Intermolecular interactions in ethanol solution of OABA: Raman, FTIR, DFT, M062X, MEP, NBO, FMO, AIM, NCI, RDG analysis

In silico identification for flavor antioxidant compounds in Chrysanthemi flos uncovers the interactions between saccharides and secondary metabolites

Secondary metabolites and saccharides are responsible for antioxidant activity and flavor of Chrysanthemi flos (CF). However, the flavor antioxidant compounds of CF and their intermolecular interactions remain unclear. Here, we primarily employed in silico methods to identify CF antioxidants. After characterizing by physicochemical properties, FT-NIR and HPLC fingerprint, the "spectrum-effect" fusion correlation was established to select the spectral features of CF antioxidants. Quercetagitrin (QU), chlorogenic acid (CA) and saccharides fragments were clarified based on their characteristic spectrum. The antioxidant efficacy as well as the sweet and bitter taste of these compounds were verified by molecular docking. Quantum chemical calculations demonstrated that non-covalent interactions dominant facilitated the stable existence of CF antioxidants. The most significant binding types between CA, QU and saccharides fragments were hydrogen bonding. These results indicate a novel approach and theoretical support to discovery of new information pertinent to the bioactive compounds related to CF or other tea.

Theoretical study of the interaction of the potentially toxic contaminants Hg2+, CH3Hg+, CH3CH2Hg+, and C6H5Hg+ with a B3O3 monolayer matrix

CONTEXT

The mercury ion Hg2+, and its derivatives, organomercurials are high toxicity to humans due their ability to bioaccumulate. In view of these problems, studies of the interaction of these potentially toxic compounds with matrices allow verify if they can be detected, or help determine their adsorptive capacity. In this context, the work aims to theoretically evaluate the interaction between the B3O3 matrix and the potentially toxic compounds Hg2+, CH3Hg+, CH3CH2Hg+, and C6H5Hg+. The binding energy values showed that the interaction occurs effectively; being spontaneous and exothermic for all the interactions evaluated. The structural properties demonstrate that mercury interacts with the oxygen atoms of the B3O3 matrix, with bond lengths ranging from 2.365 to 3.777 Å and that all organomercurials form hydrogen bonds. The topological parameters of quantum theory of atoms in molecules (QTAIM) categorized the nature of the interactions in electrostatic for Hg…O. The non-covalent interaction analyses presented a bluish color, between Hg and matrix oxygen indicating a strong attraction interaction and Van der Waals interactions ( green color) for the interaction of the organic group and B3O3. Thus, it can be confirmed that the study showed that the B3O3 matrix is efficient for the interactions, enabling future experimental studies of the application of this matrix in adsorptive processes or for molecular filters.

METHODS

All calculations of density functional theory were performed using the program Gaussian 16 and the structures of B3O3 matrix, Hg2+, CH3Hg+, CH3CH2Hg+, and C6H5Hg+ were generated using the GaussView program. The optimization and vibrational frequency calculations were performed using the functional ωB97XD and 6-31G(d,p) basis set for the H, B, C, and O atoms, while for the Hg atom the basis set used was CEP-31G with compact effective pseudopotential. All analyses were conducted at this level of theory. The quantum theory of atoms in molecules analysis were performed using AIMALL software. Non-covalent interaction calculations were carried out using Multiwfn software, and the structures were visualized using the visual molecular dynamics program.

Investigating the molecular interactions of two long-chain PFASs with human serum albumin: Insights from multispectral analysis and computational methods

Long-chain perfluoroalkyl substances (FPAS) are commonly detected in environmental and biological contexts. This study investigated the interactions of perfluoroundecanoic acid (PFUnDA) and perfluorotridecanoic acid (PFTrDA) with human serum albumin (HSA). Fluorescence quenching experiments demonstrated static quenching of HSA's intrinsic fluorescence by both PFUnDA and PFTrDA, resulting in the formation of stable HSA-PFAS complexes. At 298 K, PFUnDA exhibited a higher binding constant (5.50 × 107 L/mol) than PFTrDA (1.01 × 105 L/mol), indicating stronger binding affinity. Thermodynamic analysis indicated that hydrogen bonds and van der Waals forces were the predominant interactions in the binding processes. Molecular docking confirmed that both PFASs bind to the IIA subdomain of HSA, with PFUnDA exhibiting lower binding energy (-8.690 kcal/mol) than PFTrDA. Molecular dynamics simulations further supported these findings, with PFUnDA showing stronger binding energy (-13.894 kcal/mol) driven primarily by van der Waals forces and electrostatic interactions. Quantum chemical analysis reveals that the carbonyl groups in PFUnDA and PFTrDA exhibit significant molecular reactivity, indicating a propensity for more vigorous chemical interactions. This study not only reveals the potential biological activity of PFUnDA and PFTrDA, but also provides scientific basis for evaluating their biosafety and risks.

