Types Of Hydrogen Bonds Research Articles

Mechanism Analysis of Heavy Oil Viscosity Reduction by Ultrasound and Viscosity Reducers Based on Molecular Dynamics Simulation.

Ultrasound and viscosity reducers are commonly used methods to reduce the viscosity of heavy oil. In order to compare the viscosity reduction effects of ultrasound and viscosity reducers and study their mechanism of interaction on heavy oil, molecular dynamics simulation was carried out in this paper. First, a molecular model of heavy oil composed of asphaltene, resin, aromatic hydrocarbon, and saturated hydrocarbon was established in this work. Through molecular dynamics simulation, the different effects of ultrasound and viscosity reducers on the viscosity reduction rate, hydrogen bond number, hydrogen bond type, and occupation rate were obtained, and the viscosity reduction mechanism of ultrasound and viscosity reducers was analyzed. By calculating the viscosity reduction rate and the number of hydrogen bonds of five oil-soluble viscosity reducers with or without ultrasound, it was found that the types of hydrogen bonds affecting the viscosity reduction effect were different with or without ultrasound or viscosity reducer, and the type and content of viscosity reducer would affect the effect of ultrasonic viscosity reduction. The amplitude, frequency, and temperature of ultrasound were also the factors affecting the effect of viscosity reducers. The simulation results helped to explain the mechanism of jointly reducing the viscosity of heavy oil by ultrasound and viscosity reducers from the microscopic point of view and provided a theoretical basis for the industrial application of ultrasound and viscosity reducers to reduce the viscosity of heavy oil.

New Polyketides from Mangrove Endophytic Fungus Penicillium sp. BJR-P2 and Their Anti-Inflammatory Activity.

Four new polyketide compounds, including two new unique isocoumarins penicillol A (1) and penicillol B (2) featuring with spiroketal rings, two new citreoviridin derivatives citreoviridin H (3) and citreoviridin I (4), along with four known analogues were isolated from the mangrove endophytic fungus Penicillium sp. BJR-P2. Their structures were elucidated by extensive spectroscopic methods. The absolute configurations of compounds 1–4 based on electronic circular dichroism (ECD) calculations, DP4+ analysis, and single-crystal X-ray diffraction are presented. All the new compounds were evaluated for anti-inflammatory activity. An anti-inflammatory assay indicated that compound 2 inhibited lipopolysaccharide (LPS)-induced NO production in RAW 264.7 cells, with half-maximal inhibitory concentration (IC50) values of 12 μM, being more potent than the positive control, indomethacin (IC50 = 35.8 ± 5.7 μM). Docking study showed that compound 2 was perfectly docking into the active site of murine inducible nitric oxide oxygenase (iNOS) via forming multiple typical hydrogen bonds.

Colorimetric switching and sensing of CO2 based on reversible proton movement between the two heavy atoms in low barrier hydrogen bond in PDI radical anion/b-PEI hydrogen bonding complex

The photophysical properties of the hydrogen bond complexes consisting of low-barrier hydrogen bond (LBHB) depend on their environmental condition. However, the stimuli responsive materials based on LBHB are still a challenging problem. Here, we report a novel material system which has high color response to CO2 based on the position changes of the proton between the two heavy atoms in the low barrier hydrogen bond. Perylene diimide radical anion/branched polyethyleneimine hydrogen bonding complex (TFPDI-b-PEI) linked by low-barrier hydrogen bond ([O1-----H1---N1]−1) is obtained and it shows the maximum absorption of 789 nm. Meanwhile, the maximum absorption of TFPDI-b-PEI appears at 561 nm with purple when CO2 is adsorbed in the branched polyethyleneimine. In essence, the geometry of LBHB in TFPDI-b-PEI can switch between two types of hydrogen bond ([O1----H1----N1]−1 and [O1-----H1---N1]−1) via adjusting the interaction between the surrounding molecule and amine groups in LBHB by interaction of CO2 with TFPDI-b-PEI. Further the TFPDI-b-PEI shows excellent color switching and colorimetric sensing performance for CO2 aqueous solution and its gas based on this hydrogen bond dynamic characteristic.

