A computational investigation of galactopyranoside esters as antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetics, and bioactivity prediction

One of the most common viral infections worldwide is the Human Papilloma Virus (HPV) which has been linked to cancer and other diseases in many countries. Monosaccharide esters are significant in the field of carbohydrate chemistry because they are efficient in the synthesis of pharmacologically active compounds. Therefore, the present study aimed to perform thermodynamic, molecular docking and molecular dynamics study of a series of previously designed monosaccharaides, methyl β-d-galactopyranoside (MGP, 1) esters (2-10) with along with their physicochemical and pharmacokinetic properties. We have optimized the MGP esters employing the DFT study at the B3LYP/6-311 + G (d,p) level of theory. The subsequent analysis also investigated the electronic energies, enthalpies, entropies, polarizability, and natural bond orbital (NBO) of these modified esters. Then, MGP esters were docked into CTX-M-15 extended-spectrum beta-lactamase from Escherichia coli (PDB: 4HBT) and E2 DNA-binding domain from human papillomavirus type 31 (PDB: 1A7G), and the results revealed that most of the esters can efficiently bind to the target. Desmond was used to doing molecular dynamics simulations at 200 ns in addition to molecular docking to look at the binding conformational stability of the protein-ligand complex. Based on RMSD and RMSF, it was determined that the stability of the protein-ligand combination was maintained during the whole 200 ns simulations for all compounds. Finally, a pharmacokinetic study suggests that modified esters of MGP exhibited better pharmacokinetic characteristics and were less hazardous than the parent drug. This work demonstrated that potential MGP esters can efficiently bind to 4HBT and 1A7G proteins and opened avenues for the development of newer antimicrobial agents that can target dangerous pathogens.Communicated by Ramaswamy H. Sarma.

Integrated CO2 capture and electrochemical upgradation: the underpinning mechanism and techno-chemical analysis

Coupling post-combustion CO2 capture with electrochemical utilization (CCU) is a quantum leap in renewable energy science since it eliminates the cost and energy involved in the transport and storage of CO2. However, the major challenges involved in industrial scale implementation are selecting an appropriate solvent/electrolyte for CO2 capture, modeling an appropriate infrastructure by coupling an electrolyser with a CO2 point source and a separator to isolate CO2 reduction reaction (CO2RR) products, and finally selection of an appropriate electrocatalyst. In this review, we highlight the major difficulties with detailed mechanistic interpretation in each step, to find out the underpinning mechanism involved in the integration of electrochemical CCU to achieve higher-value products. In the past decades, most of the studies dealt with individual parts of the integration process, i.e., either selecting a solvent for CO2 capture, designing an electrocatalyst, or choosing an ideal electrolyte. In this context, it is important to note that solvents such as monoethanolamine, bicarbonate, and ionic liquids are often used as electrolytes in CO2 capture media. Therefore, it is essential to fabricate a cost-effective electrolyser that should function as a reversible binder with CO2 and an electron pool capable of recovering the solvent to electrolyte reversibly. For example, reversible ionic liquids, which are non-ionic in their normal forms, but produce ionic forms after CO2 capture, can be further reverted back to their original non-ionic forms after CO2 release with almost 100% efficiency through the chemical or thermal modulations. This review also sheds light on a focused techno-economic evolution for converting the electrochemically integrated CCU process from a pilot-scale project to industrial-scale implementation. In brief, this review article will summarize a state-of-the-art argumentation of challenges and outcomes over the different segments involved in electrochemically integrated CCU to stimulate urgent progress in the field.

Tuning Functionalized Ionic Liquids for CO2 Capture

The increasing concentration of CO₂ in the atmosphere is related to global climate change. Carbon capture, utilization, and storage (CCUS) is an important technology to reduce CO₂ emissions and to deal with global climate change. The development of new materials and technologies for efficient CO₂ capture has received increasing attention among global researchers. Ionic liquids (ILs), especially functionalized ILs, with such unique properties as almost no vapor pressure, thermal- and chemical-stability, non-flammability, and tunable properties, have been used in CCUS with great interest. This paper focuses on the development of functionalized ILs for CO₂ capture in the past decade (2012~2022). Functionalized ILs, or task-specific ILs, are ILs with active sites on cations or/and anions. The main contents include three parts: cation-functionalized ILs, anion-functionalized ILs, and cation-anion dual-functionalized ILs for CO₂ capture. In addition, classification, structures, and synthesis of functionalized ILs are also summarized. Finally, future directions, concerns, and prospects for functionalized ILs in CCUS are discussed. This review is beneficial for researchers to obtain an overall understanding of CO₂-philic ILs. This work will open a door to develop novel IL-based solvents and materials for the capture and separation of other gases, such as SO₂, H₂S, NOx, NH₃, and so on.

