Journal of Molecular Modeling最新文献

{"title":"Tutton salt (NH4)2Zn(SO4)2(H2O)6: thermostructural, spectroscopic, Hirshfeld surface, and DFT investigations","authors":"João G. de Oliveira Neto,&nbsp;Jailton R. Viana,&nbsp;Kamila R. Abreu,&nbsp;Luiz F. L. da Silva,&nbsp;Mateus R. Lage,&nbsp;Stanislav R. Stoyanov,&nbsp;Francisco F. de Sousa,&nbsp;Rossano Lang,&nbsp;Adenilson O. dos Santos","doi":"10.1007/s00894-024-06089-7","DOIUrl":"10.1007/s00894-024-06089-7","url":null,"abstract":"<div><h3>Context</h3><p>Ammonium Tutton salts have been widely studied in recent years due to their thermostructural properties, which make them promising compounds for application in thermochemical energy storage devices. In this work, a detailed experimental study of the Tutton salt with the formula (NH₄)₂Zn(SO₄)₂(H₂O)₆ is carried out. Its structural, vibrational, and thermal properties are analyzed and discussed. Powder X-ray diffraction (PXRD) studies confirm that the compound crystallizes in a structure of a Tutton salt, with monoclinic symmetry and <i>P</i>2₁/<i>a</i> space group. The Hirshfeld surface analysis results indicate that the main contacts stabilizing the material crystal lattice are H···O/O···H, H···H, and O···O. In addition, a typical behavior of an insulating material is confirmed based on the electronic bandgap calculated from the band structure and experimental absorption coefficient. The Raman and infrared spectra calculated using DFT are in a good agreement with the respective experimental spectroscopic results. Thermal analysis in the range from 300 to 773 K reveals one exothermic and several endothermic events that are investigated using PXRD measurements as a function of temperature. With increasing temperature, two new structural phases are identified, one of which is resolved using the Le Bail method. Our findings suggest that the salt (NH₄)₂Zn(SO₄)₂(H₂O)₆ is a promising thermochemical material suitable for the development of heat storage systems, due to its low dehydration temperature (≈ 330 K), high enthalpy of dehydration (122.43 kJ/mol of H₂O), and hydration after 24 h.</p><h3>Methods</h3><p>Computational studies using Hirshfeld surfaces and void analysis are conducted to identify and quantify the intermolecular contacts occurring in the crystal structure. Furthermore, geometry optimization calculations are performed based on density functional theory (DFT) using the PBE functional and norm-conserving pseudopotentials implemented in the Cambridge Serial Total Energy Package (CASTEP). The primitive unit cell optimization was conducted using the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm. The electronic properties of band structure and density of states, and vibrational modes of the optimized crystal lattice are calculated and analyzed.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06089-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational study of the supramolecular complexation of azocompounds with cucurbit[7]uril: effects on the production and release of free radicals","authors":"Angie C. Forero-Girón,&nbsp;Soledad Gutiérrez-Oliva,&nbsp;Camilo López-Alarcón,&nbsp;Barbara Herrera,&nbsp;Margarita E. Aliaga","doi":"10.1007/s00894-024-06132-7","DOIUrl":"10.1007/s00894-024-06132-7","url":null,"abstract":"<div><h3>Context</h3><p>An inclusion complex between 2,2′-azobis(2-methylpropionamidine) dihydrochloride (AAPH), a widely employed azocompound, and cucurbit[7]util (CB[7]), has shown an increased yield of radicals derived from the homolytic cleavage of the azo bond. Aimed to get insights about the formation of complexes and their effect on the yield of radicals production, complexes of CB[7] with seven azocompounds were studied by computational methods. Molecular electrostatic surfaces and structural analysis showed that the inclusion of symmetrical azocompounds inside of CB[7] depends mainly on the charge density and position of the functional groups at the main chain of the azoderivative. Analysis of non-covalent interactions and thermodynamic outcomes revealed that positively charged azocompounds with amidinium or imidazolium groups presented strong favorable interactions (multiple hydrogen bonds) with the oxygens of CB[7] portals. Additionally, carbon-centered radicals generated from the complexes (azocompounds@CB[7]) were corroborated using the electron localization function (ELF). Results evidenced that the strength of the interactions and the level of inclusion (partial or complete) between the azocompound and CB[7] determined the final orientation of the radicals (located out- or inside of the CB[7] cavity). Obtained results could be employed to design new supramolecular systems based on the properties of azocomplound@CB[7] complexes for new scientific or industrial applications.