Computational Chemistry Study Research Articles

Alpinia officinarum Hance Essential Oil as Potent Antipseudomonal Agent: Chemical Profile, Antibacterial Activity, and Computational Study.

Alpinia officinarum Hance, is an aromatic and medicinal herb with a very interesting history and prominent chemical and biological prospects. We aimed to investigate the antibacterial activity of Alpinia officinarum essential oil and the preferred molecular targets of its constituents together with their pharmacokinetic properties and toxicity profile. According to GC-MS analysis, eucalyptol was the main compound (27.52 %) identified in Alpinia officinarum essential oil, followed by α-terpineol, and β-sesquiphellandrene. As opposed to the weak antiradical activity estimated by DPPH and ABTS tests, the essential oil caused inhibition of all the bacteria following well-diffusion and microdilution methods, especially the gram-negative Pseudomonas aeruginosa and Escherichia coli. It displayed exceptionally remarkable activity against Pseudomonas aeruginosa by totally inhibiting its growth on the agar plate exceeding the effect of chloramphenicol standard. This bactericidal effect was confirmed by very low MIC and MBC values of 0.82 and 6.562 μg/mL, respectively. The molecular docking showed interesting binding affinity between the major compounds and various drug targets in Pseudomonas aeruginosa, also good pharmacokinetic and toxicity behavior. These encouraging findings are particularly relevant in light of the increasingly pressing challenge to find alternative substances with antibacterial aptitude to address the issue of antibiotic resistance among infectious bacteria.

Comparative study of Sombor index and its various versions using regression models for top priority polycyclic aromatic hydrocarbons

The aromatic compounds having structural configurations with two or more fused benzene rings are the polycyclic aromatic hydrocarbons (PAHs). Topological indices are valuable tools for studying the structure property relationships of PAHs and also helps in predicting various properties and activities. They find applications widely in computational chemistry, drug design and QSPR studies. This article focuses on analysing the potential predictive index for Sombor index (SO), elliptic Sombor index (ESO), Euler Sombor index (EU), reverse Sombor index (RSO), reverse elliptic Sombor index (RESO) and reverse Euler Sombor index (REU) using regression models for top priority 38 PAHs. From the study it is evident that, SO and RSO have proved to be potential predictive indices among the considered degree-based and reverse degree-based indices. The variation of best predictive index with minimal RMSE are plotted for linear, quadratic and cubic regression models for better understanding.

Discovery of HCCCH_2CCH in TMC-1 with the QUIJOTE line survey

We present the first detection in space of 1,4-pentadiyne. It has been found towards TMC-1 with the QUIJOTE line survey in the 31-50 GHz range. We observed a total of 17 transitions with $J$ = 2 up to 13 and $K_a$ = 0,1 and 2. The observed transitions allowed us to derive a rotational temperature of 9.5 pm 0.5 K and a column density of (5.0 pm 0.5)times 1012 cm$^ $. This molecule was the last non-cyclic isomer of the C$_5$H$_4$ family that could be detected via radio astronomy. A computational chemistry study was performed to determine the energies of the five most stable isomers. The isomer ($c$-C$_3$H$_3$CCH) has a considerably higher energy than the others, and it has not yet been detected. To better understand the chemical reactions involving these species, we compared the ethynyl and cyano derivatives. The observed abundances of these species are in good agreement with the branching ratios of the formation reactions studied with our chemical model of TMC-1.

Impact of quantum size effects to the band gap of catalytic materials: a computational perspective*

The evolution of nanotechnology has facilitated the development of catalytic materials with controllable composition and size, reaching the sub-nanometer limit. Nowadays, a viable strategy for tailoring and optimizing the catalytic activity involves controlling the size of the catalyst. This strategy is underpinned by the fact that the properties and reactivity of objects with dimensions on the order of nanometers can differ from those of the corresponding bulk material, due to the emergence of quantum size effects. Quantum size effects have a deep influence on the band gap of semiconducting catalytic materials. Computational studies are valuable for predicting and estimating the impact of quantum size effects. This perspective emphasizes the crucial role of modeling quantum size effects when simulating nanostructured catalytic materials. It provides a comprehensive overview of the fundamental principles governing the physics of quantum confinement in various experimentally observable nanostructures. Furthermore, this work may serve as a tutorial for modeling the electronic gap of simple nanostructures, highlighting that when working at the nanoscale, the finite dimensions of the material lead to an increase of the band gap because of the emergence of quantum confinement. This aspect is sometimes overlooked in computational chemistry studies focused on surfaces and nanostructures.

