CONTEXT: Chronic inflammation is a risk factor for diabetes, but it can also be a complication of diabetes, leading to severe diabetes and causing many other clinical manifestations. Inflammation is a major emerging complication in both type I and type II diabetes, which causes increasing interest in targeting inflammation to improve and control diabetes. Diabetes with insulin resistance and impaired glucose utilization in humans and their underlying mechanism is not fully understood. But a growing understanding of the intricacy of the insulin signaling cascade in diabetic inflammatory cells reveals potential target genes and their proteins responsible for severe insulin resistance. With this baseline concept, the current project explores the binding affinities of the hyaluronic acid anti-diabetic compounds conjugates to such target proteins in diabetic inflammatory cells and their molecular geometries. A range of 48 anti-diabetic compounds was screened against aldose reductase binding pocket 3 protein target through in silico molecular docking, and results revealed that three compounds viz, metformin (CID:4091), phenformin (CID:8249), sitagliptin (CID:4,369,359), possess significant binding affinity out of 48 chosen drugs. Further, these three anti-diabetic compounds were conjugated with hyaluronic acid (HA), and their binding affinity and their molecular geometrics towards aldose reductase enzyme were screened compared with the free form of the drug. The molecular geometries of three shortlisted drugs (metformin, phenformin, sitagliptin) and their HA conjugates were also explored through density functional theory studies, and it proves their good molecular geometry towards pocket 3 of aldose reductase target. Further, MD simulation trajectories affirm that HA conjugates possess good binding affinity and simulation trajectories with protein target aldose reductase than a free form of the drug. Our current study unravels the new mechanism of drug targeting for diabetes through HA conjugation for inflammatory diabetes. HA conjugates act as novel drug candidates for treating inflammatory diabetes; however, it needs further human clinical trials. METHODS: For ligand structure, PubChem, ACD chem sketch, and online structure file generator platform are utilized for ligand preparation. Target protein aldose reductase obtained from protein database (PDB). For molecular docking analysis, AutoDock Vina (Version 4) was utilized. pKCSM online server used to predict ADMET properties of the above three shortlisted drugs from the docking study. Using mol-inspiration software (version 2011.06), three shortlisted compounds' bioactivity scores were predicted. DFT analysis for three shortlisted anti-diabetic drugs and their hyaluronic acid conjugates were calculated using a functional B3LYP set of Gaussian 09 software. Molecular dynamics simulation calculations for six chosen protein-ligand complexes were done through YASARA dynamics software and AMBER14 force field.

CONTEXT: Global warming is a severe problem experiencing the climate crisis due to rising CO2 emissions. Deep eutectic solvents (DESs) have recently attracted a lot of attention as potential absorbents to mitigate carbon dioxide CO2 emissions because of their large CO2 capacities and stability under diverse conditions. Designing a potent DES requires knowledge of molecular-level understanding including structure, dynamics, and interfacial properties in DESs. In this study, we investigate the CO2 sorption and diffusion in different DESs at different temperatures and pressure using molecular dynamics (MD) simulations. Our results demonstrate that CO2 molecules preferentially concentrate at the CO2-DES interface, and the diffusion of CO2 in bulk DESs increases with increasing pressure and temperature. The solubility of CO2 in the three DESs increases as ChCL-ethylene glycol < ChCL-urea < ChCL-glycerol at high pressure (58.6 bar). METHODS: The initial configuration for MD simulations included DES and CO2 and produced the solvation box using PACKMOL software. The geometries are optimized in the Gaussian 09 software at the theoretical level of B3LYP/6-311 + G*. The partial atomic charges were fitted to an electrostatic surface potential using the CHELPG method. MD simulations were carried out by using the NAMD version 2.13 software. VMD software was used to take the snapshots. TRAVIS software is used to determine spatial distribution functions.

CONTEXT: The present study aims to improve the performance of optoelectronics and photovoltaics by constructing an acceptor-donor-acceptor (A-D-A) molecule with a fullerene-free acceptor moiety. The study utilizes malononitrile and selenidazole derivatives to tailor the molecule for enhanced photovoltaic abilities. The study analyzes molecular properties and parameters like charge density, charge transport, UV absorption spectra, exciton binding energies, and electron density difference maps to determine the effectiveness of the tailored derivatives. METHODS: To optimize the geometric structures, the study used four different functionals (B3LYP, CAM-B3LYP, MPW1PW91, and ɷB97XD) along with a double zeta valence basis set 6-31G(d, p) basis set. The study compared the results of the tailored derivatives with a reference molecule (R-P2F) to determine improvements in performance. The light harvesting efficiency of the molecules was analyzed by performing simulations in the gas and solvent phases (chloroform) based on the spectral overlap between the solar irradiance and the absorption spectra of the molecules. The open-circuit voltage (VOC) of each molecule was also analyzed, representing the maximum voltage that can be obtained from the cell under illuminated conditions. The findings indicated that the M1-P2F designed derivative is a more effective, with energy gap of 2.14 eV, and suitable candidate for non-fullerene organic solar cell application, based on various analyses such as power conversion efficiency, quantum chemical reactivity parameters, and electronic features.

CONTEXT: Heparin, 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°). METHODS: Computational 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.

