...
Shiri, Faezeh Kalantari Fotooh, Forough Mosslemin, Mohammad Hossein Mohebat, Razieh
Published in
Journal of Molecular Modeling
Adsorption of hydrogen sulfide (H2S) on the surface of catalytic systems containing (8, 0) single-walled carbon nanotube decorated with Ni and Pd transition metals was investigated using plane-wave density functional theory. SWCNT was modified by adding Ni and Pd atoms to both inside and outside the nanotube and replacing carbon atoms with these me...
de la Garza, Cesar Gabriel Vera Narváez, Wilmer Esteban Vallejo Rodríguez, Luis Daniel Solís Fomine, Serguei
Published in
Journal of Molecular Modeling
The structural variability offered by 2D materials is an essential feature in materials design. Despite its significance, obtaining assemblies with suitable stability remains a challenge. In this work, we theoretically explore novel silicon, phosphorus, and germanium, analogues of haeckelites at hybrid DFT level. Both 2D systems and nanoflakes (NF)...
Isogai, Makoto Seshimo, Masataka Houjou, Hirohiko
Published in
Journal of Molecular Modeling
We applied the method of coarse-graining the intermolecular vibrations to molecular heterodimers assembled by double hydrogen bonding. This method is based on principal component analysis, by which the original atomic displacement vectors are projected onto a lower-dimensional space spanned by a basis set of translations, librations, and intramolec...
Kuo, Jenn-Kun Tsai, Yu-Ting Huang, Pei-Hsing Luo, Jheng-Yu
Published in
Journal of Molecular Modeling
To effectively capture the acidic fluid molecules in industrial exhaust, this study employed molecular dynamics to simulate the dynamic adsorption behavior of a mixture of carbon monoxide (CO), carbon dioxide (CO2), hydrogen sulfide (H2S), and water (H2O) molecules in gold (Au) nanoslits. We systematically examined the self-diffusion coefficient (D...
Kara Zaitri, Lamia Mekelleche, Sidi Mohamed
Published in
Journal of Molecular Modeling
A theoretical analysis of a series of imidazole-based Y-shaped chromophores, D1–D8, is performed in order to investigate their non(linear) optical, fluorescence, and charge-transport properties. The calculations have been carried out employing DFT and TD-DFT methods at CAM-B3LYP and M06-2X levels of theory. FMO analysis reveals that in ground state...
Yuan, Yongna Mills, Matthew J. L. Zhang, Zhuangzhuang Ma, Yan Zhao, Chunyan Su, Wei
Published in
Journal of Molecular Modeling
Force fields are actively used to study RNA. Development of accurate force fields relies on a knowledge of how the variation of properties of molecules depends on their structure. Detailed scrutiny of RNA’s conformational preferences is needed to guide such development. Towards this end, minimum energy structures for each of a set of 16 small RNA-d...
Tian, Wenchao Liu, Xianxian Wang, Lulu Zheng, Bufeng Jiang, Kun Fu, Guoyong Feng, Wenyu
Published in
Journal of Molecular Modeling
Neuroblastoma (NB), as a metastatic form of solid tumor, has a high fatality rate found in early childhood. The two anaplastic lymphoma kinase (ALK) neoepitopes nonamer and decamer used in cancer immunotherapy against NB cancer can selectively bind to the human leukocyte antigen (HLA-B*15:01) groove with high affinities, whereas the native self-pep...
Wei, Lin Liu, GuiLi Qu, YanJin Zhang, GuoYing
Published in
Journal of Molecular Modeling
Based on first-principles calculations using density functional theory, this paper systematically studies the effects of uniaxial tension-compression deformation on the stability and electrical and thermal properties of monolayer graphene and AA stacked bilayer graphene. The study shows that the original symmetry of graphene is broken by the tensil...
Furer, Victor L. Potapova, Ludmila I. Chachkov, Denis V. Vatsouro, Ivan M. Kovalev, Vladimir V. Shokova, Elvira A. Kovalenko, Valery I.
Published in
Journal of Molecular Modeling
The IR spectra of p-(3-carboxy-1-adamantyl)thiacalix[4]arene (1-AdCOOHTC4A) have been studied. IR spectra of crystalline 1-AdCOOHTC4A obtained at room temperature or upon heating to 250 °C or its dilute solutions lack bands of free hydroxyl groups. The frequency of hydroxyl groups at 3377 cm−1 indicates the formation of an intramolecular H-bond alo...