Actuating Liquid Crystals Rapidly and Reversibly by Using Chemical Catalysis.

Microtubules and catalytic motor proteins underlie the microscale actuation of living materials, and they have been used in reconstituted systems to harness chemical energy to drive new states of organization of soft matter (e.g., liquid crystals (LCs)). Such materials, however, are fragile and challenging to translate to technological contexts. Rapid (sub-second) and reversible changes in the orientations of LCs at room temperature using reactions between gaseous hydrogen and oxygen that are catalyzed by Pd/Au surfaces are reported. Surface chemical analysis and computational chemistry studies confirm that dissociative adsorption of H2 on the Pd/Au films reduces preadsorbed O and generates 1 ML of adsorbed H, driving nitrile-containing LCs from a perpendicular to a planar orientation. Subsequent exposure to O2 leads to oxidation of the adsorbed H, reformation of adsorbed O on the Pd/Au surface, and a return of the LC to its initial orientation. The roles of surface composition and reaction kinetics in determining the LC dynamics are described along with a proof-of-concept demonstration of microactuation of beads. These results provide fresh ideas for utilizing chemical energy and catalysis to reversibly actuate functional LCs on the microscale.

Solvent-mediated modification of thermodynamics and kinetics of monoethanolamine regeneration reaction in amine-stripping carbon capture: Computational chemistry study.

A major limitation of amine-based post-combustion carbon capture technology is the necessity to regenerate amines at high temperatures, which dramatically increases operating costs. This paper concludes the effect of solvent choice as a possible route to modify the thermodynamics and kinetics characterizing the involved amine regeneration reactions and discusses whether these modifications can be economically beneficial. We report experimentally benchmarked computational chemistry calculations of monoethanolamine regeneration reactions employing aqueous and non-aqueous solvents with a wide range of dielectric constants. Unlike previous studies, our improved computational chemistry framework could accurately reproduce the right experimental activation energy of zwitterion formation. From the thermodynamics and kinetics of the predicted reactions, the use of non-aqueous solvents with small dielectric constants led to reductions in regeneration Gibbs free energies, activation barriers, and enthalpy changes. This can reduce energy consumption and give an opportunity to run desorption columns at relatively lower temperatures, thus offering the possibility of relying on low-grade waste heat as an energy input.

Metal free synthesis of thermally stable blue fluorescent m-terphenyls by ring transformation of 2H-pyran-2-ones: chemical synthesis, spectroscopy and computational studies.

A simple yet convenient nucleophile-induced synthetic route for the construction of thermally stable fluorescent active functionalized stilbenes has been delineated. The nucleophile-induced base encouraged synthetic protocol was performed under mild conditions without harming the environment and products were achieved in good yields. The synthesized stilbenes showed amazing emission properties and good thermal stability. Synthesized products displayed interesting positive solvatochromism in different solvents based on variation in polarity. Further, we present a comprehensive analysis of the eight molecules, leveraging a combination of Density Functional Tight Binding (DFTB), Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. This integrated approach allowed for an in-depth exploration of the electronic structures, reactivity profiles, and dynamic behaviors of these complex molecular systems. Our findings reveal significant insights into the physicochemical properties of the synthesized molecules, contributing to a deeper understanding of their potential applications in various fields.

Design and Synthesis of D3R Bitopic Ligands with Flexible Secondary Binding Fragments: Radioligand Binding and Computational Chemistry Studies.

A series of bitopic ligands based on Fallypride with a flexible secondary binding fragment (SBF) were prepared with the goal of preparing a D3R-selective compound. The effect of the flexible linker ((R,S)-trans-2a-d), SBFs ((R,S)-trans-2h-j), and the chirality of orthosteric binding fragments (OBFs) ((S,R)-trans-d, (S,R)-trans-i, (S,S)-trans-d, (S,S)-trans-i, (R,R)-trans-d, and (R,R)-trans-i) were evaluated in in vitro binding assays. Computational chemistry studies revealed that the interaction of the fragment binding to the SBF increased the distance between the pyrrolidine nitrogen and ASP1103.32 of the D3R, thereby reducing the D3R affinity to a suboptimal level.