</p><h3>Methods</h3><p>First-principles calculations at B3LYP-D3BJ/6-311g(d,p) level theory in the gas phase and in solvent (PCM, water) were performed in Gaussian 16 software package. The dispersion energy correction was included through the Grimme’s dispersion with Becke-Johnson damping D3(BJ). Thermodynamical data and the minimum character of all structures were obtained from vibrational frequency calculations. NBO, Multiwfn, Chemcraft, and NCIPLOT software were used to perform population analysis, analyze outcomes, visualize data, and display non-covalent interactions respectively.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cu(β-diketonato)2 bathochromic shifts from the ultraviolet towards the visible region","authors":"Marrigje M. Conradie","doi":"10.1007/s00894-024-06138-1","DOIUrl":"10.1007/s00894-024-06138-1","url":null,"abstract":"<div><h3>Context</h3><p>The DFT-calculated ultraviolet/visible properties of 11 different Cu(β-diketonato)₂ complexes are presented. The selected β-diketonato ligands on the Cu complex contain none, one or two aromatic rings. The experimentally measured absorbance maxima range of the ultraviolet/visible is observed at 295–390 nm, and the calculated range is 302–425 nm, for the 11 complexes in this study. More aromatic rings on the ligand lead to bathochromic shifts of the experimentally measured absorbance maxima from the ultraviolet towards the visible region. Absorbance maxima of the Cu(β-diketonato)₂ complexes with no aromatic rings on the ligand are found to be predominantly ligand-to-metal charge transfer excitations, whereas introducing one or two aromatic rings shifts the excitations to predominantly ligand-to-ligand charge transfer.</p><h3>Methods</h3><p>DFT calculations were conducted on the neutral molecules with multiplicity 2, using the PBEh1PBE functional and the aug-cc-pVDZ basis set as implemented in the Gaussian 16 package. The selected solvent was acetonitrile, the solvent in which most of the experimental UV/Vis are reported. The molecules were all optimized in the solvent phase, using the IEFPCM. The initial coordinates for the compounds were generated using Chemcraft.</p><h3>Highlights</h3><p>TDDFT of 11 different Cu(β-diketonato)₂ complexes follow the experimental trend.</p><p>Aromatic rings on the ligand lead to Bathochromic shifts of UV/Visible spectra.</p><p>No aromatic rings on the ligand lead to ligand-to-metal charge transfer excitations.</p><p>Aromatic rings on the ligand lead to ligand-to-ligand charge transfer excitations.</p><h3>Graphical abstract</h3><p>Bathochromic shifts in eco-friendly Cu(β-diketonato)₂.</p>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06138-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparisons between full molecular dynamics simulation and Zhang’s multiscale scheme for nanochannel flows","authors":"Chuntao Jiang,&nbsp;Yongbin Zhang","doi":"10.1007/s00894-024-06115-8","DOIUrl":"10.1007/s00894-024-06115-8","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;In a very small surface separation, the fluid flow is actually multiscale consisting of both the molecular scale non-continuum adsorbed layer flow and the intermediate macroscopic continuum fluid flow. Classical simulation of this flow often takes over large computational source and is not affordable owing to using molecular dynamics simulation (MDS) to model the adsorbed layer flow, if the flow field size is on the engineering size scale such as of 0.01–10 mm or even bigger like occurring in micro or macro hydrodynamic bearings. The present paper uses full MDS to validate Zhang’s multiscale flow model, which yields the closed-form explicit flow equations respectively for the adsorbed layer flow and the intermediate continuum fluid flow. Here, full MDS was carried out for the pressure-driven flow of methane in the nano slit pore made of silicon respectively with the channel heights 5.79 nm, 11.57 nm, and 17.36 nm. According to the number density distribution, the flow areas were respectively discriminated as the adsorbed layer zone and the intermediate fluid zone. The values of the characteristic parameters for Zhang’s multiscale scheme were extracted from full MDS and input to Zhang’s multiscale flow equations respectively for calculating the flow velocity profile and the volume flow rates of the adsorbed layers and the intermediate fluid. It was found that for these three channel heights, the flow velocity profiles calculated from Zhang’s model approximate those calculated from full MDS, while the total flow rates through the channel calculated from Zhang’s model are close to those calculated from full MDS. The accuracy of Zhang’s multiscale flow model is improved with the increase of the channel height.