CONTEXT: The evaluation of ionic conductivity through atomistic modeling typically involves calculating diffusion coefficients, which often necessitates simulations spanning several hundreds of nanoseconds. This study introduces a less computationally demanding approach based on non-equilibrium molecular dynamics applicable to a wide range of systems. METHOD: Ionic conductivity is determined by evaluating the Joule heating effect recorded during non-equilibrium molecular dynamics (NEMD) simulations. These simulations which involve applying a uniform electric field using classical force fields in LAMMPS are conducted within the MedeA software environment. The conductivity value for a specific temperature can thus be obtained from a single simulation together with an estimation of the associated uncertainty. Guidelines for selecting NEMD parameters such as electric field intensity and initial temperature are proposed to satisfy linear irreversible transport. RESULTS: The protocol presented in this study is applied to four different types of systems, namely, (i) molten NaCl, (ii) NaCl and LiCl aqueous solutions, (iii) solution of ionic liquid with two solvents, and (iv) NaX zeolites in the anhydrous and hydrated states. The main advantages of the proposed protocol are simplicity of implementation (eliminating the need to store individual ion trajectories), reliability (low electric field, linear response, no perturbation of the equations of motion by a thermostat), and a wide range of applications. The estimated contribution of field-induced drift motion of ions to kinetic energy appears very low, justifying the use of standard kinetic energy in the method. For each system, the reported influence of temperature, ion concentration, solvent nature, or hydration is correctly predicted.

CONTEXT: Some structural properties can be involved in the antioxidant capacity of several polyphenol derivatives, among them their simplified structures. This study examines the contribution of simplified structure for the antioxidant capacity of some natural and synthetic antioxidants. The resonance structures were related to the π-type electron system of carbon-carbon double bonds between both phenyl rings. Trans-resveratrol, phenyl-benzofuran, phenyl-indenone, and benzylidene-benzofuranone are the best basic antioxidant templates among the simplified derivatives studied here. Additionally, the stilbene moiety was found on the molecules with the best antioxidant capacity. Furthermore, our investigation suggests that these compounds can be used as antioxidant scaffold for designing and developing of new promising derivatives. METHODS: To investigate the structure-antioxidant capacity for sixteen simplified natural and proposed derivatives we have employed density functional theory and used Gaussian 09. Our DFT calculations were performed using the B3LYP functional and the 6-31+G(d,p) basis set. All electron transfer mechanisms were investigated by using values of HOMO, ionization potential, energy affinity, stabilization energies, and spin density distributions.

CONTEXT: In this study, the complete reaction mechanism of methanol decomposition on metallic Mo2C(001) and Mo/C-mixed Mo2C(101) hexagonal Mo2C crystalline phases was systematically investigated using plane-wave-based periodic density functional theory (DFT). The main reaction route for Mo2C(001) is as follows: CH3OH → CH3O + H → CH2O + 2H → CHO + 3H → CO + 4H → C + O + 4H. Hence, C, O, and H are the main products. It was found that the energy barrier for CO dissociation was low. Therefore, it was concluded that the Mo2C(001) surface was too active to be easily oxidized or carburized. The optimal reaction pathway for Mo2C(101) is as follows: CH3OH → CH3O + H → CH2O + 2H → CH2 + O + 2H → CH3 + O + H → CH4 + O. Therefore, CH4 is the major product. The hydrogenation of CH3 leading to CH4 showed the highest energy barrier and the lowest rate constant and should be the rate-determining step. In addition, the formation of CO + 2H2 was competitive on Mo2C(101), and the optimal path was CH3OH → CH3O + H → CH2O + 2H → CH2 + O + 2H → CH + O + 3H → C + O + 4H → CO + 2H2. The computed energy barrier and rate constant indicate that the rate-determining step is the last step in CO formation. In agreement with the experimental observations, the results provide insights into the Mo2C-catalyzed decomposition of methanol and other side reactions. METHODS: All calculations were performed by using the plane-wave based periodic method implemented in Vienna ab initio simulation package (VASP, version 5.3.5), where the ionic cores are described by the projector augmented wave (PAW) method. The exchange and correlation energies were computed using the Perdew, Burke and Ernzerhof functional with the latest dispersion correction (PBE-D3).

BACKGROUND: The 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. METHODS: The 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.

CONTEXT: Today, the treatment or prevention of cancer, which is one of the most important causes of death, has a very important place. On the other hand, the discovery of new antimicrobial agents is also important because of antibiotic resistance that can occur in humans. For these reasons, in this study, the synthesis, quantum chemical calculations, and in silico studies of a novel azo molecule with high bioactive potential were carried out. In the first step of the synthesis part, (3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)aniline compound, which is the raw material of the drug used in cancer treatments, was synthesized. In the second step, a novel product 2-hydroxy-5-((3-(4-methyl-1H-imidazol-1-yl)-5-trifluoromethyl)phenyl)diazenyl)benzaldehyde (HTB) was obtained as a result of the reaction of salicylaldehyde coupling to this compound. Then, as it was being spectroscopically described, its geometry was optimized. In order to perform quantum chemical calculations, the molecular structure, vibrational spectroscopic data, electronic transition absorption wavelengths, HOMO and LUMO analyses, molecular electrostatic potential (MEP) and potential energy surface (PES) of the molecule were all taken into consideration. Using molecular docking simulations, in silico interactions of the HTB molecule with some anticancer and antibacterial-related proteins were studied. In addition, the ADMET parameters of the HTB were also predicted. METHODS: The structure of the synthesized compound was elucidated using 1H-NMR, 13C-NMR (APT), 19F-NMR, FT-IR and UV-vis spectroscopic methods. The optimized geometry, molecular electrostatic potential diagram and vibrational frequencies of the HTB molecule were calculated at the DFT/B3LYP/6-311G(d,p) level. The TD-DFT method was used to calculate HOMOs-LUMOs and electronic transitions, and the GIAO method was used to calculate chemical shift values. It was observed that the experimental spectral data were in good agreement with the theoretical ones. Molecular docking simulations of the HTB molecule using 4 different proteins were investigated. Two of these proteins were involved in simulating anticancer activity and the other two in simulating antibacterial activity. According to molecular docking studies, the binding energies of the complexes formed by the HTB compound with the 4 selected proteins were between -9.6 and -8.7 kcal/mol. HTB showed the best affinity with VEGFR2 protein (PDB ID: 2XIR) and the binding energy of this interaction was found to be -9.6 kcal/mol. The HTB-2XIR interaction was examined with molecular dynamics simulation for 25 ns and it was determined that this complex was stable during this time. In addition, the ADMET parameters of the HTB were also calculated, and from these values, it was determined that the compound has very low toxicity and high oral bioavailability.