Multivitamin complex-loaded electrospun polyvinyl alcohol core/shell structure fibers for transdermal delivery system: In-silico and experimental studies

Transdermal delivery systems offer a controlled and targeted environment for releasing drugs compared to other delivery systems. This study presents the fabrication of polyvinyl alcohol (PVA) fibers with a multivitamin complex (MV) using the electrospinning technique (ES). The research focuses on understanding how various fiber structures, such as core/shell, simple fibers, and ES parameters, affect the MC release mechanism and cell viability behavior.The vitamin complexes were uniformly encapsulated within the polymeric chains in all structure fibers. PVA simple fibers with and without the vitamin complex don't significantly differ in diameter size. However, the core/Shell fiber has a notable decrease in fiber diameter of 45 %.The fiber with a core/shell structure resulted in a slower release rate of the vitamin complex than simple fiber. According to the Korsmeyer-Peppas model, the release mechanism observed in our study for the simple fibers is classical Fickian diffusion. Instead, core/shell fibers indicate a more anomalous or non-Fickian behavior.The structural configurations of the fibers do not result in statistically significant differences in cell viability. This could be attributed to the identical nature of materials used, including the polymer and MV, across all cases.Finally, a computational chemistry study was used to examine the interaction between polyvinyl alcohol (PVA) and vitamins K3 and B3, like a model of MV. The analysis showed four strong hydrogen bonds between PVA and vitamin B3, whereas the interaction between PVA and vitamin K3 only had one hydrogen bond. Furthermore, the PVA and vitamin B3 interaction had higher energy and was more exothermic and spontaneous than the PVA-vitamin K3 interaction. On the other hand, the PVA-vitamin K4 interaction displayed higher reactivity due to its lower separation energy. In contrast, the PVA-vitamin B3 interaction was more stable.

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

Abstract 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).

A model of pre-reaction complexes

One of the main objectives of computational chemistry studies is the interpretation of chemical mechanisms whose data were obtained from quantum mechanical software packages. In these mechanisms, starting from the reactant, the reactant and the product states are connected through intermediates and transition states, in an alternating order. Generally, the reactivity of a given pathway is determined by the overall barrier height. Sometimes, a comparison becomes necessary for a given step with another possible step that can be realized within the same mechanism, and in this case as well the step with the lowest-lying transition state is preferred. However, there are some exceptions in the order of these states. There are states known as pre-reaction complexes that reside between a reactant, or an intermediate, and a transition state. Excluding some first principle quantum dynamics studies, the effect of a pre-reaction complex is generally not discussed in most of the computational chemistry studies, and the overall barrier heights become the main considerations, as usual.In this work, a mathematical model that allows obtaining the rate constant of a pathway without a pre-reaction complex, and that of a pathway with a pre-reaction complex was described. The model was built using time-dependent quantum perturbation theory and quantum time-correlation functions. This work can improve our understanding of the nature of chemical reactions that include pre-reaction complexes by enabling us to differentiate the seemingly identical reaction pathways.

Novel Grafted Hydrogel for Iron and Ammonia Removal from Groundwater: A Synthesis and Computational Chemistry Study.

Current research is moving towards iron and ammonia elimination from groundwater. Here, we are using a poly acrylic-poly acrylamide hydrogel that is grafted with 3-chloroaniline. This copolymer was synthesized by addition polymerization technique. The effects of agitation time, dosage and adsorbent temperature on the removal process sensitivity were investigated. The copolymer was described experientially and theoretically. Isothermal kinetic adsorption models are discussed. This hydrogel could be regenerated efficiently (98.3% removal of iron and 100% removal of ammonia). The density functional theory (DFT) method, using B3LYP/6-311G(d,p), and the LANL2DZ level of the theory were managed to investigate the stationary states of the grafted copolymer and the complexation energy of the hydrogel with the studied cations. DFT has been used to investigate the Natural Bond Orbital (NBO) properties to locate the most negative centers on the hydrogel. The calculated complexation energy showed hydrogel selectivity with regard to the studied cations.

Multitarget Mechanisms of 5‐hydroxy Ferulic Acid for Cancer Prevention: A Computational Chemistry Study

AbstractThis study used computational methods to investigate the multitarget mechanisms of 5‐hydroxy ferulic acid in preventing cancer. The antiradical activity of 5‐hydroxy ferulic acid was systematically studied by using the M06‐2X/6‐311++G(d,p) method in both pentyl ethanoate (lipid‐like) and water media. The results show that 5‐hydroxy ferulic acid is more effective at scavenging the HOO• radical (koverall=5.2×108 M−1s−1) than Trolox (koverall=1.3×105 M−1s−1) in aqueous solution. The complexation ability of 5‐hydroxy ferulic acid with Cu(II) ions was investigated at the M06/6‐311++G(d,p) level of theory under physiological pH conditions. The most thermodynamically stable complexes can slow down about 107 times the Haber‐Weiss cycle's first reaction (from 4.2×109 M−1s−1 to 3.8×102 M−1s−1) and mitigate the potential damage caused by ⋅OH radical production. Furthermore, by performing molecular docking simulations on protein‐ligand adducts and comparing their activity to that of 5‐fluorouracil (a commercial anticancer drug), the existing forms of 5‐hydroxy ferulic acid at physiological pH were extremely effective at inhibiting the thymidylate synthase enzyme. Based on these findings, 5‐hydroxy ferulic acid may be an effective cancer treatment.

