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Modeling the alkylation of amines with alkyl bromides: explaining the low selectivity due to multiple alkylation J. Mol. Model. (IF 2.2) Pub Date : 2024-03-16 Luis F. Resende, Josefredo R. Pliego
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Depicted simulation model for removal of second-generation antipsychotic drugs adsorbed on Zn-MOF: adsorption locator assessment J. Mol. Model. (IF 2.2) Pub Date : 2024-03-16 Ali Abdullah Issa, Maryam Dhary Kamel, Doaa S. El-Sayed
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Mechanism of formation of p-benzylenephenol peroxide radical (p-PhC(O2•)HPhOH) J. Mol. Model. (IF 2.2) Pub Date : 2024-03-16 Gregory A. Poskrebyshev
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Theoretical exploration of the stabilities and detonation parameters of nitro-substituted 1H-benzotriazole J. Mol. Model. (IF 2.2) Pub Date : 2024-03-14 Lulin Li, Jiawei Zhang, Butong Li, Guobin Yi, Taoyu Wang, Yanhong Peng
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Probing the inhibition of MAO-B by chalcones: an integrated approach combining molecular docking, ADME analysis, MD simulation, and MM-PBSA calculations J. Mol. Model. (IF 2.2) Pub Date : 2024-03-13
Abstract Context Monoamine oxidase B (MAO-B), an enzyme of significant relevance in the realm of neurodegenerative disorders, has garnered considerable attention as a potential target for therapeutic intervention. Natural compounds known as chalcones have shown potential as MAO-B inhibitors. In this particular study, we employed a multimodal computational method to evaluate the inhibitory effects of
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Exploring Jahn-Teller distortions: a local vibrational mode perspective J. Mol. Model. (IF 2.2) Pub Date : 2024-03-13 Mateus Quintano, Renaldo T. Moura, Elfi Kraka
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Counter-ion adsorption and electrostatic potential in sodium and choline dodecyl sulfate micelles — a molecular dynamics simulation study J. Mol. Model. (IF 2.2) Pub Date : 2024-03-11 Rafaela Eliasquevici, Kalil Bernardino
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A theoretical study on 1H-indole-2,3-dione complexes with lithium, sodium, and potassium cations J. Mol. Model. (IF 2.2) Pub Date : 2024-03-11
Abstract Context A comparative study of the change in different properties of electronic and structural of the free 1H-indole-2,3-dione molecule and its complexes has been obtained. HOMA analysis was performed to investigate the effects of lithium sodium and potassium cations on the aromaticity of lithium sodium and potassium complexes of 1H-indole-2,3-dione. Methods Several 1H-indole-2,3-dione complexes
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The structural, stability, electronic, optical and thermodynamic properties of MoX2 (X= S, Se, and Te) under hydrostatic pressures: a plasmon approach and first-principle study J. Mol. Model. (IF 2.2) Pub Date : 2024-03-11 R. Santosh, S. Chandra, V. Kumar, B. M. M. Tripathi, Pankaj Kumar
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Bistriazolotriazole-tetramine: commendable energetic moiety and cation J. Mol. Model. (IF 2.2) Pub Date : 2024-03-09
Abstract Context Various 7H,7′H-[6,6′-bi[1,2,4]triazolo[4,3-b][1,2,4]triazole]-3,3′,7,7′-tetramine (A) based nitrogen-rich energetic salts were designed and their properties explored. All energetic salts possess relatively high nitrogen content (> 48%), positive heats of formation (> 429 kJ/mol) and stability owing to a significant contribution from fused backbone. The cationic component shows a very
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Toxicity of persistent organic pollutants: a theoretical study J. Mol. Model. (IF 2.2) Pub Date : 2024-03-07 Ana Martínez
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Chemical reactivity of graphene doped with 3d transition metals: nothing compares to a single vacancy J. Mol. Model. (IF 2.2) Pub Date : 2024-03-06
Abstract Context Finding catalysts that do not rely on the use of expensive metals is one of the requirements to achieve sustainable production. The reactivity of graphene doped with 3d transition metals was studied. All dopants enhanced the reactivity of graphene and performed better than Stone–Wales defects and divacancies, but were inferior to monovacancies. For hydrogenation of doped-monovacancies
