ContextHeavy metal ion removal from wastewater has become a global concern due to its extensive negative effects on human health and the environment. The density functional theory is employed to investigate the possibility of removing Pb2+, Hg2+, and Cd2+ ions from wastewater using nano-graphene. Researchers have shown that NG can efficiently remove heavy metals from media. Additionally, it was shown that the adsorption of Pb2+, Hg2+, and Cd2+ ions might reduce the large pristine NG (HOMO–LUMO) gap.MethodsHSE06 may accurately represent NG electrical characteristics. The DFT-D3 method was also used to account for Van der Waals interactions in the present study. The results demonstrated that charge transfer and binding energy remained greater in cation-NG systems with greater electron transfer rates. Pb2+, Hg2+, and Cd2+ adsorption results indicated that Egap was significantly reduced by 68%, 15%, and 21%, respectively. The Pb2+@NG complex exhibited the strongest oscillator strength. This may be explained by the enormous occupation number difference between the 2px orbital of the C atoms and the 6 s orbital of the Pb2+ cations. The greater Ebin value of Pb2+@NG is consistent with the increased predicted redshifts (199 nm). DFT (hybrid functional HSE06) studies that rely on time showed that the relevant complexes have “ligand-to-metal charge transfer” excitations. In general, it was found that Pb2+@NG had the greatest k value, binding energy, redshifts, and charge transfer rate among the complexes. The theoretical insights of this study may influence experimental efforts to identify NG-based compounds that are effective and efficient at removing pollutants from wastewater.

ContextThe organic solar cells (OSCs) are being developed with the goal of improving their photovoltaic capabilities. Here, utilizing computational methods, six new nonfullerene acceptors (NFA) comprising dyes (A1–A6) have been created by end-group alterations of the Y123 framework as a standard (R).MethodsThe DFT-based investigations at B3LYP/6-31G + (d,p) level were applied to evaluate their properties. The planar geometries associated with these structures, which lead to improved conjugation, were validated by the estimation of molecular geometries. Dyes A1–A6 have shorter Egap than R, according to a frontier molecular orbital (FMO) investigation, which encourages charge transfer in them. The dyes with their maximum absorption range were shown by optical properties to be 692–711 nm, which is significantly better than R with its 684 nm range. Their electrostatic and Mulliken charge patterns provided additional evidence of the significant separation of charges within these structures. All the dyes A1–A6 had improved light harvesting efficiency (LHE) values as compared to Y123, highlighting their improved capacity to generate charge carriers by light absorption. With the exception of dye A4, all newly developed dyes might have a superior rate of charge carrier mobility than R, according to reorganization energies λre. Dyes A3 and A4 had the greatest open-circuit voltage (Voc). Dye A3 exhibited improvement in all of its examined properties, making it a promising choice in DSSC applications.Graphical Abstract

ContextEnergetic materials are a class of materials containing explosive groups or containing oxidants and combustibles. The optimization of energetic materials has a significant impact on the development of industry and national defense. For high-energy density compounds (HEDC) that have not been synthesized or are dangerous to experimental operation, it is of guiding significance to predict its energy level, physicochemical properties, and safety through molecular design and theoretical calculation. Cyclic urea nitramine series compounds are a type of energetic compounds with high density and excellent detonation performance. In this study, 2,5,7,9-tetranitro-2,5,7,9-tetraazabicyclo[4,3,0]nonane-8-one (K-56) was used as the parent structure, and 36 energetic derivatives were designed. The effects of introducing single and multiple substituents on the electronic structure, energy gap, heat of formation, detonation performance, thermal stability, thermodynamic parameters, and surface electrostatic potential of K-56 and its derivatives were discussed in detail. The results exhibit the following: (1) the single substitution of -C(NO2)3 (A6) can reduce the detonation velocity of K-56 by 11.9 % and the detonation pressure by 19.8 %, while the double substitution of -C(NO2)3 (B6) can increase the density of K-56 by 11.6 %, the detonation velocity by 10.9 %, and the detonation pressure by 31 %. (2) The heat of formation of K-56 (−110.0 kJ mol−1) increased by 324.18 % and 628.81 %, respectively, proving that -N3 is an extremely effective group to improve HOF. (3) The thermal stability of the derivatives generated by the monosubstitution of the target group on the six-membered ring is better than that of the parent compound.MethodsGaussian16 and Multiwfn 3.8 packages are the software for calculation. In this study, the parent structure K-56 and its derivatives were optimized at the B3LYP/6-311G (d,p) level to obtain the zero point energy and thermal correction data of all compounds. Then the vibration analysis of the optimized structure is carried out to confirm that its configuration is stable. Then the M06-2X-D3/def2-TZVPP basis set is used to calculate the single point energy.