T- and pH-dependent OH radical reaction kinetics with glycine, alanine, serine, and threonine in the aqueous phase

Glycine, alanine, serine, and threonine are essential amino acids originating from biological activities. These substances can be emitted into the atmosphere directly. In the present study, the aqueous phase reaction kinetics of hydroxyl radicals (˙OH) with the four amino acids is investigated using the competition kinetics method under controlled temperature and pH conditions. The following T-dependent Arrhenius expressions are derived for the ˙OH reactions with glycine, k(T, H₂A⁺) = (9.1 ± 0.3) × 10⁹ × exp[(-2360 ± 230 K)/T], k(T, HA^±) = (1.3 ± 0.1) × 10¹⁰ × exp[(-2040 ± 240 K)/T]; alanine, k(T, H₂A⁺) = (1.4 ± 0.1) × 10⁹ × exp[(-1120 ± 320 K)/T], k(T, HA^±) = (5.5 ± 0.2) × 10⁹ × exp[(-1300 ± 200 K)/T]; serine, k(T, H₂A⁺) = (1.1 ± 0.1) × 10⁹ × exp[(-470 ± 150 K)/T], k(T, HA^±) = (3.9 ± 0.1) × 10⁹ × exp[(-720 ± 130 K)/T]; and threonine, k(T, H₂A⁺) = (5.0 ± 0.1) × 10¹⁰ × exp[(-1500 ± 100 K)/T], k(T, HA^±) = (3.3 ± 0.1) × 10¹⁰ × exp[(-1320 ± 90 K)/T] (in units of L mol^-1 s^-1). The energy barriers of the ˙OH-induced H atom abstractions were simulated by the density functional theory (DFT) calculation performed with GAUSSIAN using the method of M06-2X and the basis set of 6-311++G(3df,2p). According to the calculation results, the -COOH and -NH₃⁺ groups with strong negative inductive effects increase the energy barriers and thus decrease the ˙OH reaction rate constants. In contrast, the presence of a -OH or -CH₃ group with weak negative or positive inductive effects can reduce energy barriers and hence increase the ˙OH reaction rate constants. To improve the previous structure-activity relationship, the contribution factors of -NH₃⁺ at C_α-atom and C_β-atom are determined as 0.07 and 0.15, respectively. Aqueous phase ˙OH oxidation acts as an important sink of the amino acids in the atmosphere, and can be accurately described by the obtained Arrhenius expressions under atmospheric conditions.

A combined DFT and FT-IR study on the surface interactions in alumina supported ionic liquid [H-Pyr]+[HSO4]. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020;226:117545. [PMID: 31710889 DOI: 10.1016/j.saa.2019.117545]

The surface interactions in [H-Pyr]⁺[HSO₄]^-/γ-Al₂O₃ system (prepared by wetness impregnation method) are investigated theoretically and experimentally. For that purpose, atoms in molecules theory, natural bond orbital and natural charge population analyses in a combination with a vibrational spectroscopy (FT-IR) are used. It is established that a bond formation between the hydrogen sulfate anion and the alumina influences the IL-support interaction in a great extent. However, a support-cation and a cation-anion interaction in the immobilized [H-Pyr]⁺[HSO₄]^- present as well. A comparative analysis between the experimental and the calculated vibrational modes is carried out and a significant number of infrared bands are assigned. The results indicate a good correlation between the experimental and the theoretical IR frequencies. It is found that the aforementioned interactions affected the vibrational frequencies in the supported IL.