CONTEXT: Nanosensor 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. METHODS: Electronic 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.

CONTEXT: Energetic 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. METHODS: Gaussian16 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.

CONTEXT: High-energy density materials (HEDMs) have emerged as a research focus due to their advantageous ultra-high detonation performance and better sensitivity. The primary aim of this study revolves around crafting HEDMs that strike a delicate balance between exceptional performance and minimal sensitivity. Density functional theory (DFT) was utilized to evaluate the geometric structures, energies, densities, energy properties, and sensitivities of 39 designed derivatives. The theoretical density (ρ) and heat of formation (HOF) were used to estimate the detonation velocity (D) and pressure (P) of the title compounds. Our study shows that the introduction of fluorine-containing substituents or fluorine-free substituents into the CHOFN backbone or the CHON backbone can significantly enhance the detonation performance of derivatives. Derivative B1 exhibits the better overall performance, including superior density, detonation performance, and sensitivity (P = 58.89 GPa, D = 8.02 km/s, ρ = 1.93 g/cm3, and characteristic height H50 = 34.6 cm). Our molecular design strategy contributes to the development of more novel HEDMs with excellent detonation performance and stability. It also marks a significant step towards a material engineering era guided by theory-based rational design. METHODS: GaussView 6.0 was used for construction of molecular system coordinates, and Gaussian 16 was used to obtain optimal structures, energies, and volumes of all compounds at the B3LYP/6-31+G(d,p) level of theory. It was characterized to be the local energy minimum on the potential energy surface without imaginary frequencies at the same theory level. Molecular weight, isosurface area, and overall variance were obtained using the Multiwfn 3.3. The detonation properties of the materials were analyzed using the C-J thermodynamic detonation theory. Our broad analysis facilitated an extensive assessment of these properties.

CONTEXT: In this study, theoretical and experimental analysis of the electrical, optical, and structural properties of a wurtzite-like zinc oxide (ZnO) nanostructure has been done. To investigate how quantum confinement affects the optical characteristics, two distinct ZnO clusters in nanowire structures have been investigated. The [(ZnO)55(H2O)4] system's HOMO-LUMO band gap (BG) was calculated to be 2.99 eV, which is quite close to the experimental measurement. It was found that the BG decreases with the increase in the number of atoms in the cluster in connection with the quantum confinement in nanoclusters. In addition, the lowest excitation energy in TD-DFT calculations of the identical system is in fairly good agreement with the experimental value with a difference of 0.1 eV. We conclude that the CAM-B3LYP functional has highly successful in reproducing the experimental data reported in the present study and previously reported experimental data. METHODS: The geometrical optimization of two different sizes of ZnO clusters ([(ZnO)25(H2O)4] and [ZnO)55(H2O)4]) was performed using the CAM-B3LYP functional with no symmetry constraints applied in the gas phase. LANL2DZ basis sets were used for the Zinc (Zn) atom and 6-31G* basis sets for the O and H atoms. To determine their optical and electronic properties, excited state calculations of the pre-optimized structures were performed using the Time-Dependent DFT (TD-DFT) method. Multiwfn, Gaussum 3.0, and GaussView 5.0 programs were used to visualize the results.

CONTEXT: Proton transfer in acid-base systems is not well understood. Some acid-base reactions do not proceed to the extent that is expected from the difference in the pKa values between the base and acid in aqueous solutions, yet some do. In that regard, we have computationally studied the process of proton transfer from the acids of varying strength (benzenesulfonic acid (BSu), methansulfonic acid (MsO), and sulfuric acid (SA)) to the amines with different numbers of propyl substituents on the nitrogen atom (propylamine (PrA), dipropylamine (DPrA), and tripropylamine (TPrA)) upon complexation. Density functional theory calculations were used to thoroughly examine the energetic and structural aspects of the molecular complexes and/or ionic pairs resulting from the acid-base interaction. The potential energy curves along the proton transfer coordinate in these acid-amine systems were analyzed. The change in free energies accompanying the molecular complexes and ionic pair formations was calculated, and the relationship between the energy values and the ΔРА parameter (difference in proton affinity of the acid anion and amine) was established. The larger ΔРА values were found to be unfavorable for the formation of ionic pairs. Using structural, energy, QTAIM, and NBO analyses, we determined that the hydrogen bonds in the molecular complexes PrA-MsO and PrA-BSu are stronger than those in their corresponding ionic pairs. The ionic pairs with the TPrA cation possess the strongest hydrogen bonds of all the ionic pairs being studied, regardless of the anion. The results showed that hydrogen bonding interactions in the molecular complexes contribute significantly to the energies of the acid-base interaction, while in the ionic pairs, the most important energy contribution comes from Coulomb interactions, followed by hydrogen bonding and dispersion forces. The ionic pairs with propylammonium, dipropylammonium, and tripropylammonium cations have stronger ion-ion interactions than tetrapropylammonium (TetPrA)-containing ionic pairs with the same anions. This effect rises with the order of the cation: TetPrA → TPrA → DPrA → PrA, and the sequence of anions is SA → BSu → MsO. The results obtained here expand the concept of acid-base interaction and provide an alternative to experimental searches for suitable acids and bases to obtain new types of protic ionic liquids. METHODS: All quantum-chemical calculations were carried out by using the DFT/B3LYP-GD3/6-31++G(d,p) level as implemented in the Gaussian 09 software package. For the resulting structures, the electron density distribution was analyzed by the "atoms in molecules" (QTAIM) and the natural bond orbital (NBO) methods on the wave functions obtained at the same level of theory by AIMAll Version 10.05.04 and Gaussian NBO Version 3.1 programs, respectively.