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Strain-induced modification in thermal properties of monolayer 1 T-ZrS2 and ZrS2/ZrSe2 heterojunction J. Mol. Model. (IF 2.2) Pub Date : 2024-03-06
Abstract Context This paper systematically analyzes the phonon dispersion curves of single-layer ZrS2, ZrSe2, and ZrS2/ZrSe2 heterostructures under different strains. The phonon spectra and thermal parameters of the three structures were obtained based on the density functional perturbation theory method. The upper limits of strain that different monolayers and heterojunctions can withstand were studied
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Bending deformation modulation of the optoelectronic properties of molybdenum ditelluride doped with nonmetallic atoms X (X = B, C, N, O): a first-principles study J. Mol. Model. (IF 2.2) Pub Date : 2024-03-05 Ying Dai, Guili Liu, Jianlin He, Zhonghua Yang, Guoying Zhang
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Computational insight into the crystal structures of cubane and azacubanes J. Mol. Model. (IF 2.2) Pub Date : 2024-03-04
Abstract Context Using quantum chemistry and atom–atom potential methods, the molecular and crystal structures of cubane 1 and all types of unsubstituted azacubanes 2–22 were calculated. Alternative possible polymorphs of cubane 1 have been proposed. The thermochemical properties of azacubanes in the gas and solid phases were assessed. Thermodynamic aspects of stability are considered, and a significant
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Electronic structure and optical properties of In- and Vacancy-doped 6H-SiC: a first-principles study J. Mol. Model. (IF 2.2) Pub Date : 2024-03-02
Abstract Purposes The paper aims to investigative the cacuses and impacts of In- and Vacancy-doped to 6H-SiC, expecting that improving optical properties of materials. Design-Using the first-principles calculations, we discuss the electronic structure and optical properties of different doped 6H-SiC systems. Findings The results show that In-doped 6H-SiC becomes a direct bandgap p-type semiconductor
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Effect of tensile deformation on the optoelectronic properties of black phosphine-doped lithium atoms J. Mol. Model. (IF 2.2) Pub Date : 2024-03-01 Zenan Huang, Ying Wang, Congrui Wang, Guili Liu, Guoying Zhang, Jindong Niu
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Study on the electronics and structural properties of transition metal–doped La2Mo2O9 J. Mol. Model. (IF 2.2) Pub Date : 2024-03-01 Priyanshi Gaur, Brijesh Kumar Pandey, Mayank Shriwastav, Abhishek Kumar Gupta, Priyanshu Srivastava
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A B3LYP-D3 computational study of electronic, structural and torsional dynamic properties of mono-substituted naphthalenes: the effect of the nature and position of substituent J. Mol. Model. (IF 2.2) Pub Date : 2024-02-29 Amina Benalia, Abdelali Boukaoud, Rachid Amrani, Adel Krid
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A molecular dynamics simulation of the effect of the toluene catalytic ratios and initial temperature on the catalytic combustion of air/methane inside a microchannel J. Mol. Model. (IF 2.2) Pub Date : 2024-02-29 Seyed Masoud Badakhshian, Babak Mehmandoust, Davood Toghraie, Sobhan Emami, Mohammad Hashemian
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Computational-based investigation of antioxidative potential polyphenolic compounds of Salvia officinalis L.: combined DFT and molecular docking approaches J. Mol. Model. (IF 2.2) Pub Date : 2024-02-28 Ridha Bendaas, Yahia Bekkar, Lyamine Messaadia, Lotfi Bourougaa, Abdelatif Messaoudi, Samir Kiamouche, Benamira Messaoud
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Temperature-dependent failure of atomically thin MoTe2 J. Mol. Model. (IF 2.2) Pub Date : 2024-02-28 A. S. M. Redwan Haider, Ahmad Fatehi Ali Mohammed Hezam, Md Akibul Islam, Yeasir Arafat, Mohammad Tanvirul Ferdaous, Sayedus Salehin, Md. Rezwanul Karim
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Cobalt group transition metals (TM: Co, Rh, Ir) coordination of S-doped porphyrins (TM_S@PPR) as sensors for molecular SO2 gas adsorption: a DFT and QTAIM study J. Mol. Model. (IF 2.2) Pub Date : 2024-02-27 Monsurat Alarape Raimi, Abdullah Ola Rajee, Terkumbur E. Gber, Temple Okah Arikpo, Anthony M. S. Pembere, Hitler Louis