ContextNanosensor materials for the trapping and sensing of CO2 gas in the ecosystem were investigated herein to elucidate the adsorption, sensibility, selectivity, conductivity, and reactivity of silicon-doped carbon quantum dot (Si@CQD) decorated with Ag, Au, and Cu metals. The gas was studied in two configurations on its O and C sites. When the metal-decorated Si@CQD interacted with the CO2 gas on the C adsorption site of the gas, there was a decrease in all the interactions with the lowest energy gap of 1.084 eV observed in CO2_C_Cu_Si@CQD followed by CO2_C_Au_Si@CQD which recorded a slightly higher energy gap of 1.094 eV, while CO2_C_Ag_Si@CQD had an energy gap of 2.109 eV. On the O adsorption sites, a decrease was observed in CO2_O_Au_Si@CQD which had the least energy gap of 1.140 eV, whereas there was a significant increase after adsorption in CO2_O_Ag_Si@CQD and CO2_O_Cu_Si@CQD with calculated ∆E values of 2.942 eV and 3.015 eV respectively. The adsorption energy alongside the basis set supposition error (BSSE) estimation reveals that CO2_C_Au_Si@CQD, CO2_C_Ag_Si@CQD, and CO2_C_Cu_Si@CQD were weakly adsorbed, while chemisorption was present in the CO2_O_Ag_Si@CQD, CO2_O_Cu_Si@CQD, and CO2_O_Au_Si@CQD interactions. Indeed, the adsorption of CO2 on the different metal-decorated quantum dots affects the Fermi level (Ef) and the work function (Φ) of each of the decorated carbon quantum dots owed to their low Ef values and high ∆Φ% which shows that they can be a prospective work function–based sensor material.MethodsElectronic structure theory method based on first-principle density functional theory (DFT) computation at the B3LYP-GD3(BJ)/Def2-SVP level of theory was utilized through the use of the Gaussian 16 and GaussView 6.0.16 software packages. Post-processing computational code such as multi-wavefunction was employed for result analysis and visualization.

BackgroundThe presence of volatile organic compounds (VOCs) in the exhaled breath of lung cancer patients is the only available source for detecting the disease at its initial stage. Exhaled breath analysis depends purely on the performance of the biosensors. The interaction between VOCs and pristine MoS2 is repulsive in nature. Therefore, modifying MoS2 via surficial adsorption of the transition metal nickel is of prime importance. The surficial interaction of six VOCs with Ni-doped MoS2 led to substantial variations in the structural and optoelectronic properties compared to those of the pristine monolayer. The remarkable improvement in the conductivity, thermostability, good sensing response, and recovery time of the sensor exposed to six VOCs revealed that a Ni-doped MoS2 exhibits impressive properties for the detection of exhaled gases. Different temperatures have a significant impact on the recovery time. Humidity has no effect on the detection of exhaled gases upon exposure to VOCs. The obtained results may encourage the use of exhaled breath sensors by experimentalists and oncologists to enable potential advancements in lung cancer detection.MethodsThe surface adsorption of transition metal and its interaction with volatile organic compounds on a MoS2 surface was studied by using Spanish Initiative for Electronic Simulations with Thousands of Atoms (SIESTA). The pseudopotentials used in the SIESTA calculations are norm-conserving in their fully nonlocal forms. The atomic orbitals with finite support were used as a basis set, allowing unlimited multiple-zeta and angular momenta, polarization, and off-site orbitals. These basis sets are the key for calculating the Hamiltonian and overlap matrices in O(N) operations. The present hybrid density functional theory (DFT) is a combination of PW92 and RPBE methods. Additionally, the DFT+U approach was employed to accurately ascertain the coulombic repulsion in the transition elements.