The molecular structure, vibrational spectra, solvation effect, non-covalent interactions investigations of psilocin

Psilocin, or 4-HO-DMT (or 3-(2-dimethylaminoethyl)-1H-indol-4-ol), is a psychoactive alkaloid substance from the tryptamine family, isolated from Psilocybe mushrooms. This substance is being studied by various research groups because it has a clear therapeutic effect in certain dosages. In this work, the study of the structure and properties of psilocin was carried using theoretical methods: the effects of polar solvents (acetonitrile, dimethylsulfoxide, water, and tetrahydrofuran) on the structural parameters, spectroscopic properties (Raman, IR, and UV-Vis), frontier molecular orbital (FMO), molecular electrostatic potential (MEP) surface, and nonlinear optical parameters (NLO). Theoretical calculations were performed at the B3LYP/6-311++G(d,p) level by the density functional theory (DFT) method. IEFPCM was used to account for solvent effects. The types and nature of non-covalent interactions (NCI) between psilocin and solvent molecules were determined using Atoms in Molecules (AIM), the reduced density gradient method (RDG), the electron localization function (ELF), and the localization orbital locator (LOL). Experimental and calculated FT-IR, FT-Raman, and UV-Vis spectra were compared and found to be in good agreement.

Applied Investigation of Methyl, Ethyl, Propyl, and Butyl Mercaptan as Potential Poisons in the Gas Phase Polymerization Reaction of Propylene

The polypropylene (PP) synthesis process is crucial in the plastics industry, requiring precise control as it directly impacts the catalytic activity and the final product's performance. This study investigates the effects of trace amounts of four different mercaptans on the polymerization of propylene using a fourth-generation Ziegler-Natta (ZN) catalyst. Various concentrations of these mercaptans were tested, and results showed that their presence significantly reduced the melt flow index (MFI) of the final PP. The most notable MFI decrease occurred at 37.17 ppm of propyl mercaptan and 52.60 ppm of butyl mercaptan. Methyl and ethyl mercaptan also reduced the MFI at lower concentrations, indicating that mercaptans act as inhibitors by slowing down the polymerization process and reducing the fluidity of molten PP. The highest MFI increase was observed at lower concentrations of each mercaptan, suggesting that smaller molecular inhibitors require less concentration. This trend was also seen in the catalyst's productivity, where lower concentrations of methyl mercaptan reduced PP production more effectively than higher concentrations of butyl mercaptan. Fourier transform infrared spectroscopy (FTIR) identified interactions between the mercaptans and the ZN catalyst. Computational analysis further supported these findings, providing insights into the molecular interactions and suggesting possible inhibition mechanisms that could impact the final properties of polypropylene.

Intermolecular interactions in water and ethanol solution of ethyl acetate: Raman, DFT, MEP, FMO, AIM, NCI-RDG, ELF, and LOL analyses

CONTEXT

The intermolecular interactions of ethyl acetate (EtOAc)-water (H2O)/ethanol (EtOH) mixtures were investigated using a combination of Raman spectroscopy and quantum chemical calculations. The computational approach was used to analyze the structure of hydrogen-bonded complexes of ethyl acetate with water/ethanol molecules, based on density functional theory (DFT). The calculated frequencies closely matched the experimental Raman values, with differences being under 4%. Experimental data show that when the concentrations of ethyl acetate in the ethyl acetate/water/ethanol solutions were reduced, almost all Raman spectral bands are blue-shifted. The AIM analysis reveals that all the given complexes possess a positive energy density, indicating that the molecules interact electrostatically. The energy and bond length indicate that the methyl group forms relatively weak hydrogen bonds. Analysis indicates that EtOAc forms weak H-bonding C = O∙∙∙H and C-H∙∙∙O, which are recognized as van der Waals interactions. As the amount of ethyl acetate decreases in the complex, the interaction forces also decrease. This could also explain why the bands are blue-shifted. It was discovered that the title complexes' hydrogen bond energy decreased exponentially as bond length increased.