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The regulation of high-energy insensitive compound 2,6-diamino-3,5-dinitropyrazine-1-oxide by external electric field J. Mol. Model. (IF 2.2) Pub Date : 2024-02-26 Jun Chen, Jiani Xu, Tingting Xiao, Zikai Gao, Mengjie Bo, Zhihui Gu, Peng Ma, Congming Ma
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A physical organic strategy to predict and interpret stabilities of chemical bonds in energetic compounds for the discovery of thermal-resistant properties J. Mol. Model. (IF 2.2) Pub Date : 2024-02-26 Haitao Liu, Peng Chen, Xin Huang, Xianfeng Wei
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Anisotropies in electronic densities and electrostatic potentials of Halonium Ions: focus on Chlorine, Bromine and Iodine J. Mol. Model. (IF 2.2) Pub Date : 2024-02-23 Ponnadurai Ramasami, Jane S. Murray
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Theoretical investigation of hydrogen sulfide capture from methane binary mixture using s-heptazine-based metal–organic framework J. Mol. Model. (IF 2.2) Pub Date : 2024-02-22 Mohamed Essalhi, Najmeddine Ferhi, Adela Abidi
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Structural, electronic and thermoelectric properties of monolayer TiSe2 J. Mol. Model. (IF 2.2) Pub Date : 2024-02-22 Uttam Paliwal, Pradeep Tanwar, K. B. Joshi
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In silico elucidation for the identification of potential phytochemical against ACE-II inhibitors J. Mol. Model. (IF 2.2) Pub Date : 2024-02-22 Ekambaram Gayathiri, Palanisamy Prakash, Kuppusamy Selvam, Thangaraj Pratheep, Somdatta Y. Chaudhari, Subramanian Deepika Priyadharshini
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First-principles study of the effects of doping B, N, and O on the photoelectric properties of Cr adsorbed GaS J. Mol. Model. (IF 2.2) Pub Date : 2024-02-20
Abstract Context To lessen the impact of the dangerous metal Cr, this paper applies the first principles to investigate the adsorption behavior and photoelectric properties of GaS on Cr. The effects of doped GaS on Cr adsorption behavior are investigated with four GaS systems, which are pure, boron (B)-doped, nitrogen (N)-doped, and oxygen (O)-doped, in order to maximize the characteristics of GaS
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Lead-free alternative cation (Ethylammonium) in organometallic perovskites for thermoelectric applications J. Mol. Model. (IF 2.2) Pub Date : 2024-02-20
Abstract Context Hybrid halide perovskites are gaining prominence as a promising option in the advancement of photovoltaic devices. Ethylammonium-based hybrid halide perovskites have demonstrated impressive characteristics, such as a reduced band gap, enhanced stability, and non-toxic properties. In this study, we have explored the structural, electronic, optical, and thermoelectric characteristics
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Star-shaped small donor molecules based on benzotriindole for efficient organic solar cells: a DFT study J. Mol. Model. (IF 2.2) Pub Date : 2024-02-20 Faiza Shafiq, Adeel Mubarik, Mahira Rafiq, Saad M. Alshehri
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Non-relativistic energy equations for diatomic molecules constrained in a deformed hyperbolic potential function J. Mol. Model. (IF 2.2) Pub Date : 2024-02-19
Abstract Context In this paper, the approximate analytical energy equations for the deformed hyperbolic potential have been obtained for arbitrary parameters of the potential. The potential function was transformed to a molecular potential by subjecting it to the Varshni conditions which allows for the determination of the energy levels of diatomic molecules. The molecular vibrational energy spectra
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COSMO-RS-based assessment of thermodynamic tools in predicting the polar and non-polar solvents efficiency in vegetable oil extraction J. Mol. Model. (IF 2.2) Pub Date : 2024-02-17 Mohammed Abobakr Al-Maari, Hanee F. Hizaddin, Muhammad Zulhaziman Mat Salleh, Adeeb Hayyan
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Enhancement of gas adsorption on transition metal ion–modified graphene using DFT calculations J. Mol. Model. (IF 2.2) Pub Date : 2024-02-17 Jie Li, Xiaozhen Fan, Junjie Chen, Guosheng Shi, Xing Liu