ContextAs a result of the diversity of microstructures encountered in cis-1,4-polybutadiene and the variety of measurement methods used, experimental values of variation of glass transition temperature (Tg) with pressure are relatively dispersed. However, atomistic simulations enable access to valuable information for very well-controlled chemistry and structures with a well-defined and systematic acquisition protocol. By varying the temperature and pressure, the specific volume of the melt was computed, yielding results that deviated by only 2% from experimental data. A linear relationship between Tg and pressure was observed, with Tg predicted to be 162 K at zero pressure and a rate of change of Tg with respect to pressure (dTg/dP) of 0.24 K/MPa.MethodThe atomistic dilatometry experiments were conducted on a model of amorphous cis-1,4 polybutadiene with an approximate molecular weight of 5400 g/mol using the LAMMPS code and the all-atom forcefield pcff + . The dilatometry process involved cooling and heating at a rate of 9 × 1012 K/min. The specific volume was calculated by averaging over seven independent configurations for each temperature. The Tait equation was employed to fit the specific volume evolution within the temperature range of 10 to 700 K under different pressures of 0, 60, and 100 MPa.

ContextSeveral descriptors from conceptual density functional theory (cDFT) and the quantum theory of atoms in molecules (QTAIM) were utilized in Random Forest (RF), LASSO, Ridge, Elastic Net (EN), and Support Vector Machines (SVM) methods to predict the toxicity (LD50) of sixty-two organothiophosphate compounds. The A-RF-G1 and A-RF-G2 models were obtained using the RF method, yielding statistically significant parameters with good performance, as indicated by R2 values for the training set (R2Train) and R2 values for the test set (R2Test), around 0.90.MethodsThe molecular structure of all organothiophosphates was optimized via the range-separated hybrid functional ωB97XD with the 6–311 + + G** basis set. Seven hundred and eighty-seven descriptors have been processed using a variety of machine learning algorithms: RF LASSO, Ridge, EN and SVM to generate a predictive model. The properties were obtained with Multiwfn, AIMALL and VMD programs. Docking simulations were performed by using AutoDock 4.2 and LigPlot + programs. All the calculations in this work are carried out in Gaussian 16 program package.

ContextFrom a nuclear spin prospective, water exists as para and ortho nuclear spin isomers (isotopomers). Spin interconversions in isolated molecules of water are forbidden, but many recent reports have shown them to happen in bulk, through dynamic proton exchanges happening between interconnected networks of a large array of water molecules. In this contribution, a possible explanation for an unexpected slow or delayed interconversion of ortho-para water in ice observed in an earlier reported experiment is provided. Using the results of quantum mechanical investigations, we have discussed the roles played by Bjerrum defects in the dynamic proton exchanges and ortho-para spin state interconversions. We guess that at the sites of the Bjerrum defects, there are possibilities of quantum entanglements of states, through pairwise interactions. Based on the perfectly correlated exchange happening via a replica transition state, we speculate that it can have significant influences on ortho-para interconversions of water. We also conjecture that the overall ortho-para interconversion is not a continuous process, rather can be imagined to be happening serendipitously, but within the boundary of the rules of quantum mechanics.MethodsAll computations were performed with Gaussian 09 program. B3LYP/6-31++G(d,p) methodology was used to compute all the stationary points. Further energy corrections were computed using CCSD(T)/aug-cc-pVTZ methodology. Intrinsic reaction coordinate (IRC) path computations were carried out for the transition states.