METHODS

The geometries of the molecular complexes were optimized using the Gaussian 09W program and the B3LYP/6-311 +  + G(d,p) set of functions. The potential energy distribution (PED) analysis was performed using VEDA 4.0 software. Raman spectra were drawn using the Origin 8.5 software. The Multiwfn 3.8 software was used to calculate topological parameters of electron density in molecular systems. GaussView 6.0 and Visual Molecular Dynamics (VMD) 1.9.3 tools were used to visualize all computational results.

An efficient and simple approach for synthesizing indazole compounds using palladium-catalyzed Suzuki-Miyaura cross-coupling

A series of indazole derivatives (6a-6i and 7a-7i) has been synthesized using Suzuki Miyaura cross-coupling with a palladium catalyst from readily available starting materials. An efficient and reliable methodology was employed for the synthesis, and the compounds were thoroughly characterized using 1H NMR, 13C NMR, FT-IR, and HRMS analysis to confirm their structural integrity and purity. Density function theory (DFT) computation identified four compounds (6g, 6h, 7g, and 7h) with significant energy band gaps. Additionally, the molecular electrostatic potential study highlighted the distinct electrical characteristics of these indazole molecules. Subsequent molecular docking investigations were carried out using the AUTODOCK method with two separate protein data bank (PDB) structures (6FEW, 4WA9) involved in renal cancer pathways. The results showed that eight substances PDB: 6FEW (6g, 6h, 7g, and 7h) and PDB: 4WA9 (6a, 6c, and 7c, 7g) had the highest binding energies, indicating their potential as therapeutic agents for treating kidney cancer.

Solid Phase Synthesis, DFT Calculations, Molecular Docking, and Biological Studies of Symmetrical N 2,N 4,N 6-Trisubstituted-1,3,5-triazines

A diversity-oriented, multicomponent convergent synthesis of symmetrical triazines through a one-pot protocol is presented in this research project. The assembly of trisubstituted triazines was initially carried out using easily available reagents through three different protocols, i.e., conventional, MW-assisted synthesis, and solid-supported MW-assisted synthesis using organic and inorganic support to carry out a comparative analysis as to which procedure best corresponds to a greener synthesis protocol. The compounds formed were characterized for structure elucidation and subjected to in vitro anticancer and antibacterial screening. Additionally, computational studies, such as DFT calculations and molecular docking analyses, were conducted.

Synthesis, X-ray Crystallography, Spectroscopic Characterizations, Density Functional Theory, and Hirshfeld Surface Analyses of a Novel (Carbonato) Picket Fence Iron(III) Complex

An Fe(III)-carbonato six-coordinate picket fence porphyrin complex with the formula [K(2,2,2-crypt)][FeIII(TpivPP)(CO3)]·C6H5Cl·3H2O (I) has been synthesized and characterized by UV-Vis and FT-IR spectra. The structure of (carbonato)(α,α,α,α-tetrakis(o-pivalamidophenyl)porphinato)ferrate(III) was also established by XRD. The iron atom is hexa-coordinated by the four nitrogen atoms of the pyrrol rings and the two oxygen atoms of the CO32- group. Complex I, characterized as a ferric high-spin complex (S = 5/2), presented higher Fe-Np (2.105(6) Å) and Fe-PC (0.654(2) Å) distances. Both X-ray molecular structure and Hirshfeld surface analysis results show that the crystal packing of I is made by C-H⋯O and C-H⋯Cg weak intermolecular hydrogen interactions involving neighboring [FeIII(TpivPP)(CO3)]- ion complexes. Computational studies were carried out at DFT/B3LYP-D3/LanL2DZ to investigate the HOMO and LUMO molecular frontier orbitals and the reactivity within the studied compound. The stability of compound I was investigated by analyzing both intra- and inter-molecular interactions using the 2D and 3DHirshfeld surface (HS) analyses. Additionally, the frontier molecular orbital (FMO) calculations and the molecular electronic potential (MEP) analyses were conducted to determine the electron localizations, electrophilic, and nucleophilic regions, as well as charge transfer (ECT) within the studied system.