CONTEXT: SF6 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. METHODS: The 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.

CONTEXT: Natural 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. ([Formula: see text]) 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. METHODS: 1N2PE was obtained from Aniba canelilla, whose essential oil is constituted of [Formula: see text] 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 [Formula: see text]C during 7 days and after that, 50 mg of 1N2PE (80%) were diluted in 100 [Formula: see text]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 [Formula: see text] 0.25 mm [Formula: see text] 0.25 [Formula: see text]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[Formula: see text]. 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.

CONTEXT: The present work describes the synthesis, structural characterization, and catalytic activity of a Co(II)-based one-dimensional coordination polymer (CP1). To validate the chemotherapeutic potential of CP1, in vitro DNA binding assessment was carried out by employing multispectroscopic techniques. Moreover, the catalytic activity of CP1 was also ascertained during the oxidative conversion of o-phenylenediamine (OPD) to diaminophenazine (DAP) under aerobic conditions. METHODS: The molecular structure of CP1 was solved with the olex2.solve structure solution program using charge flipping and refined with the olex2.refine refinement package by using Gauss-Newton minimization. The DFT studies were performed by utilizing ORCA Program Version 4.1.1 to calculate the electronic and chemical properties of CP1 by calculating the HOMO-LUMO energy gap. All calculations were carried out at B3LYP hybrid functional using def2-TZVP as the basis set. Contour plots of various FMOs were visualized by using Avogadro software. Hirshfeld surface analysis was carried out by Crystal explorer Program 17.5.27 to examine the various non-covalent interactions which are crucial for the stability of crystal lattice. In addition, molecular docking studies of CP1 with DNA were performed by using AutoDock Vina software and AutoDock tools (version 1.5.6). Discovery studio 3.5 Client 2020 was used for visualization of the docked pose and binding interactions of CP1 with ct-DNA.

CONTEXT: Degradation 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. METHODS: For 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. RESULTS: Among 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.

CONTEXT: The dye-sensitized solar cell is a technology unique in its light conversion properties as it operates with record efficiencies in diffused light conditions. The choice of the appropriate sensitizer is one of the important strategies to improve photovoltaic performance of DSSC devices. This theoretical study mainly aims to determine the impact of the π-spacer on the geometric and optoelectronic parameters of sensitizer dyes. For that, we have chosen six organic dyes of Donor-π-Acceptor structure based on triphenylamine unit as electron donor, cyanoacrylic acid as electron acceptor with various π-bridges. The results indicated that the doping process modify dihedral angles and electronic properties by enhancing the planarity and decreasing the gap energy. We have examined the optoelectronic and photovoltaic properties of studied triphenylamine based-dyes. Introducing thiophene and furan as π-spacer groups in D6 dye can effectively decrease the gap energy (Egap = 2.21 eV), broaden the absorption range (λmax = 671.19 nm), and promote the light-harvesting properties. The D2 dye based on two pyrrole units presents an improved electron injection driving force (ΔGinject = - 2.269 eV) and regeneration driving force corresponding to better charge separation. The π-bridge groups can efficiently tune the optoelectronic and photovoltaic properties of sensitizers, which contribute to the efficiency of solar cells. METHODS: The geometrical and electronic properties of all systems were studied by the DFT method using the correlation exchange functional B3LYP combined with 6-31G(d, p) basis set. On the other hand, the maximum absorption wavelengths λmax and the corresponding oscillator strengths were calculated using the hybrid functional BHandHLYP and 6-31+G(d) basis set. The solvent tetrahydrofuran (THF) are used to study the effect of the solvent, using the "Conductor-Polarizable Continuum" (C-PCM) model. All calculations were performed using Gaussian 09 program.

CONTEXT: Heavy 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. METHODS: HSE06 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.

CONTEXT: Organic-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. METHODS: To 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.

CONTEXT: The 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). METHODS: The 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.

CONTEXT: Due to the expected decrease in the availability of conventional oils, numerous studies are currently underway to find complementary sources of energy. Among the explored avenue is that of biofuels. Ethyl valerate (ETV) and tripropionin (TPP) are two biofuels whose thermal decomposition has not received the attention it deserves. Herein, we have evaluated the bond dissociation enthalpies (BDHs) to predict how easy it is to break some bonds in these compounds, and subsequently contribute to revealing the initiation step in their combustion reactions. Our computations consistently predict C4-C5 and C1-C2 bonds in ETV and TPP as the weakest bonds, likely to break first and initiate the thermal decomposition of these two compounds, respectively. The conformational changes in ETV and TPP have only a small influence on the BDHs of 1 kcal/mol at M06-2X/6-311 + G(3df,2p). B3LYP and ωB97XD appear to be the most affordable methods for estimating BDHs at 6-31G(d,p) as they give good results for ETV (RMSD: 2.94 kcal/mol and 3.22 kcal/mol) and performed better than CBS-QB3 (RMSD: 3.64 kcal/mol). Using a larger basis set, the M06-2X (RMSD: 3.61 kcal/mol) and ωB97XD (RMSD: 3.51 kcal/mol) functionals are found to provide the most accurate predictions at 6-311 + G(3df,2p) as compared to G4MP2. METHODS: BDHs of ETV and TPP are computed using density functional theory (DFT) and quantum chemistry composite methods at 6-31G(d,p) and 6-311 + G(3df,2p) levels. Because of its reliability and accuracy in thermochemical calculations, the G4MP2 theory is used as a reference to gauge the performance of DFT methods. All the calculations were carried out using the Gaussian 09 program.

CONTEXT: Cationic 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. METHODS: The 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).