ContextSF6 is widely used in electrical equipment due to its chemical stability and insulation strength, but it is a strong greenhouse gas and its use has been restricted internationally. In order to reduce the SF6 usage, it is needed to find a replacement gas for SF6. Electrical breakdown test is always adopted to select potential substitutes, but it is resource and time intensive. Thus, a structure-activity relationship model is needed to effectively predict the gas insulation strength. In this work, we calculated the isosurface electrostatic potential of 68 gas molecules in case of electron probability density, Laplacian of electron density, electron localization function, and localized orbital function. The distribution characteristics of these four real space functions were analyzed. Furthermore, correlation between the electrostatic potential parameters and insulation strength was presented. Finally, a prediction model for insulation strength of gaseous medium was established. Using the electrostatic potential parameter on the localized orbital locator function with a threshold of 0.05 a.u., the prediction model achieved the best performance with a coefficient of determination of 0.860 and a mean squared error of 0.0663.MethodsThe quantization calculation tool used in this work is the GAUSSIAN 16 software. The M06-2X method with the 6-311G++(d, p) basis set is used to optimize the molecular structure and output stable wavefunction files. Then the wavefunction analysis software Multiwfn is used to plot the contour map of the gas molecules and calculate the radial distribution patterns.

ContextMolecular docking is an important and rapid tool that provides a comprehensive view of different molecular mechanisms. It is often used to verify the binding interactions of many pairs of molecules and is much faster than more rigorous approaches. However, its application requires carefully preprocessing each molecule and selecting a series of simulation parameters, which is not always done correctly. We show how preprocessing and simulation parameters can positively or negatively impact molecular docking performance. For example, the inclusion of hydrogen atoms leads to better redocking scores, but molecular dynamics simulations must be performed under certain constraints; otherwise, it may worsen performance rather than improve it. This study clarifies the importance and influence of these different parameters in the simulation results.MethodsWe analyzed the influence of different parameters on the predictive ability of molecular docking techniques using two software packages: AutoDock Vina and AutoDock-GPU. Thus, 90 receptor-ligand complexes were redocked, evaluating the root mean square deviation (RMSD) between the original position of the ligand (receptor-ligand complex obtained experimentally) and that obtained by the software for every analysis. We investigated the influence of hydrogen atoms (on the receptor and on the receptor-ligand complex), partial charges (QEq, QTPIE, EEM, EEM2015ha, MMFF94, Gasteiger-Marsili, and no charge), search boxes (size and exhaustiveness), ligand characteristics (size and number of torsions), and the use of molecular dynamics (of the receptor or the receptor-ligand complex) before docking analyses.

ContextOrganic–inorganic nanoparticles have received extensive attention in various fields due to their unique physicochemical properties and biological activities. Among these nanoparticles, graphene oxide (GO) has emerged as a promising material, and thus, its application in biomedical fields is of great interest. Coating graphene oxide on the surface of implants can enhance its properties such as antibacterial and cell proliferation promotion, but the osteogenic properties of graphene oxide coating need further improvement, and the chance of acute inflammation triggered by local reactive oxygen species accumulation needs to be reduced. High-precision modulation of graphene oxide surface micro/nanomorphology and chemical composition can be achieved using femtosecond laser processing technology to improve its performance while also reducing the oxygen content of the graphene oxide surface to some extent. In this paper, the properties of graphene oxide were investigated by kinetic simulations based on the first-principle. The results show that the band gap of graphene oxide changes from 0.386 to 0.021 eV; the work function changes from 4.882 to 4.64 eV; the size and number of peaks in the radial distribution function decreases; and the intensity of the scatter X-ray peak becomes smaller under the action of femtosecond laser, indicating that the oxygen-containing functional groups on the surface of graphene oxide are disrupted, which provides a basis for its potential application in the medical field.MethodsTo investigate the properties of graphene oxide, SEM, XPS, Raman, and FTIR characterizations were first used to determine the oxygen-containing functional group species on the surface of graphene oxide. The structural model of graphene oxide was then modeled for density flooding theory (DFT) simulations using Biovia Materials Studio software, which was implemented in the CASTEP code. Our DFT calculations were performed using the generalized gradient approximation (GGA) as parameterized by the Perdew-Burke Ernzerhof (PBE) exchange-correlation functional. Additionally, we employed the norm-conserving pseudopotential to treat core electrons.