&lt;/p&gt;&lt;h3&gt;Method&lt;/h3&gt;&lt;p&gt;The recent modification of the optimized potential for liquid simulation (MOPLS) model was used to calculate the interaction force between two methane molecules. In order to calculate the interaction force between the wall atoms and the methane molecules accurately, our previous non-equilibrium multiscale MDS was used. The interaction forces between the methane molecule and the wall atom were obtained from the coupled potential function by the L-B mixing rule when the fluid molecules arrived at near wall. The methane molecule diameter was obtained from the radial distribution function by using equilibrium MDS under the same initial conditions. The local viscosities across the adsorbed layer were obtained from the local velocity profile by using the Poiseuille flow method. The motion equation of the methane molecule was solved by the leapfrog method. The temperature of the simulation system was checked by Bhadauria’s method, i.e., the system temperature was rectified by the velocities in the &lt;i&gt;y&lt;/i&gt;- and &lt;i&gt;z&lt;/i&gt;-directions. The flow velocity distributions across the channel height and the volume flow rates through the channel were also calculated from Zhang’s closed-form explicit flow equations resp","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A statistical physics–based physicochemical study of l-phenylalanine adsorption on activated carbon","authors":"Salah Knani,&nbsp;Sarra Wjihi,&nbsp;Mohamed Bouzid,&nbsp;Luis Felipe Oliveira Silva,&nbsp;Marcos Leandro Silva Oliveira,&nbsp;Safwat A. Mahmoud,&nbsp;Abdulaziz Alenazi,&nbsp;Ridha Selmi,&nbsp;Abdulmajeed Alshammari","doi":"10.1007/s00894-024-06142-5","DOIUrl":"10.1007/s00894-024-06142-5","url":null,"abstract":"<div><h3>Context</h3><p>In this comparative study of the adsorption of <span>l</span>-phenylalanine (<span>l</span>-Phe) on two modified low-activated carbons (ACK and ACZ) at four temperatures (293–313 K), steric and energetic characteristics of adsorption were investigated. An advanced statistical physics multilayer model involving single-layer and double-layer adsorption scenarios was developed to interpret the <span>l</span>-Phe adsorption phenomenon. Modeling results indicate that two and three <span>l</span>-Phe layers were arranged depending on the tested adsorption systems. The estimated number of <span>l</span>-Phe molecules per leading adsorption site varied from 1.71 to 2.09 and from 1.76 to 1.86 for systems <span>l</span>-Phe-ACK and <span>l</span>-Phe-ACZ, respectively. The results show that a multimolecular adsorption mechanism might connect this amino acid molecule on ACZ and ACK surfaces in a non-parallel location. These parameters changed as follows, according to the adsorbed quantity at saturation analysis: <i>Q</i>_asat (<span>l</span>-Phe-ACK) ˃ <i>Q</i>_asat (<span>l</span>-Phe-ACZ). This indicates that ACK material was more efficient and valuable for <span>l</span>-Phe adsorption than ACZ. It was also shown that the adsorption capacity decreases as the temperature increases, proving the exothermicity of the adsorption process. This analytical substantiation is confirmed by calculating the binding energies, suggesting the occurrence of physical bonds between <span>l</span>-Phe amino acid molecules and ACK/ACZ binding sites and among <span>l</span>-Phe–<span>l</span>-Phe molecules. Pore size distribution was interpreted and calculated by applying the Kelvin theory to data from single adsorption isotherms. All used temperatures depicted a distribution of pores below 2 nm. The docking analysis involving <span>l</span>-Phe and the ACZ and ACK adsorbents reveal a significant resemblance in how receptors detect ligands. Consequently, the findings from the docking process confirm that the calculated binding affinities fall within the spectrum of adsorption energy.</p><h3>Methods</h3><p>This study analyzed the adsorption capacity of the <span>l</span>-Phe through a model proposed by statistical physics formalism. Molecular docking was used to determine the various types of interactions between the two activated carbons. Two aspects, including orientation of <span>l</span>-Phe on the site, number of molecules per site <i>n</i>, interaction energy, density of receptor site, and adsorption capacity, were discussed to elucidate the influence of activation on the two adsorbents.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the link between the reaction force constant and conceptual DFT","authors":"Carlos Cárdenas,&nbsp;Paul W. Ayers,&nbsp;Debajit Chakraborty,&nbsp;Tatiana Gómez,&nbsp;Andrea Echeverri,&nbsp;Francisco Munoz,&nbsp;Patricio Fuentealba","doi":"10.1007/s00894-024-06137-2","DOIUrl":"10.1007/s00894-024-06137-2","url":null,"abstract":"<div><h3>Context</h3><p>The reaction force constant (<span>(kappa )</span>), introduced by Professor Alejandro Toro-Labbé, plays a pivotal role in characterizing the reaction pathway by assessing the curvature of the potential energy profile along the intrinsic reaction coordinate. This study establishes a novel link between <span>(kappa )</span> and the reactivity descriptors of conceptual density functional theory (c-DFT). Specifically, we derive expressions that relate the reaction force constant to nuclear softness and variations in chemical potential. Our findings indicate that regions of the reaction pathway where <span>(kappa )</span> is negative match with significant electronic structure rearrangements, while positive <span>(kappa )</span> regions match mostly with geometric rearrangements. This correlation between <span>(kappa )</span> and c-DFT reactivity descriptors enhances our understanding of the underlying forces driving chemical reactions and offers new perspectives for analyzing reaction mechanisms.