Red-emitting 4-methyl coumarin fused barbituric acid as an electrochemical sensor for catechol detection and probe for latent fingerprints

Herein, we have reported a red-emitting 4-methyl coumarin fused barbituric acid azo dye (4-MCBA) synthesized by conventional method. Density functional theory (DFT) studies of tautomer compounds were done using (B3LYP) with a basis set of 6-31G(d,p). NLO analysis has shown that tautomer has mean first-order hyperpolarisabilities (β) value of 1.8188 × 10-30 esu and 1.0470 × 10-30 esu for azo and hydrazone forms, respectively, which is approximately nine and five times greater than the magnitude of urea. 4-MCBA exhibited two absorption peaks in the range of 290-317 and 379-394 nm, and emission spectra were observed at 536 nm. CV study demonstrated that the modified 4-MCBA/MGC electrode exhibited excellent electrochemical sensitivity towards the detection of catechol and the detection limit is 9.39 μM under optimum conditions. The 4-MCBA employed as a fluorescent probe for the visualisation of LFPs on various surfaces exhibited Level-I to level-II LFPs, with low background interference.

Metal-Organic Frameworks/Heterojunction Structures for Surface-Enhanced Raman Scattering with Enhanced Sensitivity and Tailorability

Metal-organic frameworks (MOFs), which are composed of crystalline microporous materials with metal ions, have gained considerable interest as promising substrate materials for surface-enhanced Raman scattering (SERS) detection via charge transfer. Research on MOF-based SERS substrates has advanced rapidly because of the MOFs' excellent structural tunability, functionalizable pore interiors, and ultrahigh surface-to-volume ratios. Compared with traditional noble metal SERS plasmons, MOFs exhibit better biocompatibility, ease of operation, and tailorability. However, MOFs cannot produce a sufficient limit of detection (LOD) for ultrasensitive detection, and therefore, developing an ultrasensitive MOF-based SERS substrate is imperative. To the best of our knowledge, this is the first study to develop an MOFs/heterojunction structure as an SERS enhancing material. We report an in situ ZIF-67/Co(OH)2 heterojunction-based nanocellulose paper (nanopaper) plate (in situ ZIF-67 nanoplate) as a device with an LOD of 0.98 nmol/L for Rhodamine 6G and a Raman enhancement of 1.43 × 107, which is 100 times better than that of the pure ZIF-67-based SERS substrate. Further, we extend this structure to other types of MOFs and develop an in situ HKUST-1 nanoplate (with HKUST-1/Cu(OH)2). In addition, we demonstrate that the formation of heterojunctions facilitates efficient photoinduced charge transfer for SERS detection by applying the Mx(OH)y-assisted (where M = Co, Cu, or other metals) MOFs/heterojunction structure. Finally, we successfully demonstrate the application of medicine screening on our nanoplates, specifically for omeprazole. The nanoplates we developed still maintain the tailorability of MOFs and perform high anti-interference ability. Our approach provides customizing options for MOF-based SERS detection, catering to diverse possibilities in future research and applications.

WO3-x nanorods/rGO/AgBiS2 Z-scheme heterojunction with comprehensive spectrum response and enhanced Fenton and photocatalytic activities

Tetracycline (TC) antibiotics and dyes are the prevalent water contaminants, and their removal from the water through photocatalysis is a plausible approach. However, most semiconductors in their pristine form need to be improved to be exploited in photocatalysis owing to poor photoresponse, intense carrier recombination, and inertness without irradiation. Herein, we demonstrate the modification of defective WO3-x by rGO and AgBiS2 in the form of WO3-x/rGO/AgBiS2 (R2). It exploits the superior conductivity and synergism of rGO to inhibit carrier recombination; thereby, Z-scheme heterojunction with AgBiS2 provides high redox potential. Defects in WO3-x enable electron (e-) storage in R2, which decomposes H2O2 to generate ROS without irradiation. Owing to these essences and broad-spectrum response, it removed 93.72, 82.77, and 84.82% of TC during photo-Fenton (PFR), night-Fenton (NFR), and photocatalytic (PCR) reactions, respectively. Its removal rates reached 94.74, 81.54, and 87.50% against rhodamine B (RhB) during PFR, NFR, and PCR, respectively. It is superior to memory catalysis (MC) and conventional Fenton reactions (CFR) because it can perform without and with irradiation across a broader pH range. So, this work is conducive to designing WO3-x-based catalysts to combat environmental and energy crises.