X-ray diffraction, IR spectrum, optical properties, AIM, NBO, RDG, HS, Fukui function, biological and molecular docking analysis of a novel hybrid compound (C9H15N3)[CuCl4(H2O)

The paper reports the preparation and structural characterization of a novel hybrid complex (C9H15N3)[CuCl4(H2O)] grown by slow evaporation technique in aqueous solution at room temperature and characterized by X-ray diffraction, spectroscopy measurement, optical absorption, photoluminescence proprieties, Hirshfeld surface analysis, thermal and biological study. The title organic-inorganic material, (C9H15N3)[CuCl4(H2O)], crystallizes in monoclinic space group P21/n. The crystal arrangement consists of [CuCl4(H2O)]n2n− chains spreading alone c axis at x= 1/2 and y= 1/2. To build the three-dimensionality of the structure, the organic cations are linked to the chains through hydrogen bond type N – H···Cl, OW1 – H···Cl and C – H···Cl. The new prepared compound was screened for its antioxidant activity. The Photoluminescence proprieties were also reported. The nature and proportion of contacts and the rapport of enrichment in the crystal packing were studied by the Hirshfeld surfaces. The vibrational properties FT-IR and UV–VIS spectral analyses of present compound have been researched by theoretical calculations. Energy gap (Eg) of the molecule was found using LUMO and HOMO calculation. The local reactivity analyses (Fukui functions) were evaluated to identify the reactive sites in the protonated organic part. Intermolecular interactions were analyzed by molecular electrostatic potential surface (MEPS), the reduced density gradient (RDG), natural bond orbital (NBO) and topological AIM are reported. The thermal analysis (ATD/TG) reveals the decomposition of title compound. The NBO analysis of title compound shows that the maximum energy is equal to 37.61 Kcal.mol−1 confirmed the charge transfer between organic and inorganic groups. The activation of thermodynamic parameters is calculated by DFT/ B3LYP/LanL2DZ. Photoluminescence measurements (PL) showed two peaks at around 331 and 393 nm. The biological activities of (C9H15N3)[CuCl4(H2O)] were investigated by DPPH and ABTS tests. Finally, docking studies have been conducted to predict 2PPCU anti-tubercular activity and as a potential therapeutic target for anticancer treatment against transaminase- Bio A and VEGFR-2 kinase inhibitor respectively type PDB's.

Theoretical study on L-H+-L with identical donors: Short strong hydrogen bond or not?

Short strong hydrogen bonds (SSHBs) play a crucial role in many chemical processes. Recently, as the representative of SSHBs, [F-H-F]- was experimentally observed. [F-H-F]- has a symmetric structure, which can be described as a H+ acid shared by two terminal F- donors (F--H+-F-). To explore whether two identical donors are bound to result in SSHBs, we performed theoretical studies on a series of compounds (L-H+-L) with two identical electron donors (L corresponds to donors containing group 14, 15, 16, and 17 elements). The results show that identical donors do not definitely lead to SSHBs. Instead, typical hydrogen bonds also exist. Both electronegativity and basicity contribute to the patterns of hydrogen bonds, where more electronegative and weaker donors benefit to SSHBs. In addition, it was found that zero-point energies also respond to the hydrogen bonding systems. This systemic work is expected to provide more insights into SSHBs.

The effect of surface functional groups on the wettability of graphene oxide coated alumina substrate: Molecular dynamics simulations