</p><h3>Methods</h3><p>The internal reaction path for the proton transfer in SNOH, chemical potential, and nuclear softness were computed using DFT with B3LYP exchange-correlation functional and 6-311++G(d,2p) basis set.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrogen bonding in 2,2,2-trifluoroethanol","authors":"Soon Ng,&nbsp;Yaoming Xie,&nbsp;Henry F. Schaefer III","doi":"10.1007/s00894-024-06135-4","DOIUrl":"10.1007/s00894-024-06135-4","url":null,"abstract":"<div><h3>Context</h3><p>2,2,2-Trifluoroethanol (TFE) is known as a membrane mimetic solvent. The IR spectrum, ¹H NMR spectrum, ¹³C NMR spin‒lattice relaxation times (T₁), and nuclear Overhauser effect (NOE) data are consistent with extensive hydrogen bonding in TFE, but do not lead to structural features of the hydrogen bonding. Hence, DFT computations were carried out. The results predict the existence of a set of H-bonded dimers and trimers. The bond lengths and dihedral angles in these complexes are obtained, together with their dissociation energies. Computations were also performed for the geometry of the two conformers of the isolated monomer. The structure of one of the dimers consists of a 7-member cyclic fragment with a free CF₃CH₂ side chain. One set of the trimer structures involves the OH of a third monomer H-bonding to one of the F atoms in the CF₃ group of the side chain of this dimer, thereby creating three trimer isomers. A fourth trimer cluster is formed from three monomers in which three OH∙∙∙O bonds create a cyclic fragment with three CF₃CH₂ side chains. The high dissociation energy (with respect to three monomers) indicates the high stability of the trimer complexes. The structural features of the trimer complexes resemble the structure of a conventional liquid crystal molecule and are postulated to resemble the latter in properties and function in solution, but at <i>a much shorter timescale</i> because of the noncovalent bonding. This hydrogen bonding phenomenon of TFE may be related to its function as a membrane memetic solvent.</p><h3>Methods</h3><p>Initially, IR and NMR spectroscopic methods were used. Standard procedures were followed. For the computations, a hybrid DFT method with empirical dispersion, ωB97X-D, was used. The basis set, 6-311++G**, is of triple-ζ quality, in which polarization functions and diffuse functions were added for all atoms.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydroxyl radical-induced C1′-H abstraction reaction of different artificial nucleotides","authors":"N. R. Jena,&nbsp;P. K. Shukla","doi":"10.1007/s00894-024-06126-5","DOIUrl":"10.1007/s00894-024-06126-5","url":null,"abstract":"<div><h3>Context</h3><p>Recently, a few antiviral drugs viz Molnupiravir (EIDD-1931), Favipiravir, Ribavirin, Sofosbuvir, Galidesivir, and Remdesivir are shown to be beneficial against COVID-19 disease. These drugs bind to the viral RNA single strand to inhibit the virus genome replication. Similarly, recently, some artificial nucleotides, such as P, J, B, X, Z, V, S, and K were proposed to behave as potent antiviral candidates. However, their activity in the presence of the most reactive hydroxyl (OH) radical is not yet known. Here, the possibility of RNA strand break due to the OH radical-induced C1′-hydrogen (H) abstraction reaction of the above molecules (except Remdesivir) is studied in detail by considering their nucleotide conformation. The results are compared with those of the natural RNA nucleotides (G, C, A, and U). Due to low Gibbs barrier-free energy and high exothermicity, all these nucleotides (except Remdesivir) are prone to OH radical-induced C1′-H abstraction reaction. As Remdesivir contains a C1′-CN bond, the OH radical substitution reactions at the CN and C1′ sites would likely liberate the catalytically important CN group, thereby downgrading its activity.</p><h3>Method</h3><p>Initially, the B3LYP-D3 dispersion-corrected density functional theory method and 6–31 + G* basis set were used to optimize all reactant, transition state, and product complexes in the implicit aqueous medium. Subsequently, the structures of these complexes were further optimized by using the ωB97X-D dispersion-corrected density functional theory method and cc-PVTZ basis set in the aqueous medium. The IEFPCM method was used to model the aqueous medium.