ContextCationic amino acid transporters (CATs) facilitate arginine transport across membranes and maintain its levels in various tissues and organs, but their overexpression has been associated with severe cancers. A recent study identified the alternating access mechanism and critical residues involved in arginine transportation in a cationic amino acid transporter from Geobacillus kaustophilus (GkApcT). Here, we used molecular dynamics (MD) simulation methods to investigate the transportation mechanism of arginine (Arg) through GkApcT. The results revealed that arginine strongly interacts with specific binding site residues (Thr43, Asp111, Glu115, Lys191, Phe231, Ile234, and Asp237). Based on the umbrella sampling, the main driving force for arginine transport is the polar interactions of the arginine with channel-lining residues. An in-depth description of the dissociation mechanism and binding energy analysis brings valuable insight into the interactions between arginine and transporter residues, facilitating the design of effective CAT inhibitors in cancer cells.MethodsThe membrane-protein system was constructed by uploading the prokaryotic CAT (PDB ID: 6F34) to the CHARMM-GUI web server. Molecular dynamics simulations were done using the GROMACS package, version 5.1.4, with the CHARMM36 force field and TIP3P water model. The MM-PBSA approach was performed for determining the arginine binding free energy. Furthermore, the hotspot residues were identified through per-residue decomposition analysis. The characteristics of the channel such as bottleneck radius and channel length were analyzed using the CaverWeb 1.1 web server. The proton wire inside the transporter was investigated based on the classic Grotthuss mechanism. We also investigated the atomistic details of arginine transportation using the path-based free energy umbrella sampling technique (US).

ContextA remarkable change in lattice parameters and bulk modulus is achieved by the suitable addition of Al (Al1-x Lax Sb) and In (Al1-x Inx Sb) atoms in the AlSb compound. Electronic responses like band structure, the total partial density of states, and the elemental density of states are thoroughly investigated. The computed values indicate that the binary compound AlSb is an indirect band gap and an optically inactive response. After increasing the doping concentrations (0.25, 0.5, 0.75) of La and In in AlSb, the band gap changes from indirect to direct nature. Hence, Al1-0.75 La0.25 Sb, Al1-0.50 La0.50 Sb, Al1-0.75 In0.25Sb, and Al1-0.50 In0.50Sb become optically active. The illustrious roles of Al-3p and In-4d states on the band gap and nonlinear responses of these compounds are extensively explored by the comparison between the computed results of ultra-soft and norm converging pseudopotentials. The excess specific heat (CV), enthalpy of mixing (Hm), and phonon dispersion curves resulting from the concentrations “x” are estimated in order to investigate the thermodynamic stability responses of the pristine and doped AlSb. The obtained CV and thermal coefficient statistics for Al1-x Lax Sb and Al1-x Inx Sb may be useful for a good mapping of experimental results and examining these compounds’ enharmonic responses. There is a valuable change in optical characteristics like dielectric functional, absorption, conductivity, and refractive index due to the addition of (La, In) impurities in AlSb. It is further observed that Al1-0.75 La0.25 Sb, Al1-0.50 La0.50 Sb, Al1-0.75 In0.25Sb, and Al1-0.50 In0.50Sb are significantly mechanically stable compared to pristine AlSb. The above results suggest that Al1-x Lax Sb and Al1-x Inx Sb are high-performance optical materials and can be promising potential candidates for optoelectronic applications.MethodsThe structural, electronic, mechanical, vibrational, and optical responses of the pure and doped Al1-0.75 La0.25 Sb, Al1-0.50 La0.50 Sb, Al1-0.75 In0.25Sb, and Al1-0.50 In0.50Sb are investigated, using Heydscuseria-Ernzerhof screened hybrid functional (HSEO6) and generalized gradient approximation (GGA) with norm-converging and ultra-soft pseudopotential techniques in the density functional theory.