CONTEXT: Heavy metals are highly noxious, and their presence can cause diverse effects on living organisms and the environment. Crown ether porphyrins and phthalocyanines are known to effectively extract these pollutants and are also used in photovoltaic devices. This study aims to evaluate various factors that govern intramolecular charge transfer (ICT) and photo-injection processes, including maximum absorption wavelength (λmax), density of states (DOS), charge transfer dipole (μCT), light harvesting efficiency (LHE), open-circuit voltage (Voc), and free energy change of electron injection (ΔGinj) in order to investigate the performance of different compounds designed from metalloporphyrins for bulk-heterojunction organic solar cell (BHJ-OSC) applications. The porphyrin complex showed the best optoelectronic properties, with remarkable LHE values and CT amounts compared to phthalocyanine derivatives. The central metal played a significant role in optimizing the optical properties of the materials for use in solar cells. HgPr4O and CdPr4O were found to have optimal Voc values, resulting in effective injection, high electron, and hole mobilities, making them ideal materials for highly efficient BHJ-OSC devices. METHODS: Density functional theory (DFT) approach was employed with the B3LYP functional and the def2TZVP basis set as implemented in the Gaussian 16 revision C.01 program to investigate the designed complexes and to compute geometrical parameters, frontier molecular orbitals (FMOs), and natural bond orbital (NBO). Furthermore, the time-dependent density functional theory (TD-DFT) method was used to analyze the optical properties and photovoltaic characteristics of selected metalloporphyrins by examining the UV-Vis spectra. In summary, the study presents a thorough description of the structural and electronic properties of the investigated complexes and provides insights into their potential use in photovoltaic applications.

CONTEXT: Staphylococcus aureus is a highly pathogenic organism that is the most common cause of postoperative complications as well as severe infections like bacteremia and infective endocarditis. By mediating the formation of biofilms and the expression of virulent genes, the quorum sensing (QS) mechanism is a major contributor to the development of these diseases. By hindering its QS network, an innovative approach to avoiding this bacterial infection is taken. Targeting the AgrA of the Agr system serves as beneficial in holding the top position in the QS system cascade. METHODS: Using known AgrA inhibitors, the machine learning algorithms (artificial neural network, naïve Bayes, random forest, and support vector machine) and pharmacophore model were developed. The potential lead compounds were screened against the Zinc and COCONUT databases using the best pharmacophore hypothesis. The hits were then subjected second screening process using the best machine learning model. The predicted active compounds were then reranked based on the docking score. The stability of AgrA-lead compounds was studied using molecular dynamics approaches, and an ADME profile was also carried out. Five lead compounds, namely, CNP02386963,4,5-trihydroxy-2-[({7,13,14-trihydroxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.04,16.011,15]hexadeca-1(14),4,6,8(16),11(15),12-hexaen-6-yl}oxy)methyl]benzoic acid, CNP0129274 4-(dimethylamino)-1,5,6,10,12,12a-hexahydroxy-6-methyl-3,11-dioxo-3,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, CNP0242717 3-Hydroxyasebotin, CNP0361624 3,4,5-trihydroxy-6-[(2,4,5,6,7-pentahydroxy-1-oxooctan-3-yl)oxy]oxane-2-carboxylic acid, and CNP0285058 2-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}-2-(4-hydroxyphenyl)acetonitrile were obtained using the two-step virtual screening process. The molecular dynamics study revealed that the CNP0238696 was found to be stable in the binding pocket of AgrA. ADME profiles show that this compound has two Lipinski violations and low bioavailability. Further studies should be performed to assess the anti-biofilm activity of the lead compound in vitro.

CONTEXT AND RESULTS: 2,4,6-triazide-1,3,5-triazine (TAT) has received widespread attention for its great potential to synthesize or convert to nitrogen-rich high energy density materials (HEDMs). The TAT structure alteration in the compression process up to 30 GPa has characteristics as follows: (a) [N3] groups straighten; (b) [N3] groups gather toward the six-membered C-N heterocycles. At about 5 GPa, Raman peak split at 700 cm-1 was observed both in calculation and in-situ Raman experiment, which is caused by pressure-induced intramolecular stress. Besides, the broad band of the amorphous two-dimensional C=N network (centered at 1630 cm-1) occurred at about 12 GPa. Meantime, the study on electronic features suggests the pressure-induced deformation in TAT molecular structure cause the discontinuous change of band gap at about 4.5 GPa and 8.0 GPa, respectively. COMPUTATIONAL AND THEORETICAL TECHNIQUES: The static compression process of TAT was explored in the range of 0-30 GPa by using dispersion corrected density functional theory (DFT-D) calculations combined with in-situ Raman experiment. The GGA/PBE+G06 method that has less errors than other calculation methods was used to predict the geometry structure, vibrational properties and electronic structure of TAT under pressure.

CONTEXT: We investigated the interaction between glycine and Li+ in water environment based on the Gly·Li+(H2O)n (n = 0-8) cluster. Our study shows that for Gly·Li+, Li+ binds to both carbonyl oxygen and amino nitrogen to form a bidentate structure, and the first three water molecules preferentially interact with Li+. For n = 0-5, the complexes of Gly·Li+(H2O)n exist in neutral form, and when the water number reached 6, the complex can coexist in neutral and zwitterionic form, then zwitterionic structures are dominant for n = 7, 8. The analyses by RDG, AIM, and ESP in conjunction with the calculated interaction energies show that the interaction between Li+ and Gly decreases gradually with the water molecules involved successively from n = 1 to 6 and then increases for n = 7-8. Additionally, the infrared spectra of Gly·Li+(H2O)n (n = 0-8) are also calculated. METHODS: The initial structures were optimized using Gaussian 09 program package in B3LYP-D3 (BJ)/6-311G(d, p) method, and the frequency was calculated with 6-311 + G(2d, p) basis set. GaussView5.0.9 was used to view simulation infrared spectra. The noncovalent interaction method (NCl), energy decomposition (EDA), atoms in molecules (AIM) analysis, and electrostatic potential (ESP) analyses were conducted using Multiwfn software to gain a deeper understanding of the interaction properties of Gly, Li+, and water.