The Interplay between Charge Transport and CO2 Capturing Mechanism in [EMIM][SCN] Ionic Liquid: A Broadband Dielectric Study

The hoisted increment in the CO₂ emission in the atmosphere is a noteworthy environmental problem. Gas-liquid absorption is a well-known strategy that can be used to control CO₂ emissions from an increased rate of fossil fuel industrializations. In this work, a combination of broadband dielectric spectroscopy, Fourier infrared (FTIR) spectroscopy, and quantum chemical calculations were used to study the absorption, desorption and kinetic mechanism of a room temperature imidazolium ionic liquid (IL) with cyanide anion, 1-ethyl-3-methylimidazolium thiocyanate ([EMIM][SCN]) on CO₂ exposure. Initially, the charge transport and glassy dynamics of [EMIM][SCN] is investigated in a wide frequency and temperature range using broadband dielectric spectroscopy and differential scanning calorimetry. The conductivity relaxation was well fitted with Havriliak-Negami function in the modulus formalism, while the dc conductivity correlated well with the Barton-Nakajima-Namikawa relation. Then, the conductometric approach was taken to monitor the interplay between the ionic conductivity of [EMIM][SCN] and diffusion of captured CO₂ in it. The resistance of the IL increases upon CO₂ exposure, indicating a chemical change at the molecular level of [EMIM][SCN]. The possible CO₂ capturing mechanisms for [EMIM][SCN] were investigated with density functional theory calculations and FTIR spectroscopy. Thus, this work proposes a new strategy to explain the mechanism underlined in chemisorption of CO₂ in the [EMIM][SCN]. This can be extended to more promising CO₂ capturing materials including ionic liquids especially imidazolium-based ionic liquids with cyanide anions like dicyanimide, tricyanometanide, tetracyanoborate, etc.

New Coordination Complexes Based on the 2,6-bis[1-(Phenylimino)ethyl] Pyridine Ligand: Effective Catalysts for the Synthesis of Propylene Carbonates from Carbon Dioxide and Epoxides

We aimed to develop new effective catalysts for the synthesis of propylene carbonate from propylene oxide and carbon dioxide. A kind of M^x+LCl_x coordination complex was fabricated based on the chelating tridentate ligand 2,6-bis[1-(phenylimino)ethyl] pyridine (L). The obtained products were characterized by elemental analysis, infrared spectroscopy, ultraviolet spectroscopy, thermogravimetric analysis, and single-crystal X-ray diffraction. It was found that the catalytic activity of the complexes with different metal ions, the same ligand differed and co-catalyst, where the order of greatest to least catalytic activity was 2 > 3 > 1. The catalytic system composed of complex 2 and DMAP proved to have the better catalytic performance. The yields for complex 2 systems was 86.7% under the reaction conditions of 100 °C, 2.5 MPa, and 4 h. The TOF was 1026 h⁻¹ under the reaction conditions of 200 °C, 2.5 MPa, and 1 h. We also explored the influence of time, pressure, temperature, and reaction substrate concentration on the catalytic reactions. A hypothetical catalytic reaction mechanism is proposed based on density functional theory (DFT) calculations and the catalytic reaction results.

Molecular dynamics, physical and thermal stability of neat amorphous amlodipine besylate and in binary mixture

In this paper, a stable amorphous solid dispersion of an antihypertensive drug, amlodipine besylate (AMB) was prepared by entrapping it in a polymer matrix, polyvinyl pyrrollidone, in different weight ratios (AMB/PVP 05:95, 10:90, 20:80, 30:70). The glass forming ability of all binary dispersions were studied by means of differential scanning calorimetry and found good correlation between experimental T_g and Fox Flory's prediction. By considering the daily dosage limit of 5 mg, a weight ratio of 05:95 was further considered for the study. The structures of neat and binary of AMB were characterized by density functional theory, Fourier transform infrared spectroscopy, Fourier transform Raman spectroscopy and UV-visible spectroscopy. Further, detailed molecular dynamics of both pure and binary were investigated using broadband dielectric spectroscopy to judge the physical stability of the amorphous dispersions. Translation-rotation coupling of AMB possibly explains the dual conductivity and dipolar nature of the secondary relaxation in neat AMB. Thus, the binary dispersion of AMB with commercially acceptable weight ratio with strong glass forming behaviour and better shelf life was prepared and characterized for practical applications.

Fluorinated graphene as an anticancer nanocarrier: an experimental and DFT study

Both experimental and theoretical research was conducted to explore the performance of fluorinated graphene as a novel anticancer nanocarrier, and we also reported its first application in cancer chemo-photothermal therapy.