ContextThe property transition between metal and semiconductor is the key to improving the properties of transition metal dichalcogenides (TMDCs). The adsorption of the NbS2 compound in the defect state was adjusted for the first time. The hybrid system overwrites the original surface mechanism of NbS2 and induces indirect band gaps. This modulation mode makes NbS2 convert into a semiconductor and effectively improves the catalytic activity of the material in the system. In addition, the original local magnetic moment of the compound is concentrated in the vacancy region and is improved. The optical properties of the adsorption system indicate that NbS2 compounds can be effectively applied in visible and low-frequency ultraviolet regions. This provides a new idea for the design of the NbS2 compound as a two-dimensional photoelectric material.MethodsIn the study, we assume that only one atom is adsorbed on the NbS2 supercell of the defect, and the distance between the two adjacent atoms exceeds 12.74 Å, so the interaction between atoms is ignored in the study. Adsorbed atoms include nonmetallic elements (H, B, C, N, O, F), metallic elements (Fe, Co), and noble metal elements (Pt, Au, Ag). The density functional theory (DFT) was used in the experiment. The non-conservative pseudopotential method was used in the calculation to optimize the crystal structure geometrically. The approximate functional is Heyd-Scuseria-Ernzerhof (HSE06). The calculation method includes the spin-orbit coupling (SOC) effect. The crystal relaxation optimization uses a 7 × 7 × 1 k point grid to calculate niobium disulfide’s photoelectric and magnetic properties. A vacuum space of 15Å is introduced in the direction outside the plane, and the free boundary condition is adopted to avoid the interaction between atomic layers. For the convergence parameter setting, the interatomic force of all composite systems is less than 0.03 eV/Å, and the lattice stress is less than 0.05 Gpa.

ContextPlastic waste pyrolysis offers a potential solution to reduce plastic accumulation, but prioritizing monomer recovery from the process is crucial to effectively address the environmental consequences of plastic accumulation. This study focuses on enhancing the yield of styrene during the pyrolysis of polystyrene by investigating thermal and kinetic data. A comprehensive investigation into the thermal degradation pathways of polystyrene is imperative to overcome the challenges associated with its waste management. The calculated bond dissociation energies reveal that the cleavage of non-terminal carbon–carbon bonds is energetically favorable, resulting in the formation of high molecular weight benzylic radicals. Based on these findings, four pyrolysis pathways are proposed, and the associated thermodynamic and kinetic parameters are determined using the DFT method. The major products identified in this study include styrene, α-methylstyrene, isopropylbenzene, methylbenzene, ethylbenzene, and methane. Furthermore, optimizing the temperature profile of the reactor is shown to enhance the recovery of styrene, thereby contributing to the reduction of plastic waste. This study provides valuable insights into the effective resource recovery from polystyrene waste pyrolysis, emphasizing the significance of managing pyrolysis conditions to achieve maximum yield. By controlling the temperature profile during the pyrolysis process, it is possible to obtain a high yield of styrene, facilitating the efficient recovery of the monomer from waste polystyrene and addressing the environmental concerns associated with plastic accumulation.MethodsIn this study, all calculations were performed using the B3LYP/6-31G(d) level of theory with the Gaussian 16 program package. The proposed model underwent geometry optimization and frequency calculations. Transition states were optimized using the TS Berny method, and energy profiles along reaction pathways were refined using the QST3 method. The IRC method validated proposed mechanisms and investigated energy profiles. Structural models were visualized using GaussView 6.0.