Synthesis, characterization, DFT studies and evaluation of the potential anti-tumour activity of nicotinic hydrazide based Schiff base using in vitro and molecular docking techniques

Breast cancer, one of the most serious issues worldwide, has been raising day by day. It has now become a necessary to develop a suitable drug to combat this terrible illness. Schiff bases are increasingly being used as powerful medications for a number of illnesses. BNH has now synthesized from Benzil and Nicotinic hydrazide and characterized experimentally by FT-IR, UV, 1H NMR,13CNMR and Mass analysis. DFT calculations were done using Gaussian 16 W with B3LYP/6-311 + G (d,p) and geometry of the compound is optimized. Frontier Molecular orbit (FMO), Mullikan atomic charges and Molecular Electrostatic Potential (MEP) were studied. Invitro antimicrobial studies were done using various bacteria and fungi. The synthesized compound is appropriate against bacterial and fungal actions. Invitro study were done using MCF-7 cell lines to analyze the anticancer property of the ligand. The outcome suggests that BNH may be employed in the future as a novel anticancer medication.

Quantum chemical framework for tailoring N/B doped phenalene derivatives to achieve high performance nonlinear optical materials

Nonlinear optical (NLO) response materials are among the smartest materials of the era and are employed to modulate the phase and frequency of the laser. The present study presents a quantum chemical framework for tailoring nitrogen/boron doped derivatives of Dihydrodibenzo [de,op]pentacene through terminal and central core modifications. The derivatives of these compounds have been designed by introducing various π-conjugated connectors as well as B/N heteroatoms in the phenalene rings. Density functional theory (DFT) methods are used to optimize the ground state molecular geometries of designed compounds, represented as 1 to 4 (phenalene derivatives) and 1-BN to 4-BN (B/N doped phenalene derivatives) at the M06-2X/6-311G* level of theory. The highest value of 116.9 × 10-24 esu and 240.2 × 10-24 esu for isotropic and anisotropic linear polarizability is shown by compound 4. Among the designed compounds, 4-BN has achieved the highest γ amplitude of 1858 × 10-36 esu owing to its unique molecular structural design. Further analysis of electronic parameters, such as electron density difference (EDD) maps, the density of states, electrostatic potentials, transition density matrix (TDM) analysis, and frontier molecular orbitals analysis (FMOs), demonstrated the more effective intramolecular charge transfer (ICT) for the best compounds, resulting in a good NLO response. The compounds were also analyzed for their potential in photovoltaic applications based on factors such as open circuit voltage values determined to be between (0.14 eV and 1.82 eV), and light harvesting efficiency (0.425-0.909).

Theoretical and experimental approach on investigation of ethylurea-water clusters

Alkylated urea derivatives have found wide application as starting materials for the production of many drugs, including anticancer drugs, as well as in many other areas. In this work, we studied ethylurea crystalline hydrates using a complex of theoretical and experimental methods. The nature of the intermolecular interactions between ethylurea and water molecules is investigated using topological analyses such as atoms in molecules (AIM), non-covalent interaction (NCI), reduced density gradient (RDG), electron localized functions (ELF), and localized orbital locator (LOL). The hydrogen bond energy is in the range of 1.1295–14.4327 kcal/mol. Also, a highly correlated parabolic relationship between topological parameters (E HB, ρ, and ∇2 ρ) and H-bond length was determined. According to RDG data, with an increase in the number of water molecules in ethylurea clusters, the area corresponding to hydrogen bonds increases. The initial ethylurea and its crystalline hydrate were studied by FTIR spectroscopy and X-ray diffraction. The introduction of water molecules into the ethylurea crystal was proved by IR spectroscopy by the appearance of the corresponding absorption bands. X-ray diffraction showed that the initial ethylurea has intense peaks at 11.2, 16.8, 21.4, 22.24, 25.06, 25.78° 2Ɵ, the intensity of which changes when water molecules are introduced into the crystal.

Synthesis molecular docking and DFT studies on novel indazole derivatives

The amide bond is an important functional group used in various fields of chemistry, including organic synthesis, drug discovery, polymers, and biology. Although normal amides are planar, and the amide has an N-C(O) bond, herein, the 26 indazole derivatives were reported via amide cross-coupling (8a-8z). Using IR, 1H NMR, 13C NMR, and mass spectrometry, all of the produced compounds were analysed. A DFT computational study was also conducted using GAUSSIAN 09-Gaussian View 6.1, which revealed that 8a, 8c, and 8s had the most substantial HOMO-LUMO energy gap. The effectiveness of indazole moieties with renal cancer-related protein (PDB: 6FEW) was assessed by docking the derivatives using Autodock 4. The analysis showed that derivatives 8v, 8w, and 8y had the highest binding energies.