CONTEXT: In 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. METHODS: Density 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.

CONTEXT: Plastic 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. METHODS: In 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.

CONTEXT: The detection and monitoring of CO gas are essential to avoid human health problems. Therefore, the CO adsorption on Pd2 and PdCo dimers deposited on pyridinic Nx-doped graphene (PNxG; x = 1 - 3) was investigated employing the auxiliary density functional theory. In the most stable arrangements for the Pd2 dimer supported on PNxG, a Pd atom is in the PNxG vacancy, and the other Pd atom is placed on C atoms. For the PdCo dimer deposited on PNxG, the most stable interaction is like Pd2 dimer supported on PNxG, but with the Co atom centered over the vacancy site. Concerning the stability of the Pd2 and PdCo dimers supported on PNxG, the interaction energies (Eint) of the PdCo dimer deposited on PNxG are higher than those obtained with the Pd2 dimer. Also, the Eint of Pd2 and PdCo dimers deposited on PNxG are higher than those supported on pristine graphene. The CO adsorption energies on Pd2/PNxG and PdCo/PNxG composites are higher than those reported in the literature for pristine graphene, showing that the Pd2/PNxG and PdCo/PNxG composites have a good sensitivity toward the CO molecule. METHODS: All electronic structure calculations were performed using the auxiliary density functional theory implemented in the deMon2k program. For exchange and correlation functional, the revised PBE was used. The Pd atoms were treated with an 18-electron QECP|SD basis set, while the remaining atoms were subjected to a DZVP-GGA basis set. The GEN-A2* auxiliary-function-set was used for all computations.

CONTEXT: Molecular 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. METHODS: We 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.

CONTEXT: As 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. METHOD: The 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.

CONTEXT: Since 1991 when Grätzel et al. improved the conversion efficiency of dye-sensitized solar cells to 7.1% by applying nano technology as the first time, the researches on dye-sensitized solar cells have received widely attentions. The organic dye without precious metals has a lower cost, which is easily to get synthesized and its structure is easily decorated, owing a higher photoelectric conversion efficiency at the same time. Therefore, in recent years, the organic dye has attracted people's attentions more and more. In order to better understand the relationship between structure and properties of dye molecules, with ZL003 as a prototype, molecular modifications are then made and a scheme, with rigid fused π-bridge comprising electron-rich and deficient segments. The calculated results indicate that the π-bridge containing dithienopyrrolobenzothiadiazole and dipyrrolo-dithienobenzothiadiazole as π-bridge has been demonstrated to be successful to significantly redshift the absorption maximum wavelength, extend the lifetime of the first excited state, and decrease the energy gap between the highest occupied molecule orbital (HOMO) and the lowest unoccupied molecule orbital (LUMO). It is hoped that the calculation result of this paper would provide theoretical basis for the experimental synthesis of more efficient dye molecules. METHOD: All calculations were performed in Gaussian 09 program package. The ground state geometries (S0) and the first excited state (S1) were optimized using density function theory (DFT) with the hybrid function B3LYP functional, coupled with the 6-31G(d, p) basis set for optimization of molecule ground state conformations. TD-DFT calculations of excited state energies and absorption spectra were performed using MPWPW91 functional combined with the 6-31 + G (d) basis set.

CONTEXT: At the interface of W-Cu after direct jointing, diffusion layers with a thickness of approximately 22 nm are present but often overlooked in simulations of mechanical properties. In this study, an interface model with a W-Cu diffusion layer is developed using molecular dynamics (MD). The effects of the diffusion layers on the elastic-plastic behaviors, dissipation mechanisms, and fracture properties of the interface are analyzed under mode-I (perpendicular to the interface) and mode-II (parallel to the interface). The results demonstrate that the interface model with a diffusion layer exhibits superior mechanical properties under mode-I and mode-II loading compared to the model without a diffusion layer. Furthermore, a multi-scale method based on the classical Paris law is proposed, combining MD and finite element methods to investigate the fatigue crack propagation of W-Cu bimetallic composites under cyclic loading and predict their fatigue life. The findings of this study are meaningful for improving the mechanical properties of W-Cu interface materials, predicting the material's lifespan, and guiding related engineering applications. METHODS: In this study, the molecular dynamics simulations have been carried out by using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The visualization of results is performed using the Open Visualization Tool (OVITO). Common neighbor analysis (CNA) and dislocation analysis (DXA) in OVITO have been employed to capture the structural evolution. Finite element method simulations are performed in Ansys Workbench.

CONTEXT: How to elucidate the effect of alkali metal promoters on gold-catalyzed water-gas shift reaction intrinsically remains a challenging, because that the complex synergy effects such as strong metal-support interactions, interfacial effects, and charge transfer of supported metal catalysts makes people difficulty in the understanding the alkali promotion phenomenon in nature. Herein, we report a systematically study of whole water-gas shift reaction mechanism on pure and the K-modified defected-Au(211) (i.e., by removing one surface Au atom from perfect Au(211) and make one model with the Au-Au coordination number is six) by using the microkinetic modeling based on first principles. Our results indicate that the presence of K can increase the adsorption ability of oxygen-containing species via the attractive coulomb interaction, has no significant effect on the adsorption of H species, but inhibits the adsorption of CO due to the steric effect. K promoter stabilizes the water adsorption by ~0.3 eV, which results in one order increasing of whole reaction rate. Interestingly, the strong promotion effect of the K can be assigned to the significant direct space interaction between K and the adsorbate H2O* through the inducted electric field, which can be further confirmed by the posed negative electric field on the unpromoted D-Au(211). Microkinetic modeling results revealed that the carboxyl mechanism is the most likely to occur, redox mechanism is the next one, and the formate mechanism is the least likely to occur. For different kinds of alkali metal additives, the adsorption strength of water molecules gradually weakens from Li to Cs, but Na shows the best promoter behavior at the low temperature. By considering the effect of K contents on the reactivity of water-gas shift reaction, we found that the K with the medium coverage (~0.2~0.3 ML) has the strongest promoting effect. It is expected that the conclusion of this work can be extended to other WGSR catalytic systems like Cu(or Pt). METHODS: All calculations were performed by using the plane-wave based periodic method implemented in Vienna ab initio simulation package (VASP, version 5.4.4), where the ionic cores are described by the projector augmented wave (PAW) method. The exchange and correlation energies were computed using the Perdew, Burke and Ernzerhof functional with the vdw correction (PBE-D3). The transition states (TSs) were searched using the climbing image nudged elastic band (CI-NEB) method. Some electronic structure properties like work function was predicated by the DS-PAW software. Microkinetic simulation was carried out using MKMCXX software.