ContextIn spite of the fact that molecular acidity is a fundamental physicochemical property of molecular systems, the vast majority of theoretical studies have focused attention on monoprotic acids and on the prediction of pKa’s. Polyprotic acids, represent a challenge for electronic structure calculations since the multiple acidic sites result in a vast group of species with different conformations and reactivities. In this work, Information-theoretic (IT) concepts of localizability, order and uniformity are applied to the Citric Acid and its deprotonated species through the one-electron density functionals: Shannon entropy (S), Fisher information (I) and Disequilibrium (D), respectively. We pursue the goal of characterizing the acidity of the aforementioned species with the aim to associate the IT concepts to chemical features such as the polarizability of the protonated/deprotonated species, the liability of the acidic sites, atomic electrostatic potentials, covalent bonding. IT analyses looks very promising for future studies on the acidity of specific deprotonation-sites of polyprotic acids.MethodsDensity functional theory (DFT) calculations were performed with Gaussian 09 program. A sensitivity analysis of the IT-measures was performed for the citric acid and the citrate using B3LYP, B3PW91, BPW91, M05-2X, M06-2X and PBEPBE functionals with the 6-311++g(3df,2p), 6-311++g(d,p), 6.311+g(d,p) and aug-cc-pVDZ basis sets. The rest of the analysis was performed with the M05-2X/6-311+G(d,p) level of theory. Additionally, aqueous media was considered by use of the SMD solvent model. The IT-measures were calculated using a suite of programs developed in our laboratory jointly with the DGRID software package.

ContextDegradation reactions of micropollutants such as antibiotics with OH radicals are very important in terms of environmental pollution. Therefore, in this study, the degradation kinetic mechanism of 6-aminopenicillanic acid (6-APA) with OH radical was investigated by density functional theory (DFT) methods.MethodsFor the calculations, different functionals such as B3LYP, MPW1PW91, and M06-2X were used with a 6-31 g(d,p) basis set. The aquatic effect on the reaction mechanism was investigated by conductor-like polarizable continuum model (CPCM). For the degradation kinetics in aqueous media, the addition of explicit water molecules was also calculated. Subsequent reaction mechanism for the most probable reaction product was briefly discussed.ResultsAmong the functionals used, B3LYP results were consistent with the experimental results. Calculated kinetic parameters indicated that the OH-addition path was more dominant than the H-abstraction paths. With the increase of explicit water molecules in the models, the energy required for the formation of transition state complexes decreased. The overall rate constant is calculated as 2.28 × 1011 M−1 s−1 at 298 K for the titled reaction.

ContextHeparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations. Later, we evaluate the biological compatibility of the nanosystems, in the target of the spike protein, through molecular docking. The results show that graphene oxide interacts with the heparin with an increase in the affinity energy with the spike protein, indicating a possible increment in the antiviral activity. Experimental analysis of synthesis and morphology of the nanostructures were carried out, indicating heparin absorption by graphene oxide, confirming the results of the first principle simulations. Experimental tests were conducted on the structure and surface of the nanomaterial, confirming the heparin aggregation on the synthesis with a size between the GO layers of 7.44 Å, indicating a C–O type bond, and exhibiting a hydrophilic surface characteristic (36.2°).MethodsComputational simulations of the ab initio with SIESTA code, LDA approximations, and an energy shift of 0.05 eV. Molecular docking simulations were performed in the AutoDock Vina software integrated with the AMDock Tools Software using the AMBER force field. GO, GO@2.5Heparin, and GO@5Heparin were synthesized by Hummers and impregnation methods, respectively, and characterized by X-ray diffraction and surface contact angle.