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Computational studies of the influence of auxiliary acceptors in the D-A'-π-A structure of organic dyes on the photovoltaic performance of dye solar cells J. Mol. Model. (IF 2.2) Pub Date : 2024-02-13 Omar Britel, Hanane Etabti, Asmae Fitri, Adil Touimi Benjelloun, Mohammed Benzakour, Mohammed Mcharfi
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Exploring the binding mechanism of a small molecular Hsp70-Bim PPI inhibitor through molecular dynamic simulation J. Mol. Model. (IF 2.2) Pub Date : 2024-02-13
Abstract Context The interface of Hsp70-Bim protein–protein interaction (PPI) has been identified as a specific target for Chronic Myeloid Leukemia (CML) therapy and the specific inhibitors were developed to exhibit in vivo anti-leukemia activities. Herein, we explored the binding mechanism of a Hsp70-Bim inhibitor, 6-(cyclohexylthio)-3-((2-morpholinoethyl) amino)-1-oxo-1H-phenalene-2-carbonitrile
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Nano-friction behavior and deformation study of hydroxyapatite in ultra-precision polishing process J. Mol. Model. (IF 2.2) Pub Date : 2024-02-13 Weixi Lu, Jiachun Li
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Phillyrin: an adipose triglyceride lipase inhibitor supported by molecular docking, dynamics simulation, and pharmacological validation J. Mol. Model. (IF 2.2) Pub Date : 2024-02-13 Chenyu Zhou, Lanmeng Yan, Jing Xu, Hamizah Shahirah Hamezah, Tongsheng Wang, Fangping Du, Xiaohui Tong, Rongchun Han
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Formic acid stability in different solvents by DFT calculations J. Mol. Model. (IF 2.2) Pub Date : 2024-02-12 Raphael da Silva Alvim, Antonio Esio Bresciani, Rita Maria Brito Alves
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Total absorption spectrum of benzene aggregates obtained from two different approaches J. Mol. Model. (IF 2.2) Pub Date : 2024-02-12 Ricardo Montserrat, Ricardo R. Oliveira, Alexandre B. Rocha
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Employing neural density functionals to generate potential energy surfaces J. Mol. Model. (IF 2.2) Pub Date : 2024-02-10 B Jijila, V. Nirmala, P. Selvarengan, D. Kavitha, V Arun Muthuraj, A. Rajagopal
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Influence of chloride salt erosion on the adhesion of asphalt-aggregate interfaces considering mineral anisotropy: insights from molecular dynamics J. Mol. Model. (IF 2.2) Pub Date : 2024-02-08 Enyong Sun, Yanqing Zhao, Guozhong Wang
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N2 reduction to NH3 on surfaces of Co-Al18P18, Ni-Al21N21, Fe-B24N24, Mn-B27P27, Ti-C60 and Cu-Si72 catalysts J. Mol. Model. (IF 2.2) Pub Date : 2024-02-07 Chou-Yi Hsu, Mohammed Ahmed Mustafa, Anupam Yadav, Khalid Mujasam Batoo, Mandeep Kaur, Sajjad Hussain, Salim B. Alsaadi, Ahmed Read Al-Tameemi, Zahraa F. Hassan, Eftikhaar Hasan Kadhum, Laith H. Alzubaidi, Liguan Nai
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Disaggregation of amyloid-beta fibrils via natural metabolites using long timescale replica exchange molecular dynamics simulation studies J. Mol. Model. (IF 2.2) Pub Date : 2024-02-07
Abstract Context Amyloid fibrils are self-assembled fibrous protein aggregates that are associated with several presently incurable diseases such as Alzheimer’s. disease that is characterized by the accumulation of amyloid fibrils in the brain, which leads to the formation of plaques and the death of brain cells. Disaggregation of amyloid fibrils is considered a promising approach to cure Alzheimer’s
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First principle study of the effect of doping on the optoelectronic properties of Cr-adsorbed MoS2 J. Mol. Model. (IF 2.2) Pub Date : 2024-02-07
Abstract Context This study explores, for the first time, using first principles, the impact of substitutional doping with boron (B), carbon (C), and nitrogen (N) on the adsorption of chromium (Cr) on monolayer MoS2. The effects of doping on the Cr adsorption behavior of MoS2 were investigated using four MoS2 systems, namely, pure, boron (B)-doped, carbon (C)-doped, and nitrogen (N)-doped, in order
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Evaluation of the inhibitory potential of bioactive compounds against SARS-CoV-2 by in silico approach J. Mol. Model. (IF 2.2) Pub Date : 2024-02-07 J Mariya Sneha Rani, P Akkarshana, V Neelaveni, Shalini Mohan, P. D. Rekha, Rajas M. Rao, Lakshmanan Muthulakshmi