In this article, molecular dynamic simulation was used to simulate the wetting process of graphene oxide coated alumina substrate. By changing the density of hydroxyl and epoxy groups on the surface of graphene oxide, the influence mechanism of two functional groups on the wetting process of water molecules was explored. From the simulation results, the increase of hydroxyl density can enhance the wettability of the substrate and reduce the wettability angle from 64.32° to 54.20°. By calculating the formation of the hydrogen bond in the wetting process, it is found that hydroxyl can significantly raise the hydrogen bond lifetime in the system. This increasing effect is particularly prominent in the observation of the hydrogen bond between water molecules and graphene oxide. The hydrogen bond lifetime increases from 2.20 ps to 12.77 ps. The result also reflects the reason why hydroxyl increases the wettability of the substrate. In addition, the increase of hydroxyl density also brings changes in hydrogen bond behavior and the number of hydrogen bonds. Under the condition of high epoxy density, most of the hydrogen bonds between water molecules and the substrate exist in the form of single hydrogen bonds, and the number is small. When the hydroxyl density increases, double-hydrogen bond, triple-hydrogen bond and single hydrogen bond appear in the model. In this process, the number of hydrogen bonds between the water droplet and the substrate is also increasing. Temperature is an important influence on the formation and lifetime of the hydrogen bond. High temperatures can promote the formation of the hydrogen bond between alumina and water molecules. In addition, it can also decrease the lifetime of all types of hydrogen bonds. Through the free energy perturbation theory, we get the free energy of different models in the wetting process. The results show that high hydroxyl density can improve the free energy of the wetting process, reduce the ability of spontaneous desorption and increase the stability of wetting. High temperatures can reduce the free energy and lead to the occurrence of desorption behavior. This article reveals the wetting mechanism of water molecules on graphene oxide coated alumina substrate, mainly reveals the influence of hydrogen bond and the change of free energy in the wetting process, which lays a theoretical foundation for the application of graphene oxide wetted coating on the aluminum alloy surface.

Effect ofGOagglomeration on the mechanical properties of graphene oxide and nylon 66 composites and micromechanical analysis

AbstractNanoparticles are prone to aggregation in the matrix under the action of surface energy, chemical bonding, electrostatic attraction, and van der Waals forces. Based on the molecular dynamics method, the tensile properties of graphene oxide (GO)‐reinforced nylon 66 composites were simulated and calculated, and the stress–strain curves, atomic stress clouds, and changes in the number of hydrogen bonds were obtained for the composites under tensile loading, and the effects of GO agglomeration on the mechanical properties of GO/PA66 composites were analyzed. When the GO mass fraction accounted for 90.3%, 80.5%, and 70.6% of the model, respectively, the mechanical properties of the composites decreased by 15.4%, 4.5%, and 4.2%, respectively. Because GO agglomeration in the composites made it difficult to bond effectively between GO and PA66, the number of hydrogen bonds and the type of hydrogen bonds within the model, varied with the degree of aggregation. The changes in the number of hydrogen bonds and the type of hydrogen bonds during uniaxial stretching were simulated by molecular dynamics. The number of hydrogen bonds and the type of hydrogen bonds directly affect the mechanical properties of the composites. It can be seen from the atomic stress cloud diagram that the aggregation of GO makes the mechanical properties of GO fail to exert effectively. The main stress is on the C atoms in the outermost layer of GO, while the stress on the inner layer C atoms is relatively small. As the degree of GO agglomeration decreases, the stress on each C atom of GO lamellae tends to be uniform, which effectively brings into play the excellent mechanical properties of GO and improves the mechanical properties of the composite.

Exploring dithiolate-amine binary ligand systems for the supramolecular assemblies of Ni(II) coordination compounds: Crystal structures, theoretical studies, cytotoxicity studies, and molecular docking studies

Dithiolate-amine binary ligand systems based two novel supramolecular structures of Ni(II) coordination compounds [Ni(2-ap)2(i-mnt)] (1) and [Ni2(i-mnt)2(tn)2]n (2) [where i-mnt−2: 1,1-dicyanoethylene-2,2-dithiolate, 2-ap: 2-amino pyridine, tn: 1,3-diaminopropane] have been designed, synthesized and characterized by spectroscopic techniques and X-ray crystallography. In complex 1, the N2S2 coordination kernel around Ni+2 attains distorted square planar geometry (Okuniewski parameter τ/4 = 0.17) and its supramolecular array has a dominant influence of N H···N type hydrogen bonds forming significant ring geometry of graph-set-motifR428. The i-mnt−2 adopts a diverse coordination mode in 2 contrary to 1 resulting in a binuclear one-dimensional infinite polymeric chain structure of consecutive NiS4 [square planar, S4 donor set τ/4 = 0] and NiN6 (octahedral) coordination kernels linked by i-mnt−2 that runs along [1 0 0] axis wherein N H···S, N H···N, C H···S type hydrogen bonds are believed to be crystal structure stabilizers. The Hirshfeld surface analyses (HS) at the molecular and atomic levels have been extensively studied to quantify all non-covalent interactions/contacts and the nature of ligand - metal interactions. The prominent N···H/H···N [28.1 % (1), 27.3 % (2A, NiS4), 20 % (2B, NiN6)] and S···H/H···S contacts [10.4 % (1), 32.8 % (2A), 29 % (2B)] presumably play vital role in crystal packing. The non-covalent interactions were further investigated by Molecular Electrostatic Potential (MEP) surface at PBE0-D3/def2-TZVP level and QTAIM optimizations (for 1). The MTT assay study using SW620 metastatic colon cancer cells shows a significant dose-dependent decline in cell proliferation with increasing concentration for 1 but for 2, the reverse trend is followed. A molecular docking study with the APC protein has further investigated the antiproliferative activity of 1 (MTT assay).