Interactions between DNA and the acridine intercalator: A computational study

Cancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and makes replication impossible. In this context, this study aimed to computationally investigate how acridine intercalators interact with DNA by evaluating the mechanism of interactions, binding, and interaction energies using quantum mechanics calculations. Molecular electrostatic potential (MEP) analysis revealed that acridine has well- distributed negative charges in the center of the molecule, indicative of a dominant electron-rich region. Acridine exhibits well-defined π orbitals (HOMO and LUMO) on the aromatic rings, suggesting that charge transfer occurs within the molecule and may be responsible for the pharmacological activity of the compound. Structural analysis revealed that acridine interacts with DNA mainly through hydrogen bonds between HAcridine… ODNA with bond lengths ranging from 2.370 Å to 3.472 Å. The Binding energy (ΔEBind) showed that acridine interacts with DNA effectively for all complexes and the electronic energy results (E+ZPE) for complexes revealed that the complexes are more stable when the DNA-centered acridine molecule. The Laplacian-analysis topological QTAIM parameter (∇2ρ(r)) and total energy (H(r)) categorized the interactions as being non-covalent in nature. The RGD peak distribution in the NCI analysis reveals the presence of van der Waals interactions, predominantly between the intercalator and DNA. Accordingly, we confirm that acridine/DNA interactions are relevant for understanding how the intercalator acts within nucleic acids.

Synthesis, molecular modeling, quantum chemical calculations and in silico drug profiling of the novel (4-phenylpiperazin-1-ium) hydrogenfumarate as a tyrosinase inhibitor

The complexation between fumaric acid (FA) and 1-phenylpiperazine (1 PP) is a fruitful cooperation that allowed the preparation of a new organic crystal entitled (4-phenylpiperazin-1-ium) hydrogenfumarate denoted by 4PPHFUM, which is reported in the present manuscript. This new substance is created by the slow evaporation that occurs when 1-phenylpiperazine and fumaric acid are combined in a stoichiometric 1:1 ratio. The stacking of the crystal is provided by O–H⋯O, N–H⋯O and C–H⋯O hydrogen bonds, also supported by C–H⋯π interactions between the organic cations. The importance of these interactions in the formation of this new crystal is confirmed by the Hirshfeld surface analysis which showed that H-bonds and supramolecular C–H⋯π interactions account for about half of the non-covalent interactions existing in this compound. These non-covalent bonds that encompass the synthesis and design of this supramolecule have also been analyzed in detail using a quantum chemical computational study. Using the docking – based drug design strategy, we investigated the therapeutic effect of this cooperative outcome between fumaric acid and 1-phenylpiperazine to demonstrate the improved therapeutic property of this novel non-covalent compound as a tyrosinase inhibitor. 4PPHFUM was found to be a potent tyrosinase inhibitor with high interaction energy with its protein, higher than that of the most potent tyrosinase inhibitors (thiamidol, hydroquinone, resorcinol, hexylresorcinol and kojic acid).

Bonding and noncovalent interactions effects in 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid: DFT calculation, topological analysis, NMR and molecular docking studies

The pharmaceutical proprieties of the 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid compound have been studied and the relevant drug design has been considered. The investigated organic compound with formula (2,6-(CH3)C4H10N2)2(C2O4)2·H2C2O4 (2DPOA) has been synthesized by slow evaporation technique at room temperature of a molar ratio 3:2 mix of oxalic acid and 2,6-dimethylpiperazine. Then 2DPOA has been characterized by IR, 13C NMR, UV–visible and the DFT calculation at the B3LYP level of theory has been made. The molecular structure and parameters (bond angles and lengths) of the molecule have been optimized using the Gaussian 09 software and compared with the XRD data. The atoms-in-molecules (AIM), electron localization function (ELF), and localized orbital locator (LOL) methods have been utilized to determine the types and nature of noncovalent interactions present within the 2DPOA molecule. These methods offer insights into the characteristics and behavior of these interactions. Furthermore, the presence of these interactions has been confirmed through the Hirshfeld Surface (HS) and reduced density gradient (RDG) analysis. The NBO analysis is employed to assess the charge exchange occurring within the studied compound. The molecular reactive sites have been examined using the molecular potential surface and Mulliken atomic charges. The energy gap between HOMO–LUMO and chemical properties of 2DPOA have been determined within the frontier molecular orbital theory. The UV–Vis spectrum of the 2DPOA molecule has been recorded and examined. The calculated and experimental infrared absorption and nuclear magnetic resonance spectra of 2DPOA molecule have been investigated. Finally, the molecular docking simulation has been used to find novel inhibitors and drugs for the cancer and epilepsy disease treatment.