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Codoped germanene with 3p and 4p elements elements","authors":"Pablo A. Denis,&nbsp;Jose A. S. Laranjeira,&nbsp;Nicolas F. Martins,&nbsp;Julio R. Sambrano","doi":"10.1007/s00894-024-06133-6","DOIUrl":"10.1007/s00894-024-06133-6","url":null,"abstract":"<div><h3>Context</h3><p>The relentless need for new materials to be used in electronic devices has opened new research directions in materials science. One of them involves using two-dimensional materials, among which there is current interest in using germanene. The heteroatom doping of germanene has been proposed as a possible approach to fine-tuning its electronic properties. However, this procedure is complicated because locating the dopants with a specific arrangement is challenging, thus achieving reproducibility. To avoid this problem, we propose the codoping of germanene to understand if dopants prefer to be agglomerated as observed for graphene or if they prefer to adopt a random disposition. Herein, we employed first-principles calculations to study 21 codoped germanene systems with one <i>3p</i> (Al, Si, P, and S) and one <i>4p</i> (Ga, As, and Se) element. Our results indicate that in the cases of AlP, AlS, GaP, GaS, GaAs, and GaSe codoped germanene, the dopants show a tendency to be located in specific lattice positions. The ortho disposition of dopants is preferred for AlP, AlS, GaP and GaS codoped germanene and their <i>4p</i> counterparts GaAs and GaSe codoped germanene, and the materials showed interesting electronic properties making them suitable to develop germanene-based electronic materials.</p><h3>Methods</h3><p>We utilized the M06-L, HSE06 methods accompanied by the 6-31G* basis sets to perform periodic boundary conditions calculations as implemented in Gaussian 09. The unit cells were sampled employing 100 k-points for geometry optimizations and 2000 k-points for electronic properties The ultrafine grid was employed. Results were visualized employing Gaussview 5.0.1. In addition to this, we performed B3LYP-D3 periodic calculations as implemented in CRYSTAL17.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on low-rank coal flotation collector screening and performance based on molecular polarity index","authors":"Lei Zhang,&nbsp;Shengyu Liu,&nbsp;Beilei Sun,&nbsp;Jianying Guo,&nbsp;Bao Li","doi":"10.1007/s00894-024-06129-2","DOIUrl":"10.1007/s00894-024-06129-2","url":null,"abstract":"<div><h3>Context</h3><p>Extensive studies using a trial-and-error approach have been conducted on low-rank coal flotation collectors. However, screening efficient collectors remains a considerable challenge due to the lack of suitable screening principles. It has proven that polar compounds such as carboxylic acids and esters are effective collectors for low-rank coal flotation. In this work, the effects of carboxylic acid, alcohol, and methyl ester on the floatability of low-rank coal were compared, the flotation performance of the polar collector was evaluated with theoretical calculations, a suitable evaluation parameter was determined and a screening principle based on this parameter was determined. The results show that the enhancement effects of polar collectors on low-rank coal floatability follow the order of methyl decanoate &gt; methyl laurate &gt; methyl octanoate &gt; sec-octanol &gt; methyl oleate (or methyl oleate &gt; sec-octanol) &gt; n-octanoic acid. Compared with the molecular polarity index, the hydrophobicity indices log P and dipole moment cannot be used to accurately evaluate different types of collectors and the same type of collectors, respectively. At room temperature, liquid polar compounds with molecular polarity indices in the range of 6.0 ~ 8.0 kcal/mol effectively enhance the floatability of low-rank coal. The molecular polarity index of the collector is used for the first time to screen effective collectors of low-rank coal in this work. This parameter is anticipated to be highly important for the development and research of low-rank coal and other mineral collectors.</p><h3>Methods</h3><p>To obtain reasonable and accurate molecular structure, geometry optimization and frequency calculations of the studied collectors were conducted via the Gaussian 09 software package based on density functional theory at the B3LYP/6–311 + G (d, p) level. The integral equation formalism for the polarizable continuum model (IEF-PCM) was utilized with water as the solvent (dielectric constant = 78.36, T = 298 K) for all the calculations. Then, the atomic charge distributions (MPA and NPA) and electrostatic potential maps, the dipole moment and molecular polarity index, and the log P and water solubilities of studied collectors were shown or calculated by Gauss View 5.0, Mutiwfn program and website (https://www.molsoft.com/mprop/mprop.cgi), respectively.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}