Co-Assembly of Chiral Amines and a Four-Armed Cyano-Substituted Luminophore through Hydrogen Bonds for Potential Development of Smart Chiroptical Materials.

Chirality transfer from chiral molecules to assemblies is of vital importance to the design of functional chiral materials. In this work, selective co-assembly behaviors between chiral molecules and an achiral luminophore, potentially driven by the intermolecular salt-bridge type hydrogen bonds are reported. Cyano-substituted tetrakis(arylthio)benzene carboxylic acid (TA) served as the luminophore and hydrogen bond donors, which underwent co-assembly with different chiral amines. It was found that structures of chiral amines affect the chirality transfer and the properties of co-assemblies due to effects on hydrogen bonds and stacking pattern. Only in specific co-assemblies, the chiroptical properties occurred at both ground state and excited states based on the emerged Cotton effects and circularly polarized luminescence (CPL) signals, revealing that the chirality was successfully transferred from molecular level to supramolecular level. In addition, accurate quantitative examination of chiral amines was realized by circular dichroism (CD) spectra. This work demonstrates the characteristic chirality response and transfer through co-assembly, providing a potential method to develop smart chiroptical materials.

Investigations of cysteine isomers using Terahertz and Raman spectroscopies

The properties of chiral compounds are closely related to their molecular interactions, and differences in their interactions are usually manifested in their corresponding vibrational spectra. In this study, we measured the vibrational spectra of L- and DL-cysteine over a wide range of frequencies from 20 to 4000 cm−1 using terahertz time-domain spectroscopy, far-infrared spectroscopy, and Fourier-transform Raman spectroscopy. To analyze the origins of the characteristic peaks in the measured spectra, the vibrational spectra of L- and DL-cysteine were first calculated using density functional theory, and the intermolecular/intramolecular interaction regions were graphed using the Interaction Region Indicator. The results showed that the intramolecular interactions between L- and DL-cysteine were very similar, but there were some differences in the types of hydrogen bonds that formed between the different molecules, and the positions of the intermolecular interactions were related to the positions of the intramolecular functional groups. These calculated differences in interactions between L- and DL-cysteine molecules also were seen in the measured vibrational spectra. This study provides a framework and unique approach to understanding polymorphisms in molecular crystals as well as intermolecular interactions.

Syntheses and crystal structures of 4-(4-nitro-phen-yl)piperazin-1-ium benzoate monohydrate and 4-(4-nitro-phen-yl)piperazin-1-ium 2-carb-oxy-4,6-di-nitro-phenolate.

Crystal structures are reported for two mol-ecular salts containing the 4-(4-nitro-phen-yl)piperazin-1-ium cation. Co-crystallization from methanol/ethyl acetate solution of N-(4-nitro-phen-yl)piperazine with benzoic acid gives the benzoate salt, which crystallizes as a monohydrate, C10H14N3O2·C7H5O2·H2O, (I), and similar co-crystallization with 3,5-di-nitro-salicylic acid yields the 2-carb-oxy-4,6-di-nitro-phenolate salt, C10H14N3O2·C7H3N2O7, (II). In the structure of (I), a combination of O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds links the components into sheets, while in the structure of (II), the supra-molecular assembly, generated by hydrogen bonds of the same types as in (I), is three dimensional. Comparisons are made with the structures of some related compounds.

