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Journal of Molecular Modeling

Subject:
Catalysis
Publisher:
Springer Berlin Heidelberg
Springer Journals
ISSN:
1610-2940
Scimago Journal Rank:
71
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Effect of graphene on the key electrical, optical, and magnetic properties of polymethylmethacrylate: a study based on molecular modeling

López-Chávez, Ernesto; Garcia-Quiroz, Alberto; Díaz-Góngora, José Antonio Irán; López-Barrera, J. Antonio; Mendoza-Espinoza, José Alberto; Peña-Castañeda, Yesica Antonia; de Landa Castillo-Alvarado, Fray

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06172-zpmid: 39400734

ContextIn this work, a new polymeric structure was designed consisting of a nanometric sheet of graphene (G) and a polymethylmethacrylate (PMMA) repeat unit, which was designated as PMMA-G. Three degrees of polymerization of PMMA-G were considered: monomer (PMMA-G1), dimer (PMMA-G2), and trimer (PMMA-G3). The effect of incorporating a nanometric sheet of graphene into the molecular structure of PMMA on the modification of some of its main optical, magnetic, and electrical properties was investigated. Currently, the study presented here is of great relevance since various areas of technology require new materials with specific properties for the development of new devices. The results of our study reveal that the dielectric constant of PMMA is reduced when graphene is incorporated. However, a percentage increase of 14.48% in the refractive index of PMMA when graphene is inserted to form the nanocomposite is observed. It is found that the absolute value of molar magnetic susceptibility of PMMA increases considerably when reinforced with graphene. Finally, when reinforcing PMMA with graphene to obtain the PMMA-G nanocomposite, the electrical resistivity increases by almost an order of magnitude.MethodsWe used computational tools under Materials Studio (MS) software. We built a PMMA molecule with three degrees of polymerization, graphene sheet, and polymethylmethacrylate-graphene composite (PMMA-G) was built also with three degrees of polymerization using a concentration of 50% graphene over the PMMA polymer. For each structure, we used computational code DMol3 of MS, which is based on the Density Functional Theory, and the geometry optimization process was carried out to obtain the most stable structures. Finally, using the connectivity indices method together with topological properties of the molecular structures, implemented in Synthia computational code of MS software, we calculated the dielectric constant, magnetic susceptibility, refractive index, and electrical resistivity, for pure PMMA and PMMA-G structures for their three degrees of polymerization. The results were analyzed, and the changes in these properties were discussed in terms of the effect of an electric and magnetic field on the molecular structures of PMMA-G with respect to PMMA.
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Computational chemistry facilitates the development of second near-infrared xanthene-based dyes

Yuan, Qinlin; Wang, Mingyu; Ma, Mingyue; Sun, Pingping; Zeng, Chaoyuan; Chi, Weijie

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06179-6pmid: 39467901

ContextThe dyes in the second near-infrared (NIR-II) region play a crucial role in advancing imaging technology. However, developing small-molecule dyes in NIR-II poses a significant bottleneck to meet the substantial demands in biological fields, which may be attributed to the lack of a rational design strategy. Herein, we designed a series of rhodamine analogs with more red-shifted emission by replacing the oxygen-bridge atom in xanthene-based dyes with –C(CH3)2, –Si(CH3)2, –SO2, and –P(O)Ph. We investigated the frontier molecular orbital, electrostatic potential surfaces, the interaction region indicator, electron–hole distribution, and absorption and emission spectrum of xanthene-based dyes using (time-dependent) density functional theory. Our results demonstrated that these designed small molecular dyes exhibit long emission wavelengths covering 1377–1809 nm. We expected these findings to enable the targeted design of long-wavelength rhodamines.MethodGeometry optimization of dyes in the ground and excited states was carried out at ω-B97XD/Def2SVP level using Gaussian 16 A03. The absorption and emission wavelengths were evaluated using 13 functional, including TPSSH, O3LYP, B3LYP*, B3LYP, PBE0, MPW1B95, PBE-1/3, PBE38, MPWB1K, MN15, BHandHLYP, ω-B97XD, and CAM-B3LYP.
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A DFT study of the effect of hydrostatic pressure on the structure and electronic properties of sarcosine crystal

de Moura, Geanso M.; Lage, Mateus R.; Santos, Adenilson; Gester, Rodrigo; Stoyanov, Stanislav R.; Andrade-Filho, Tarciso