An atomistic scale simulation study of structural properties in the silk-fibrohexamerin complex

The use of Bombyx mori silk fibroin in composite materials has been extensively explored in many studies, owing to its remarkable mechanical properties. Recently, the N-glycan-engineered P25 protein was utilized to improve the mechanical properties of silk. However, the mechanism by which N-glycan-engineered P25 protein enhances the mechanical properties of silk remains unclear. This study analyzed the interaction between the P25 protein and silkworm silk using quantum mechanics/molecular mechanics multiscale simulations and discovered stronger hydrogen bonding between the amorphous domain and the P25 protein. The results confirmed that glycoengineering of the mannose molecule in N-glycan in orders of three, five, and seven increased the hydrogen bonding of the amorphous structures. However, P25 has fewer binding interactions with the crystalline domain. Silk amino acids and mannose molecules were analyzed using QM simulations, and hydroxyl and charged amino acids in the amorphous domains were found to have relatively higher reactivity with mannose molecules in N-glycans than basic and aliphatic amino acids in the crystalline domain. This study demonstrates how the N-glycan-engineered P25 protein can improve the mechanical properties of silk fibroin and identifies a key factor for N-glycan-engineered proteins.

Molecular simulation of Cu, Ag, and Au-decorated Si-doped graphene quantum dots (Si@QD) nanostructured as sensors for SO2 trapping

In view of the numerous environmental hazards and health challenges linked to sulfur (iv) oxide (SO2), an indirect greenhouse gas, and the resultant need to develop efficient gas nanosensor devices, this research had as its principal focus on the theoretical evaluation of the gas sensing potential of metals: Ag, Au and Cu functionalized silicon-doped quantum dots (Si@QD) for the detection and adsorption of SO2 gas investigated using the first-principles density functional theory (DFT) computation at the B3LYP-D3(BJ)/def2-SVP level of theory. Eight (8) possible adsorption modes: SO2_O_Si@QD, SO2_O_Ag_Si@QD, SO2_O_Au_Si@QD, SO2_O_Cu_Si@QD, SO2_S_Si@QD, SO2_S_Ag_Si@QD, SO2_S_Au_Si@QD, and SO2_S_Cu_Si@QD were considered based on SO2 interactions with the studied materials at the -S and -O sites of the SO2 molecule. The counterpoise correction (BSSE) showed that five of the eight interactions had favorable Ead + BSSE values ranging from -0.31 to -1.98 eV. All the eight interactions were observed to be thermodynamically favorable with ΔG and ΔH ranging from -129.01 to -200.24 kcal/mol and -158.26 to -229.73 kcal/mol respectively. Results from the topology analysis reveal that van der Waals forces occurred the greatest at the gas-sensor interphase while SO2_S_ Cu_Si@QD is predicted to have the highest sensing potency based on the conductivity and recovery time estimations. These results confirm the potential efficient feasibility of real-world device application of the metals (Ag, Au, Cu) functionalized Si-doped QDs.

A theoretical protocol for the rational design of the bioinspired multifunctional hybrid material MIP@cercosporin

CONTEXT

Rational design of polymeric materials prepared with the molecular imprinting technology is gaining even more space, as it can provide the optimal conditions to direct the laboratory molecularly imprinting polymer (MIP) preparation, maximizing their efficiency while reducing costs and preparation time, when compared to try-and-error approaches. We perform a rational design of an MIP with specific cavities for cercosporin accommodation by means of computational tools. The main steps of an MIP preparation were simulated and it was found that the most appropriated functional monomer to be used in the MIP preparation for cercosporin is the acrylamide, while the most suitable crosslinking agent is found to be p-divinylbenzene. Also, the most suitable solvents to remove cercosporin from the cavity are those with low dielectric constant, such as chloroform. This kind of solvent can then be used in washing step, in the case of use the MIP for sensing destinations. On the other hand, solvents like water, which has high dielectric constants, can efficiently improve the interactions between cercosporin and the functional monomer acrylamide, being indicated when the objective is to attract or maintain the cercosporin inside the MIP cavity. Thus, a MIP@cercosporin hybrid material can be used in aqueous solutions more reliably, or even the cercosporin detection in this media can be favoured. In the selectivity analysis of the material prepared in this specific condition, the results point that this MIP can also detect elsinochrome A with high efficiency, and could be more selective for hypericin, altertoxin, hypocrelin A, and phleichrome mycotoxins.