Theoretical Investigations of Palladium-Catalyzed [3+2] Annulation via Benzylic and meta C-H Bond Activation.

The palladium-catalyzed reaction of aromatic amides with maleimides results in the formation of a double C-H bond activation product, which occurs at both the benzylic and meta positions. Computational chemistry studies suggest that the first C-H bond activation unfolds via a six-membered palladacycle, maleimide insertion, protonation of the Pd-N bond, and then activation of the meta C-H bond. The process concludes with reductive elimination, producing an annulation product. The energy decomposition analysis (EDA) showed that the deformation energy favors the ortho C-H bond activation process. However, this route is non-productive. The interaction energy controls the site where the maleimide is inserted into the Pd-C(sp3 ) bond, which determines its site selectivity. The energetic span model indicates that the meta C-H bond activation step is the one that determines the turnover frequency. Regarding the directing group, it has been concluded that the strong Pd-S bonding and the destabilizing effect of the deformation energy allow the 2-thiomethylphenyl to function effectively as a directing group.

How generic is iodide-tagging photoelectron spectroscopy: An extended investigation on the Gly·X- (Gly = glycine, X = Cl or Br) complexes.

We report a joint negative ion photoelectron spectroscopy (NIPES) and quantum chemical computational study on glycine-chloride/bromide complexes (denoted Gly·X-, X = Cl/Br) in close comparison to the previously studied Gly·I- cluster ion. Combining experimental NIPE spectra and theoretical calculations, various Gly·X- complexes were found to adopt the same types of low-lying isomers, albeit with different relative energies. Despite more congested spectral profiles for Gly·Cl- and Gly·Br-, spectral assignments were accomplished with the guidance of the knowledge learned from Gly·I-, where a larger spin-orbit splitting of iodine afforded well-resolved, recognizable spectral peaks. Three canonical plus one zwitterionic isomer for Gly·Cl- and four canonical conformers for Gly·Br- were experimentally identified and characterized in contrast to the five canonical ones observed for Gly·I- under similar experimental conditions. Taken together, this study investigates both genericity and variations in binding patterns for the complexes composed of glycine and various halides, demonstrating that iodide-tagging is an effective spectroscopic means to unravel diverse ion-molecule binding motifs for cluster anions with congested spectral bands by substituting the respective ion with iodide.

Design and synthesis of a new bifunctional chelating agent: Application for Al 18F/177Lu complexation

Theranostic and personalized medicine are blooming strategies to improve oncologic patients' health care and facilitate early treatment. While 18F-radiochemistry for theranostic application is attractive due to its imaging properties, combining diagnosis by positron emission tomography (PET) via aluminum-fluoride-18 and β− therapy with lutetium-177 is relevant. Nevertheless, it requires the use of two different chelating agents, which are NOTA and DOTA for aluminum-fluoride-18 and lutetium-177 radiolabeling, respectively. To overcome this issue, we propose herein the synthesis of a new hybrid chelating agent named NO2A-AHM, which can be labeled with different types of emitters (β+, β− and γ) using the mismatched Al18F/177Lu pair. NO2A-AHM, is based on a hydrazine moiety functionalized by a NOTA cycle, a chelating arm, and a linker with a maleimide function. This design is chosen to increase the flexibility and allow the formation of 5 up to 7 coordination bonds with metal ions. Moreover, this agent can be coupled to targeting moieties containing a thiol function, such as peptides, to increase selectivity towards specific cancer cells. Experimental complexation and computational chemistry studies are performed to confirm the capacity of our chelating agent to label both aluminum-fluoride and lutetium using molecular modeling approaches at Density Functional Theory (DFT) level.The proof of concept of the ability of NO2A-AHM to complex both aluminum-fluoride-18, for PET imaging applications, and lutetium-177 for radiotherapy has shown encouraging results which is prominent for the development of a fully consistent theranostic approach.

Organic-inorganic hybrid salt and mixed ligand Cr(III) complexes containing the natural flavonoid chrysin: Synthesis, characterization, computational, and biological studies.