Identification of egg protein-derived peptides as xanthine oxidase inhibitors: virtual hydrolysis, molecular docking, and in vitro activity evaluation

The purpose of this study was to screen the xanthine oxidase (XO) inhibitory peptides from egg white proteins through virtual hydrolysis, in vitro activity validation, and molecular docking. The results demonstrated that tripeptide EEK from ovalbumin exhibited potent XO inhibitory activity with an IC50 value of 141 µmol/L. The molecular docking results showed that tripeptide EEK bound with the active center of XO via 3 carbon hydrogen bond interactions, 2 salt bridges, 5 conventional hydrogen bond interactions, and 4 attractive charge interactions. The residues Glu802, Phe1009, and Arg880 may play key roles in the XO catalytic reaction. Especially, the key intermolecular forces of inhibiting XO activity may be special type of hydrogen bonds including carbon hydrogen bond interactions and attraction charge interactions. The novel tripeptide EEK is potential candidates for controlling hyperuricemia.

Synthesis, structural characterization, and evaluation of new peptidomimetic Schiff bases as potential antithrombotic agents.

New Schiff bases functionalized with amide and phenolic groups synthesized by the condensation of 2-hydroxybenzaldehyde and 2-hydroxyacetophenone with amino acid amides which in turn were prepared in two steps from N-Boc-amino acids and homoveraltrylamine through intermediate compounds N-Boc-amino acids amides. The compounds were characterized by elemental analysis, FT-IR, UV–Vis, and NMR spectroscopy. The crystal structures of three Schiff bases were determined by single crystal X-ray diffraction. There exists O–Hcdots N, N–Hcdots O, and C–Hcdots O types of hydrogen bonds and C–Hcdotsuppi secondary bonding interactions in these crystalline solids. The Schiff bases have been screened for anticoagulant and antiplatelet aggregation activities. All the compounds showed procoagulant activity which shortens the clotting time of citrated human plasma in both platelet-rich plasma and platelet-poor plasma except the derivatives of L-methionine which showed anticoagulant activity by prolonging the clotting time. In addition, the compounds derived from benzyl cysteine and phenylalanine showed adenosine diphosphate induced antiplatelet aggregation activity, whereas others did not show any role. Moreover, all these compounds revealed non-hemolytic activity with red blood cells.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s00706-022-02936-6.

Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations

In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA. Communicated by Ramaswamy H. Sarma

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.

The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. Here, we extend an existing framework which allows arbitrarily chosen force-field correction terms to be fitted by quantification of the discrepancy between observables back-calculated from simulation and corresponding experiments. We apply a robust regularization protocol to avoid overfitting and additionally introduce and compare a number of different regularization strategies, namely, L1, L2, Kish size, relative Kish size, and relative entropy penalties. The training set includes a GACC tetramer as well as more challenging systems, namely, gcGAGAgc and gcUUCGgc RNA tetraloops. Specific intramolecular hydrogen bonds in the AMBER RNA force field are corrected with automatically determined parameters that we call gHBfixopt. A validation involving a separate simulation of a system present in the training set (gcUUCGgc) and new systems not seen during training (CAAU and UUUU tetramers) displays improvements regarding the native population of the tetraloop as well as good agreement with NMR experiments for tetramers when using the new parameters. Then, we simulate folded RNAs (a kink–turn and L1 stalk rRNA) including hydrogen bond types not sufficiently present in the training set. This allows a final modification of the parameter set which is named gHBfix21 and is suggested to be applicable to a wider range of RNA systems.

Crystal-structure studies of 4-phenyl-piperazin-1-ium 4-eth-oxy-benzoate monohydrate, 4-phenyl-piperazin-1-ium 4-meth-oxy-benzoate monohydrate, 4-phenyl-piperazin-1-ium 4-methyl-benzoate monohydrate and 4-phenyl-piperazin-1-ium tri-fluoro-acetate 0.12-hydrate.

In this study, four new piperazinium salts, namely, 4-phenyl-piperazin-1-ium 4-eth-oxy-benzoate monohydrate, C9H9O3·C10H15N2·H2O (I); 4-phenyl-piperazin-1-ium 4-meth-oxy-benzoate monohydrate, C10H15N2·C8H7O3·H2O (II); 4-phenyl-piperazin-1-ium 4-methyl-benzoate monohydrate, C10H15N2·C8H7O2·H2O (III); and 4-phenyl-piperazin-1-ium tri-fluoro-acetate 0.12 hydrate, C10H15N2·C2F3O2·0.12H2O (IV), have been synthesized. The single-crystal structures of these compounds reveal that all of them crystallize in the triclinic P space group and the crystal packing of (I)-(III) is built up of ribbons formed by a combination of hydrogen bonds of type N-H⋯O, O-H⋯O and other weak inter-actions of type C-H⋯O and C-H⋯π, leading to a three-dimensional network. In the crystal of (IV), the cations and the anions are connected by C-H⋯O, N-H⋯O and C-H⋯F hydrogen bonds and by C-H⋯π inter-actions, forming sheets which in turn inter-act to maintain the crystal structure by linking through the oxygen atoms of water mol-ecules and van der Waals inter-actions, giving the whole structure.