CONTEXT: l-Tyrosine is a naturally occurring agent that acts as a precursor in biosynthesis of monoaminergic neurotransmitters in brain such as dopamine, adrenaline, noradrenaline, and hormones like thyroxine and triiodothyronine. While l-tyrosine in vacuo adopts the canonical aminoacid form with -NH2 and -COOH functional groups, from neutral solutions, is crystallizes in the zwitterionic form possessing -NH3+ and -COO- groups. As l-tyrosine is non-innocent agent with respect to redox processes, redox ability in water expressed by the absolute oxidation and reduction potentials is investigated. The cluster analysis applied to a set of nine related neurotransmitters and trace amines confirms that l-tyrosine is mostly similar to aminoacid forms of phenylalanine, octopamine, and noradrenaline. METHODS: The energetic data at the Hartree-Fock MO-LCAO-SCF method has been conducted using def2-TZVP basis set, and improved by the many-body perturbation theory using the MP2 correction to the correlation energy. For the aminoacid form and the zwitterionic form of l-tyrosine, a set of molecular descriptors has been evaluated (ionization energy, electron affinity, molecular electronegativity, chemical hardness, electrophilicity index, dipole moment, quadrupole moment, and dipole polarizability). The solvent effect (CPCM) is very expressive to the zwitterionic form and alters the sign of the electron affinity from positive to negative values. In parallel, density-functional theory with B3LYP variant in the same basis set has been employed for full geometry optimization of the neutral and ionized forms of l-tyrosine allowing assessing the adiabatic (a) ionization/affinity processes. The complete vibrational analysis enables evaluating thermodynamic functions such as the inner energy, enthalpy, entropy, Gibbs energy, and consequently the absolute oxidation and reduction potentials. Of applied methods, the most reliable are B3LYP(a) results that account to the correlation energy and the electron and nuclear relaxation during the ionization/affinity processes.

CONTEXT: In this work, a series of heterocyclic alkenes were prepared by the reaction of 2-hydroxy-1-naphthaldehyde with various heterocyclic active methylene compounds via Knoevenagel condensation reaction using mesoporous silica, MCM 41, supported perchloric acid as an efficient green catalytic system under solvent-free conditions. A comparative study of the conventional method vs the green method was also reported with the same raw materials. 1H NMR, 13C NMR, IR, and mass spectroscopic techniques were used for the characterization of synthesized compounds. METHODS: Computational study was performed for these compounds by applying density functional theory (DFT) at M06 functional and 6-311G (d,p) basis set to interpret the electronic structures and counter check the experimental findings. The frequency analysis with aforementioned levels of DFT was performed to confirm the stability associated with optimized geometries. The true minimum for the optimized geometries for 1, 2, and 3 was achieved as indicated by the absence of negative eigenvalues in all the calculated frequencies. Additionally, natural bond orbitals (NBOs) and nonlinear optical (NLO) properties were explored utilizing the aforementioned level and basis set combination via DFT, whereas the frontier molecular orbitals (FMOs) evaluation was done at time-dependent density functional theory TDDFT at M06/6-311G(d,p). The global reactivity parameters were also calculated using the FMO data. These computation-based outcomes were found in good agreement with the experimental findings.

CONTEXT: The design and synthesis of safe and highly active sulfonylurea herbicides is still a challenge. Therefore, following some principles of structure-activity relationship (SAR) of sulfonylurea herbicides, this work focuses on evaluating two sulfonylurea derivatives bearing electron-withdrawing substituents, namely, -(CO)OCH3 and -NO2 on the aryl group, on herbicidal activity. To understand the effects caused by the substituent groups, the molecular and electronic structures of the sulfonylureas were evaluated by density functional theory. Likewise, the crystalline supramolecular arrangements of both compounds were analyzed by Hirshfeld surface, QTAIM, and NBO, with the aim of verifying changes in intermolecular interactions caused by substituent groups. Finally, through a toxicophoric analysis, we were able to predict the interacting groups in their biological target, acetolactate synthase, and verify the interactions with the binding site. METHODS: All theoretical calculations were conducted using the highly parameterized empirical exchange-correlation functional M06-2X accompanied by the diffuse and polarized basis set 6-311++G(d,p). The atomic coordinates were obtained directly from the crystalline structures, and from the energies of the frontier molecular orbitals (HOMO and LUMO), chemical descriptors were obtained that indicated the influence of the functional groups in the sulfonylureas on the reactivity of the molecules. The intermolecular interactions in the crystals were analyzed using the Hirshfeld, QTAIM, and NBO surfaces. Toxicophoric modeling was performed by the PharmaGist webserver and molecular docking calculations were performed by the GOLD 2022.1.0 software package so that the ligand was fitted to the binding site in a 10 Å sphere. For this, genetic algorithm parameters were used using the ChemPLP scoring function for docking and ASP for redocking.