Organic-inorganic hybrid salt and mixed ligand Cr(III) complexes (Cr1 and Cr2) containing the natural flavonoid chrysin were synthesized. The metal complexes were characterized using UV-Vis, Fourier-transform infrared, MS, SEM-EDX, XRD, and molar conductance measurements. Based on experimental and DFT/TD-DFT calculations, octahedral geometries for the synthesized complexes were suggested. The powder XRD analysis confirms that the synthesized complexes were polycrystalline, with orthorhombic and monoclinic crystal systems having average crystallite sizes of 21.453 and 19.600 nm, percent crystallinities of 51% and 31.37%, and dislocation densities of 2.324 × 10-3 and 2.603 × 10-3nm-2 for Cr1 and Cr2, respectively. The complexes were subjected to cytotoxicity, antibacterial, and antioxidant studies. The in vitro biological studies were supported with quantum chemical and molecular docking computational studies. Cr1 showed significant cytotoxicity to the MCF-7 cell line, with an IC50 value of 8.08μM compared to 30.85μM for Cr2 and 18.62μM for cisplatin. Cr2 showed better antibacterial activity than Cr1. The higher E HOMO (-5.959eV) and dipole moment (10.838 Debye) values of Cr2 obtained from the quantum chemical calculations support the observed in vitro antibacterial activities. The overall results indicated that Cr1 is a promising cytotoxic drug candidate.

A methodology to generate crystal-based molecular structures for atomistic simulations

We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ‘slabs’ with periodic boundary conditions (PBCs) and non-periodic solids such as Wulff structures. We also introduce a method to build crystal slabs with orthogonal PBC vectors. These methods are integrated into our code, Los Alamos Crystal Cut (LCC), which is open source and thus fully available to the community. Examples showing the use of these methods are given throughout the manuscript.

Synthesis and characterization of new Schiff base bearing bis(pyrano[3,2-c]quinolinone): Efficient cationic dye adsorption from aqueous solution

Organic compound water pollution is one of the difficult environmental issues facing the advancement of human civilization. So, New bis(pyrano[3,2-c]quinolinone) based on Schiff base adsorbent was prepared to participate in solving this problem. The synthesized adsorbent was characterized using FT-IR, 1H NMR, XRD, SEM, elemental analysis, N2- adsorption-desorption isotherm, SBET, and Pore size distribution studies. The obtained results revealed a significant improvement in the new schiff base surface texture and crystallinity. Further, pHzpc of the new adsorbent has been examined to be 3.7. Its decolorization efficiency toward methylene blue (MB) dye from an aqueous solution was examined. Also, the factors of pH, contact time, reaction temperature, and initial dye concentration were optimized. Overall, this study emphasized that the newly synthesized Schiff base act as an effective adsorbent (99%) at a very short time (5 min., 10 ppm dye concentration, pH = 9 and temperature = 25 °C) and can be regenerated for five cycles for the removal of MB dye from aqueous solutions. Freundlich isotherm model and pseudo-second order kinetic model were fit effectively for the MB dye adsorption experimental data. Also, the calculated thermodynamic parameters revealed a spontaneous and exothermic adsorption reaction. FT- IR study and computational chemistry study proved that the decolorization interaction mechanism between the positive (-N+) sites of MB dye and the negative (- OH) active sites of the new Schiff base adsorbent at the optimum conditions occurred as a physisorption process.

Chemical predictive modeling of ethyl-p-methoxycinnamate and synthesis of natural lotion from kencur (Kaempferia galanga L.) as sunscreen agents

Solar radiation is essential for the evolution of life on earth. Solar radiation, including ultraviolet radiation (UV), reaches the earth's surface. The sun emits three types of UV radiation: UVA, UVB, and UVC, which have beneficial and harmful effects on the human body. The most important benefit is the synthesis of vitamin D in the skin. However, UVB radiation also causes direct photochemical damage to DNA. This study aimed to investigate the ability of the compound ethyl-p-methoxycinnamate (EPMS) that is available in kencur as a sunscreen agent through computational chemistry studies using the Hartree-Fock (HF) method and time-dependent density functional theory (TD-DFT) and perform synthesis of lotion from kencur extract. The investigation began with creating a molecular model of a sunscreen agent optimized for geometry using the HF method and continued with spectrum analysis using TD-DFT. The study's results showed that the analysis of the EPMS spectrum could be used as a natural UVB shield. In addition, the synthesis of lotion from kencur rhizome made using oil and water phases showed organoleptic, pH, homogeneity, and spreadability test results fitted according to the Indonesian National Standard (SNI) 16-4399-1996. It indicated that kencur lotion could potentially be used as a sunscreen agent.