ContextNatural products and their biotransformation procedures are a powerful source of new chromophores with potential applications in fields like biology, pharmacology and materials science. Thus, this work discusses about the extraction procedure of 1-nitro-2-phenylethane (1N2PE) from Aniba canelilla, its biotransformation setup into 2-phenylethanol (2PE) using four fungi, Lasiodiplodia caatinguensis (phytopathogenic fungus from Citrus sinensis), Colletotrichum sp. (phytopathogenic fungus from Euterpe oleracea), Aspergillus flavus and Rigidoporus lineatus isolated from copper mining waste located in the interior of the Brazilian Amazon. A detailed experimental and theoretical vibrational analysis (IR and Raman) have allowed us to perform some charge transfer effects on the title compounds (push-pull effect) by monitoring specific vibrational modes of their electrophilic and nucleophilic molecular sites. The solvent interactions promote molecular conformations that affect the vibrational spectra of the donor and acceptor groups, as can be seen comparatively in the gas and aqueous solution spectra, an effect possibly related to the bathochromic shift in the calculated optical spectrum of the compounds. The nonlinear optical behavior shows that while the solvent reduces the response of 1N2PE, the response of 2PE increases the optical parameters, which presents low refractive index (n) and first hyperpolarizability. (\(\beta \)) is almost eight times that reported for urea (42.79 a.u.), a common nonlinear optical material. Furthermore, the bioconversion goes from an electrophilic to a nucleophilic compound, affecting its molecular reactivity.Methods1N2PE was obtained from Aniba canelilla, whose essential oil is constituted of \(\sim 80\%\) of 2PE. The A. canelilla essential oil was extracted under hydrodistillation. The biotransformation reactions were performed in autoclaved liquid media (100 mL) composed of malt extract (2%) in 250 mL Erlenmeyer flask. Each culture was incubated in an orbital shaker (130 rpm) at \(32^\circ \)C during 7 days and after that, 50 mg of 1N2PE (80%) were diluted in 100 \(\mu \)L of dimethylsulfoxide (DMSO) and added to the reactions flasks. Aliquots (2 mL) were removed using ethyl acetate (2 mL) and analyzed by GC-MS (fused silica capillary col1umn, Rtx -5MS 30 m \(\times \) 0.25 mm \(\times \) 0.25 \(\mu \)m) in order to determine the amount of 1N2PE biotransformation. FTIR 1N2PE and 2PE spectra were obtained by attenuated total reflectance (ATR), using a Agilent CARY 630 spectrometer, in the spectral region 4000-650 cm\(^{-1}\). The quantum chemical calculations were carried out in the Gaussian 09 program while the DICE code was used to perform the classical Monte Carlo simulations and generate the liquid environment using the classical All-Atom Optimized parameters for Liquid Simulations (AA-OPLS). All nonlinear optical properties, reactive parameters, and electronic excitations were calculated using the Density Functional Theory framework coupled to the standard 6-311++G(d,p) basis set.

ContextRecently, a new 2D carbon allotrope named biphenylene network (BPN) was experimentally realized. Here, we use density functional theory (DFT) calculations to study its boron nitride analogue sheet’s structural, electronic, and optical properties (BN-BPN). Results suggest that BN-BPN has good structural and dynamic stabilities. It also has a direct bandgap of 4.5 eV and significant optical activity in the ultraviolet range. BN-BPN Young’s modulus varies between 234.4\(-\)273.2 GPa depending on the strain direction.MethodsDensity functional theory (DFT) simulations for the electronic and optical properties of BN-BPN were performed using the CASTEP package within the Biovia Materials Studio software. The exchange and correlation functions are treated within the generalized gradient approximation (GGA) as parameterized by Perdew-Burke-Ernzerhof (PBE) and the hybrid functional Heyd-Scuseria-Ernzerhof (HSE06). For convenience, the mechanical properties were carried out using the DFT approach implemented in the SIESTA code, also within the scope of the GGA/PBE method. We used the double-zeta plus polarization (DZP) for the basis set in these cases. Moreover, the norm-conserving Troullier-Martins pseudopotential was employed to describe the core electrons.