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Structural, elastic, electronic, and optical properties of lead-free halide double perovskites Cs2BꞌBꞌꞌBr6 (BꞌBꞌꞌ: BeMg, CdBe, CdGe, GeMg, GeZn, MgZn): Ab initio calculations J. Mol. Model. (IF 2.2) Pub Date : 2024-02-06 Messaoud Caid, Djamel Rached, Habib Rached, Youcef Rached
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A computational study of H-bonded networks in cyclic water clusters, (H2O)n (n = 3–12) J. Mol. Model. (IF 2.2) Pub Date : 2024-02-03 Constantinos D. Zeinalipour-Yazdi
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Possible NLO response and electrical/charge transfer capabilities of natural anthraquinones as p-type organic semiconductors: a DFT approach J. Mol. Model. (IF 2.2) Pub Date : 2024-02-01 P. U. Neenu Krishna, K. Muraleedharan
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Enhanced hydrogen storage of alkaline earth metal-decorated Bn (n = 3–14) nanoclusters: a DFT study J. Mol. Model. (IF 2.2) Pub Date : 2024-01-31 Parimala devi Duraisamy, Prince Makarios Paul S, Praveena Gopalan, Abiram Angamuthu
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First-principle study on the photoelectric properties of monolayer h-BN under different strain types J. Mol. Model. (IF 2.2) Pub Date : 2024-01-31 ShaoRong Li, Hao Wang, ChengYue Wang, PengXiang Zhao, ChengFu Zhang, DongWei Qiao
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How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease? J. Mol. Model. (IF 2.2) Pub Date : 2024-01-30 Débora Feliciano Savino, João Vitor Silva, Soraya da Silva Santos, Felipe Rebello Lourenço, Jeanine Giarolla
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Energy spectrum of selected diatomic molecules (H2, CO, I2, NO) by the resolution of Schrodinger equation for combined potentials via NUFA method J. Mol. Model. (IF 2.2) Pub Date : 2024-01-29 Khalid Reggab
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Solvation energies of the ferrous ion in water and in ammonia at various temperatures J. Mol. Model. (IF 2.2) Pub Date : 2024-01-29 Ousman Boukar, Jean Jules Fifen, Jeanet Conradie, Marrigje Marianne Conradie
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Structure-based drug design and molecular dynamics studies of an allosteric modulator targeting the protein–protein interaction site of PDK1 J. Mol. Model. (IF 2.2) Pub Date : 2024-01-26
Abstract Context Protein–protein interaction interfaces play a major role in cell signaling pathways. There is always a great interest in developing protein–protein interaction (PPI) inhibitors of kinases, as they are challenging due to their hydrophobicity, flat surface, specificity, potency, etc. 3 Phosphoinositide-dependent kinase-1 (PDK1), which is involved in the PI3K/PDK1/AKT pathway, is a cancer
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Theoretical study on formation mechanism of acetic acid associating configurations and their distributions under saturated conditions J. Mol. Model. (IF 2.2) Pub Date : 2024-01-25 Xueshuang Zhao, Yunzhou Lin, Linbing Huang, Lihang Chen
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Molecular dynamics study of the mechanical properties of hydrated calcium silicate enhanced by functionalized carbon nanotubes J. Mol. Model. (IF 2.2) Pub Date : 2024-01-25 Lin Wei, GuiLi Liu, ShaoRan Qian, JingWei Zhao, Gan Jiao, GuoYing Zhang
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Investigation of dislocation and twinning behavior in HMX under high-velocity impact employing molecular dynamics simulations J. Mol. Model. (IF 2.2) Pub Date : 2024-01-25 Can-shu Yang, Shu-hai Zhang
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Quantum chemical “Aufbau” principles: how to estimate the shape of highly flexible (bio-)polymers? A recursively extendable “chemion picture” of Euler-Hückel-type J. Mol. Model. (IF 2.2) Pub Date : 2024-01-24
Abstract An outline is given of how to split the n-dimensional space of torsion angles occurring in flexible (bio-)polymers (like alkanes, nucleic acids, or proteins, for instance) into n one-dimensional potential curves. Forthcoming applications will focus on the “protein folding problem,” beginning with polyglycine. Context In accordance with Euler’s topology rules, molecules are considered to be