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06110-zpmid: 39365492

ContextWe perform density functional theory calculations to study the dependence of the structural and electronic properties of the amino acid sarcosine crystal structure on hydrostatic pressure application. The results are analyzed and compared with the available experimental data. Our findings indicate that the crystal structure and properties of sarcosine calculated using the Grimme dispersion-corrected PBE functional (PBE-D3) best agree with the available experimental results under hydrostatic pressure of up to 3.7 GPa. Critical structural rearrangements, such as unit cell compression, head-to-tail compression, and molecular rotations, are investigated and elucidated in the context of experimental findings. Band gap energy tuning and density of state shifts indicative of band dispersion are presented concerning the structural changes arising from the elevated pressure. The calculated properties indicate that sarcosine holds great promise for application in electronic devices that involve pressure-induced structural changes.MethodsThree widely used generalized gradient approximation functionals—PBE, PBEsol, and revPBE—are employed with Grimme’s D3 dispersion correction. The non-local van der Waals density functional vdW-DF is also evaluated. The calculations are performed using the projector-augmented wave method in the Quantum Espresso software suite. The geometry optimization results are visualized using VMD. The Multiwfn and NCIPlot programs are used for wavefunction and intermolecular interaction analyses.
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Unimolecular isomerizations of C6H6•+ radical cations: a computational study

Kharnaior, Kiew S.; Chandra, Asit K.; Lyngdoh, R. H. Duncan

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06148-zpmid: 39365345

ConceptEighteen concerted isomerization reactions of various C6H6•+ radical cation (RC) species are studied and found to proceed via well-defined transition states, whose relative positions along the reaction pathway generally agree with Hammond’s postulate. From the barrier heights, the rate coefficients of these reactions are estimated by using transition state theory, and the activation energies are computed. Through combination among themselves, these 18 isomerizations yielded 15 multi-step conversion routes of various C6H6•+ species to the lowest energy benzene radical cation isomer 1, which routes are compared.MethodsUse is made of DFT with the B3LYP and M06-2X functionals, along with the CBS-QB3 approach to arrive at better energies. From the barrier heights for each of the concerted reactions, canonical transition state theory was applied to evaluate rate coefficients k over the temperature range 200–500 K. The Arrhenius activation energies were computed using the plot of ln k vs. 1/T.
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Understanding and simulating mechanochromism in dye-dispersed polymer blends: from atomistic insights to macroscopic properties

Wang, Qinfan; Ottochian, Alistar; Turelli, Michele; Pucci, Andrea; Ciofini, Ilaria; Adamo, Carlo

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06174-x

ContextIn this work, we propose a computational protocol enabling the simulation of mechanochromic responses in dye-dispersed polymer blends. The main objective is the modeling of the molecular-level structural changes responsible for the modulation of the photophysical properties that lead to the mechanochromic phenomenon. In this demonstrative study, we focus on predicting the changes in optical absorption displayed by a model system consisting of a dimer of a tetraphenylethylene derivative dispersed in a polyethylene matrix. The blend is subjected to an external stimulus that causes a modulation of the polymer matrix density that translates, in turn, into the emergence of specific mechanical constraints on the optically active dimers. The accurate description of this phenomenon requires the reliable sampling of the dimer configurations induced by the interaction with the matrix under stress. These molecular geometries are associated with modified electronic structures that confer novel absorption responses to the dispersed dyes.MethodsIn the present contribution, the sampling of these structures is achieved through classical molecular dynamics (MD) simulations including a model element to apply an anisotropic mechanical force. This element allows the microscopic modeling of the chains’ and dyes’ structural rearrangements under stress. After the sampling, we compare the results of two approaches for the prediction of the optical response: (i) the calculation of a mean response from a statistical average over quantum chemical calculations on the sampled MD structures and (ii) a prediction via a more expensive hybrid scheme allowing the relaxation of the sampled molecular geometries in the presence of the matrix constraints.
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Structural and energetic properties of cluster models of anatase-supported single late transition metal atoms: a density functional theory benchmark study