DFT study on the dissolution mechanisms of α-cyclodextrin and chitobiose in ionic liquid

Density functional theory (DFT) was employed to study the dissolution mechanisms of α-cyclodextrin and chitobiose in 1-ethyl-3-methyl-imidazolium acetate ([Emim][OAc]). Geometrical analysis of the studied complexes indicated that both anion and cation in ionic liquid interacting withα-cyclodextrin and chitobiose contributed to the dissolution reaction. Intermolecular interactions in the complexes were identified as non-covalent interactions, such as hydrogen bonds, van der Waals interactions and repulsions, which were considered as the driving force of dissolution. Among them, hydrogen bonding interactions played a dominant role, which was further visualized in the real space by combination of atoms in molecules (AIM) and reduced density gradient (RDG) techniques. The nature of intermolecular orbital interactions was characterized using natural bond orbital (NBO) theory.

New insights into the chemistry of ionic alkylorganic carbonates: a computational study

A library of hydrogenated, perfluorinated aliphatic and aromatic alcohols are selected together with a combination of superbases and metal hydrides to understand the thermodynamics of the binary mixtures once serving as sorbents for the capture of CO₂via ionic organic alkylcarbonate formation.

Simultaneous CO2 and SO2 capture by using ionic liquids: a theoretical approach

Density functional theory (DFT) methods were used to analyze the mechanism of interaction between acidic gases and ionic liquids based on the 1-ethyl-3-methylimidazolium cation coupled with five different anions.

Green synthesis of 1-phenyl-1-ortho-xylene ethane in IL and reaction mechanism

In this study, 1-phenyl-1-ortho-xylene ethane (PXE) is synthesized in IL and the catalysts used were AlCl₃ in 1-butyl-3-methylimidazolium bromide ([BMIM][Br]) or 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]).

Thermal reaction of the ionic liquid 1,2-dimethyl-(3-aminoethyl) imidazolium tetrafluoroborate: a kinetic and theoretical study

Since the thermal stabilities of ionic liquids (ILs) are of significance for their application, an amine-functionalized IL 1,2-dimethyl-(3-aminoethyl) imidazolium tetrafluoroborate [aEMMIM][BF4] was chosen to study thermal decomposition mechanisms via the methods of FT-IR, (1)H NMR, TGA, TGA-MS and density functional theory (DFT) calculations. Theoretical and experimental results indicated that amine-functionalization reduces the thermal stability of [aEMMIM][BF4] compared to its non-functionalized counterpart. Moreover, we found that [aEMMIM][BF4] follows a unimolecular nucleophilic substitution (SN1) decomposition (98.8 %), whereas the bimolecular nucleophilic substitution (SN2) decomposition (1.2 %) is unfavorable. The SN1 and SN2 reactions were fully optimized at B3LYP/6-311++G(d,p) level, and the energies of reactant (R), intermediates (IM), transition state (TS) and product (P) were obtained and analyzed by reaction mechanism. The energy of the intermediate is higher than that of the reactants by 18.92 kJ mol(-1), and the energy of the TS is higher than that of the IM by 155.23 kJ mol(-1). This result indicates that the IM are also more stable than the P2 product, thus the reaction is endothermic. The chemical nature of the covalent and hydrogen bonds was analyzed by vibrational modes analysis (VMA), nature bond orbital (NBO) and the theory of atoms in molecules (AIM). Graphical Abstract Proposed thermal decomposition of [aEMMIM][BF4] via unimolecular ( SN1) and bimolecular( SN2) nucleophilic substitution mechanisms. The electrostatic potential surface (ESP) of the transition state illustrates that hydrogen bonds are generated when [BF4](-) is close to [aEMMIM](+), and SN1 decomposition is much favorable than SN2 decomposition.

Theoretical study on the mechanism of oxidative–extractive desulfurization in imidazolium-based ionic liquid

The oxidation of TH to SP by H₂O₂ with the assistance of IL experiences two steps via two transition states.

Density functional theory study on the thermodynamics and mechanism of carbon dioxide capture by CaO and CaO regeneration

The bond length between the C atom in CO₂ and O atom in CaO was about 1.39–1.42 Å, and the bond length of C–O in adsorbed CO₂ was prolonged to 1.26–1.27 Å, while the O–C–O angle of adsorbed CO₂ was about 129°.