METHOD

The main steps of a MIP synthesis were theoretically simulated trough density functional theory (DFT) calculations aiming to direct and optimize the synthesis and applications of the material before the bench tests. Initially, in order to choose the most suitable functional to be employed for cercosporin calculations, eight of the DFT functionals that had been previously used for cercosporin calculations in literature were tested, which were the LCWPBE, B3LYP, CAM-B3LYP, M062-X, mPW1PW91, PBE0, TPSSh, and ωb97Xd. The theoretical 1H NMR chemical shifts for cercosporin molecule were calculated and compared with experimental results to analyze the performance of the functionals. Of all these, the best results were obtained with the TPSSh functional, employing the 6-31G(d,p) basis set, and this level of theory was then used for all the following steps. All the simulations were performed by means of geometry optimizations and frequency calculations. Additionally, AIM calculations were employed for further analysis of the interactions between the chosen functional monomer and cercosporin template in step 1, which was functional monomer selection. In washing step, the calculations were done using implicit solvation model, and finally, in selectivity tests, the putative "solid" MIP was simulated by freezing the positions of the monomers after the template remotion, and then other structurally similar toxins were placed in its cavity for the geometry optimizations and frequency calculations.

Intramolecular hydrogen bonds interactions in the isomers of the bilirubin molecule: DFT and QTAIM analysis

CONTEXT

Bilirubin is an important molecule, used as a marker of some liver diseases, and it can also be toxic and cause jaundice, especially in newborns. The main treatment for neonatal jaundice is phototherapy with blue light, which is still widely studied because the photophysical processes involved are not fully understood.

METHODS

Calculations based on the density functional theory (DFT) at M062X/6-31G(d,p) level were performed in order to evaluate the structural, electronic, and topological properties of bilirubin isomers. It was found that the ZZ conformation can form a greater number of hydrogen bonds, which gives the isomer greater energy stabilization compared to the other ZE, EZ, and EE isomers, and that the EE isomer is the conformer with the lowest energy of stabilization. The hydrogen bonds were characterized by the quantum theory of atoms in molecules (QTAIM) and for the ZZ isomer four hydrogen bonds (HBs) were found classified as intermediate, ∇2ρ(r) > 0, H(r) > 0. The ZE, EZ, and EE isomers show weak HBs, ∇2ρ(r) > 0, H(r) > 0.

Dimethylformamide Impurities as Propylene Polymerization Inhibitor

This research study examined how the use of dimethylformamide (DMF) as an inhibitor affects the propylene polymerization process when using a Ziegler-Natta catalyst. Several experiments were carried out using TiCl4/MgCl2 as a catalyst, aluminum trialkyl as a cocatalyst, and different amounts of DMF. Then, we analyzed how DMF influences other aspects of the process, such as catalyst activity, molecular weight, and the number of branches in the polymer chains obtained, using experimental and computational methods. The results revealed that as the DMF/Ti ratio increases, the catalyst activity decreases. From a concentration of 5.11 ppm of DMF, a decrease in catalyst activity was observed, ranging from 45 TM/Kg to 44 TM/Kg. When the DMF concentration was increased to 40.23 ppm, the catalyst activity decreased to 43 TM/Kg, and with 75.32 ppm, it dropped even further to 39 TM/Kg. The highest concentration of DMF evaluated, 89.92 ppm, resulted in a catalyst productivity of 36.5 TM/Kg and lost productivity of 22%. In addition, significant changes in the polymer's melt flow index (MFI) were noted as the DMF concentration increased. When 89.92 ppm of DMF was added, the MFI loss was 75%, indicating a higher flowability of the polymer. In this study, it was found that dimethylformamide (DMF) exhibits a strong affinity for the titanium center of a Ziegler-Natta (ZN) catalyst, with an adsorption energy (Ead) of approximately -46.157 kcal/mol, indicating a robust interaction. This affinity is significantly higher compared to propylene, which has an Ead of approximately -5.2 kcal/mol. The study also revealed that the energy gap between the highest occupied molecular orbital (HOMO) of DMF and the lowest unoccupied molecular orbital (SOMO) of the Ziegler-Natta (ZN) catalyst is energetically favorable, with a value of approximately 0.311 eV.