Deraet, Xavier; Çilesiz, Umut; Aviyente, Viktorya; De Proft, Frank

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06173-ypmid: 39436438

ContextSingle-atom catalytic systems constitute an intriguing research topic due to their inherently different chemical behavior as compared to classic heterogeneous catalysts. In this study, cluster systems representing single late transition metal atoms adsorbed on anatase were constructed starting from previously generated periodic models and subjected to a density functional theory (DFT) benchmark study. The ability of different density functional approximations representing all rungs of the Jacob’s Ladder classification to accurately describe bond lengths and adsorption energies was assessed for these clusters with the aim of revealing the functional that allows to retain the structural characteristics of the initial periodic system, while also delivering reliable energetics. In this regard, our results indicate that optimisation of the clusters with the meta-GGA functionals TPSS or RevTPSS provides the lowest mean unsigned error and root-mean-square deviations with respect to the periodic models. Moreover, these functionals and, to a slightly lesser degree, PW91 were also found to provide adsorption energies that are statistically the least deviating from the CCSD(T) reference data. More complex hybrid functionals appear to be performing less well.MethodsCluster geometries were determined at the Kohn–Sham DFT level using the LANL2DZ basis set for the transition metals and the Pople 6-31G(d) basis set for O and H. The density functional approximations considered were SVWN, PBE, BP86, BLYP, PW91, TPSS, RevTPSS, M06L, M11L, B3LYP, PBE0, M06, M06-2X, MN15, ωB97X-D, CAM-B3LYP, M11, and MN12-SX. Reference adsorption energies of the metals on the support cluster were obtained at the CCSD(T)/LANL2TZ (transition metals)/6–311 +  + G(d,p)//RevTPSS/LANLD2DZ (transition metals)/6-31G*. Besides the above-mentioned functionals, energy calculations using the double-hybrid functionals, DSDPBEP86, PBE0-DH, and B2PLYP, were also performed. All adsorption energy calculations were carried out on the RevTPSS geometries.
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Influence of polypropylene fibers on the tensile mechanical properties of calcium silicate hydrate: molecular simulation

Chen, Yu; Yin, Xuyang; Udoessiet, Ndukeabasi Peter; Wang, Jiale; Zhu, Jiawen; Luo, Shimei

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06164-zpmid: 39356315

ContextThis research assesses the influence of polypropylene (PP) fibers, both homopolymer and hydroxylated (PPOH), on the tensile properties of calcium silicate hydrate (C-S–H) composites through molecular dynamics (MD) simulations. Our models explore C-S–H matrices integrated with PP and PPOH fibers at varying polymerization degrees. The results demonstrate that both PP and PPOH fibers significantly influence the tensile strength and Young’s modulus of the composites. Notably, PPOH fibers contribute to more substantial mechanical enhancements than PP, attributed to the increased polarity and enhanced intermolecular interactions from the hydroxyl groups. The study reveals a nonlinear relationship between polymer additive content and mechanical performance, with optimal properties at a polymerization degree of 20. Additionally, stress–strain analysis indicates that PPOH composites exhibit superior ductility and fracture energy, particularly at polymerization degrees of 20, showing enhanced ultimate strain and fracture energy by up to 9.6% and 13.9%, respectively, compared to PP counterparts. These results highlight the crucial role of tailored polymer additive composition and chemical modifications in maximizing the mechanical efficacy of C-S–H-based materials, enhancing their durability and structural performance.MethodsAll MD simulations were conducted using LAMMPS. The models employed a combination of Clayff and Cvff force fields. During the entire tensile simulation, the system was configured under the NPT ensemble at 300 K.
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Theoretical exploration of energetic molecular design strategy: functionalization of C or N and structural selection of imidazole or pyrazole

Chen, Qianxiong; Zhu, Jin; Jing, Suming; Deng, Jiahao; Wang, Yuanyuan; Li, Keyao; Wang, Zhineng; Liu, Jia; Bian, Shuai

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06183-wpmid: 39446185

ContextIn researching energetic materials with high energy density, it is an effective method to introduce explosophoric groups. In this study, four series of energetic compounds were designed by functionalizing with C- or N-, introducing energetic groups -CH(NO2)2, -CF(NO2)2, -C(NO2)2(NF2), -C(NO2)3, and-CH(NF2)2 into imidazole and pyrazole structures. Density functional theory was employed to optimize the structure of the target compound and subsequently to predict and evaluate its performance based on this. Meanwhile, the sensitivity of the compounds was predicted based on their electrostatic potential analysis. Following analysis of the geometric structure, detonation performance, and sensitivity of the compounds, three factors were discussed: energetic groups, functionalization methods, and skeleton structure differences. The results indicate that C-functionalization has advantages only in density, but N-functionalization is better in thermal stability, heat of formation, and sensitivity. Meanwhile, the data shows that imidazole-based compounds exhibited greater density and detonation performance in the target compounds designed within this study, while pyrazoles have a higher heat of formation and chemical stability. By analyzing the design strategy of C- or N-functionalization of novel high-energy groups on energetic imidazole or pyrazole rings and selecting a more suitable molecular construction strategy, this study provides a theoretical approach for the development of new energetic materials with excellent performance.MethodGaussian 09 and Multiwfn 3.8 packages are the software used for calculation, and the electrostatic potentials were depicted using the VMD program. In this study, the imidazole and pyrazole derivatives were optimized at the B3PW91/6-311G (d, p) level to acquire the relevant data for the compounds.
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Ursolic acid interaction with transcription factors BRAF, V600E, and V600K: a computational approach towards new potential melanoma treatments