Vibrational dynamics of ethosuximide polymorphs. Infrared absorption and inelastic neutron scattering spectroscopy and model calculations

Commercially available and administered to the patients ethosuximide is a racemic mixture of two enantiomers, each of them exist in different conformations. The presence of the species mentioned are proven by the title experimental methods aided by DFT model calculations. Results of the latter are matched against spectroscopic data by the clustering window analysis. One type of hydrogen bonds exist in the solid forms of ethosuximide NH⋯O, leading to the polymorphic variety of the substance studied.

Fabrication and Characterization of High-Performance Crosslinked PVA/ PMDA Doped with H2SO4

In the present study, pure Poly(viny1 alcohol) (PVA) and pyromellitic dianhydride (PMDA) cross linked PVA with (0,5,10,15 and 20)wt.% and doped with different molarity (5,9)M of sulfuric acid (H2SO4) were prepared by the solution casting method and were characterized as a function of frequency in the range (1-100) KHz. The FT-IR results showed that the strong broad band observed at 3738.05 and 3857.63 cm-1 may be assigned to O-H stretching due to the strong hydrogen bond of intramolecular and intermolecular type in PVA film. When PVA is doped with 5M and 9M H2SO4, a new peak was noticed at 813 cm-1, this peak may be due to the formation of hydrogen bond between the carbonyl (C=O) group of PVA and the H+ ion from the acid. As the PMDA concentration increases, the peak intensity of the O–H band 3738.05 cm−1 gradually decreases due to the reaction of more –OH groups of the PVA molecules with the –COOH group. Hence, it is difficult for the crosslinked PVA polymer chains to pack and form crystal regions, so the crosslinked PVA polymer chains become more flexible. The a.c. conductivity increases with the increase of frequency. FTIR spectra specified that the chemical reaction did occur between the PVA and the acid, therefore hydrogen ion (H+) can easily be separated from the carbonyl group and become free to move which explains proton conductivity of PVA. The increase of PMDA concentration has increased free volume and ionic mobility in the film with increasing cross-linkages. Dielectric constant decreases with increasing H2SO4 molarity for every frequency.

Delineating the RAS Conformational Landscape.

Analysis of >700 RAS structures helps define an expanded landscape of active, inactive, and druggable RAS conformations, the structural impact of common RAS mutations, and previously uncharacterized RAS inhibitor-binding modes.

Density Functional Theory Calculations of the Effect of Oxygenated Functionals on Activated Carbon towards Cresol Adsorption

The mechanism of adsorption of p-cresol over activated carbon adsorbent and the specific role of oxygen functional groups on cresol adsorption were studied using density functional theory (DFT) calculations. All the energy calculations and geometry optimization pertaining to DFT calculations were done using the B3LYP hybrid functional at basis set 6-31g level of theory in a dielectric medium of ε = 80 (corresponding to water). The interaction of cresol with different activated carbon models, namely pristine activated carbon, hydroxyl functionalized activated carbon, carbonyl functionalized activated carbon, and carboxyl functionalized activated carbon, were considered, and their adsorption energies corresponded to −416.47 kJ/mol, −54.73 kJ/mol, −49.99 kJ/mol, and −63.62 kJ/mol, respectively. The high adsorption energies suggested the chemisorptive nature of the cresol-activated carbon adsorption process. Among the oxygen functional groups, the carboxyl group tended to influence the adsorption process more than the hydroxyl and carbonyl groups, attributing to the formation of two types of hydrogen bonds between the carboxyl activated carbon and the cresol simultaneously. The outcomes of this study may provide valuable insights for future directions to design activated carbon with improved performance towards cresol adsorption.