CONTEXT: We report on atomic level of detail analyses of polymer composite models featuring epoxy resin interfaces to silica, iron oxide, and cellulose layers. Using "reactive" molecular dynamics simulations to explore epoxy network formation, resin hardening is investigated in an unprejudiced manner. This allows the detailed characterization of salt-bridges and hydrogen bonds at the interfaces. Moreover, our sandwich-type composite systems are subjected to tensile testing along the interface normal. To elucidate the role of relaxation processes, we contrast (i) direct dissociation of the epoxy-metal oxide/cellulose contact layer, (ii) constant strain-rate molecular dynamics studies featuring (visco-)elastic deformation and bond rupture of the epoxy resin, and (iii) extrapolated relaxation dynamics mimicking quasi-static conditions. While the fracture mechanism is clearly identified as interface dissociation of the composite constituents, we still find damaging of the nearby polymer phase. The observed plastic deformation and local cavitation are rationalized from the comparably large stress required for the dissociation of salt-bridges, hydrogen bonds, and van der Waals contacts. Indeed, the delamination of the contact layers of epoxy resins with slabs of silica, magnetite, and cellulose call for a maximum stress of 33, 26, and 21 MPa, respectively, as compared to 84 MPa required for bulk epoxy yielding. METHODS: Molecular dynamics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code were augmented by a Monte Carlo-type procedure to probe epoxy bond formation (Macromolecules 53(22): 9698-9705). The underlying interaction models are split into conventional Generalized Amber Force Fields (GAFF) for non-reacting moieties and a recently developed reactive molecular mechanics potential enabling epoxy bond formation and cleavage (ACS Polymers Au 1(3): 165-174).

CONTEXT: From 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. METHODS: All 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.

CONTEXT: The article explores and compares the electronic structure and magnetic properties of transition metal phosphate materials, namely FePS3, CoPS3, and NiPS3. RESEARCH FINDINGS: Analysis of the optimized configuration reveals significant insights into the electronic properties of MnPS3 clusters. Electrons within the cluster exhibit a flow from the metal atom M and the non-metal atom P to the non-metal atom S. The S atom serves as the primary site for electrophilic reactions within the cluster, while the metal atom hosts the main site for nucleophilic reactions. Configurations 2a(2), 2b(2), 3a(4), 3b(3), and 3c(2) exhibit enhanced electron mobility and optimal electronic properties. Moreover, the analysis of the magnetic properties of the optimized configurations demonstrates that the magnetic behavior of MnPS3 clusters is influenced by the spin motion of α electrons in the p orbital. Metal atoms make a relatively significant contribution to the magnetic properties of MnPS3 clusters. Configurations 1b(3), 2c(4), and 3a(4) exhibit comparatively higher magnetic properties compared to other configurations of the same size. This study identifies the optimal configuration for the magnetic and electronic properties of transition metal phosphorothioate materials. It also elucidates the trends in magnetic and electronic properties as the number of metal atoms varies, thereby providing valuable theoretical support for the application of these materials in the fields of magnetic materials and electronic devices. METHODS: In this study, the Fe-based transition elements, namely Fe, Co, and Ni, are selected as the metal atoms M. The cluster MPS3 is used to simulate the local structure of the material, allowing for an investigation into the influence of the metal atoms on its electronic and magnetic properties. By increasing the number of metal atoms and expanding the cluster size, the variations in these properties are explored. Density functional theory (DFT) calculations are performed using the B3LYP functional within the Gaussian09 software package. The MnPS3 cluster is subjected to optimal calculations and vibrational analysis at the def2-tzvp quantization level, resulting in optimized configurations with different spin multiplet degrees. Quantum chemistry software GaussView, wave function analysis software Multiwfn, and plotting software Origin are utilized for data characterization and graphical representation of the magnetic and electronic properties of the optimized configurations. Through the employment of these computational tools, valuable insights into the magnetic and electronic properties of the MnPS3 cluster and its dependency on different metal atoms are obtained.

CONTEXT: Protein-protein interaction (PPI) is a key component linked to virtually all cellular processes. Be it an enzyme catalysis ('classic type functions' of proteins) or a signal transduction ('non-classic'), proteins generally function involving stable or quasi-stable multi-protein associations. The physical basis for such associations is inherent in the combined effect of shape and electrostatic complementarities (Sc, EC) of the interacting protein partners at their interface, which provides indirect probabilistic estimates of the stability and affinity of the interaction. While Sc is a necessary criterion for inter-protein associations, EC can be favorable as well as disfavored (e.g., in transient interactions). Estimating equilibrium thermodynamic parameters (∆Gbinding, Kd) by experimental means is costly and time consuming, thereby opening windows for computational structural interventions. Attempts to empirically probe ∆Gbinding from coarse-grain structural descriptors (primarily, surface area based terms) have lately been overtaken by physics-based, knowledge-based and their hybrid approaches (MM/PBSA, FoldX, etc.) that directly compute ∆Gbinding without involving intermediate structural descriptors. METHODS: Here, we present EnCPdock ( https://www.scinetmol.in/EnCPdock/ ), a user-friendly web-interface for the direct conjoint comparative analyses of complementarity and binding energetics in proteins. EnCPdock returns an AI-predicted ∆Gbinding computed by combining complementarity (Sc, EC) and other high-level structural descriptors (input feature vectors), and renders a prediction accuracy comparable to the state-of-the-art. EnCPdock further locates a PPI complex in terms of its {Sc, EC} values (taken as an ordered pair) in the two-dimensional complementarity plot (CP). In addition, it also generates mobile molecular graphics of the interfacial atomic contact network for further analyses. EnCPdock also furnishes individual feature trends along with the relative probability estimates (Prfmax) of the obtained feature-scores with respect to the events of their highest observed frequencies. Together, these functionalities are of real practical use for structural tinkering and intervention as might be relevant in the design of targeted protein-interfaces. Combining all its features and applications, EnCPdock presents a unique online tool that should be beneficial to structural biologists and researchers across related fraternities.