Aguilera-Durán, Giovanny; Hernández-Castro, Stephanie; Loera-García, Brenda V.; Rivera-Vargas, Alex; Alvarez-Baltazar, J. M.; Cuevas-Flores, Ma Del Refugio; Romo-Mancillas, Antonio

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06165-ypmid: 39387972

ContextMelanoma is one of the cancers with the highest mortality rate for its ability to metastasize. Several targets have undergone investigation for the development of drugs against this pathology. One of the main targets is the kinase BRAF (RAF, rapidly accelerated fibrosarcoma). The most common mutation in melanoma is BRAFV600E and has been reported in 50–90% of patients with melanoma. Due to the relevance of the BRAFV600E mutation, inhibitors to this kinase have been developed, vemurafenib-OMe and dabrafenib. Ursolic acid (UA) is a pentacyclic triterpene with a privileged structure, the pentacycle scaffold, which allows to have a broad variety of biological activity; the most studied is its anticancer capacity. In this work, we reported the interaction profile of vemurafenib-OMe, dabrafenib, and UA, to define whether UA has binding capacity to BRAFWT, BRAFV600E, and BRAFV600K. Homology modeling of BRAFWT, V600E, and V600K; molecular docking; and molecular dynamics simulations were carried out and interactions and residues relevant to the binding of the inhibitors were obtained. We found that UA, like the inhibitors, presents hydrogen bond interactions, and hydrophobic interactions of van der Waals, and π-stacking with I463, Q530, C532, and F583. The ΔG of ursolic acid in complex with BRAFV600K (− 63.31 kcal/mol) is comparable to the ΔG of the selective inhibitor dabrafenib (− 63.32 kcal/mol) in complex to BRAFV600K and presents a ΔG like vemurafenib-OMe with BRAFWT and V600E. With this information, ursolic acid could be considered as a lead compound for design cycles and to optimize the binding profile and the selectivity towards mutations for the development of new selective inhibitors for BRAFV600E and V600K to new potential melanoma treatments.MethodsThe homology modeling calculations were executed on the public servers I-TASSER and ROBETTA, followed by molecular docking calculations using AutoGrid 4.2.6, AutoDockGPU 1.5.3, and AutoDockTools 1.5.6. Molecular dynamics and metadynamics simulations were performed in the Desmond module of the academic version of the Schrödinger-Maestro 2020–4 program, utilizing the OPLS-2005 force field. Ligand–protein interactions were evaluated using Schrödinger-Maestro program, LigPlot + , and PLIP (protein–ligand interaction profiler). Finally, all of the protein figures presented in this article were made in the PyMOL program.Graphical Abstract[graphic not available: see fulltext]
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The phosphodiester dissociative hydrolysis of a DNA model promoted by metal dications

de Souza Santos, Vinicius Lemes; Ribeiro, Felipe Augusto; Kim, Chang Dong; López-Castillo, Alejandro

2024 Journal of Molecular Modeling

doi: 10.1007/s00894-024-06184-9pmid: 39438344

ContextPhosphodiester bonds, which form the backbone of DNA, are highly stable in the absence of catalysts. This stability is crucial for maintaining the integrity of genetic information. However, when exposed to catalytic agents, these bonds become susceptible to cleavage. In this study, we investigated the role of different metal dications (Ca2⁺, Mg2⁺, Zn2⁺, Mn2⁺, and Cu2⁺) in promoting the hydrolysis of phosphodiester bonds. A minimal DNA model was constructed using two pyrimidine nucleobases (cytosine and thymine), two deoxyribose units, one phosphate group, and one metallic dication coordinated by six water molecules. The results highlight that Cu2⁺ is the most efficient in lowering the energy barrier for bond cleavage, with an energy barrier of 183 kJ/mol, compared to higher barriers for metals like Zn2⁺ (202 kJ/mol), Mn2⁺ (202 kJ/mol), Mg2⁺ (210 kJ/mol), and Ca2⁺ (223 kJ/mol). Understanding the interaction between these metal ions and phosphodiester bonds offers insight into DNA stability and organic data storage systems.MethodsDFT calculations were employed using Gaussian 16 software, applying the B3LYP hybrid functional with def2-SVP basis sets and GD3BJ dispersion corrections. Full geometry optimizations were performed for the initial and transition states, followed by identifying energy barriers associated with phosphodiester bond cleavage. The optimization criteria included maximum force, root-mean-square force, displacement, and energy convergence thresholds.
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