Theoretical insights into the adsorption and gas sensing performance of Fe/Cu-adsorbed graphene.

The binding mechanism of gas molecules on material surfaces is essential for understanding adsorption and sensing performance. In the present study, we examine the interaction of some volatile organic compounds (VOCs), including HCHO, C2H5OH, and CH3COCH3, on pristine graphene and its Fe/Cu-adsorbed surfaces using first-principles calculations. The results indicate that the adsorption of these molecules on graphene is regarded as physisorption, while chemisorption is observed for Fe/Cu attached surfaces. The binding of sites on molecules and surfaces primarily involves hydrogen bonds for the pure form of graphene. In contrast, stable interactions occur at functional groups such as >CO, -OH with Fe/Cu atoms, as well as CC bonds of π-rings on modified structures of graphene. It is noticeable that stronger adsorption is observed in the case of Fe addition (Gr-Fe) compared to Cu (Gr-Cu), enhancing the gas adsorption and sensing performance on graphene. Remarkably, the graphene surfaces supported by Fe and Cu improved selectivity in detecting VOC molecules, particularly C2H5OH and CH3COCH3 for Gr-Fe, and HCHO for Gr-Cu. Quantum chemical analyses reveal that the Fe/Cu⋯O/C contacts are covalent interactions, contributing significantly to the stability of configurations and sensing properties of Fe/Cu-adsorbed graphene. In summary, the observed improvements in selectivity, enhanced adsorption strength, and the identification of crucial interactions at the surface offer valuable insights into designing highly efficient gas sensors and developing advanced sensing materials.

Characteristics of nonconventional hydrogen bonds and stability of dimers of chalcogenoaldehyde derivatives: a noticeable role of oxygen compared to other chalcogens.

In this work, twenty-four stable dimers of RCHZ with R = H, F, Cl, Br, CH3 or NH2 and Z = O, S, Se or Te were determined. It was found that the stability of most dimers is primarily contributed by the electrostatic force, except for the dominant role of the induction term in those involving a Te atom, which has been rarely observed. Both electron-donating and -withdrawing groups in substituted formaldehyde cause an increase in the strength of nonconventional Csp2-H⋯Z hydrogen bonds, as well as the dimers, in which the electron donating effect plays a more crucial role. The strength of nonconventional hydrogen bonds decreases in the following order: Csp2-H⋯O ≫ Csp2-H⋯S > Csp2-H⋯Se > Csp2-H⋯Te. Remarkably, a highly significant role of the O atom compared to S, Se and Te in increasing the Csp2-H stretching frequency and strength of the nonconventional hydrogen bonds and dimers is found. A Csp2-H stretching frequency red-shift is observed in Csp2-H⋯S/Se/Te, while a blue-shift is obtained in Csp2-H⋯O. When Z changes from O to S to Se and to Te, the Csp2-H blue-shift tends to decrease and eventually turns to a red-shift, in agreement with the increasing order of the proton affinity at Z in the isolated monomer. The magnitude of the Csp2-H stretching frequency red-shift is larger for Csp2-H⋯Te than Csp2-H⋯S/Se, consistent with the rising trend of proton affinity at the Z site and the polarity of the Csp2-H bond in the substituted chalcogenoaldehydes. The Csp2-H blue-shifting of the Csp2-H⋯O hydrogen bonds is observed in all dimers regardless of the electron effect of the substituents. Following complexation, the electron-donating derivatives exhibit a stronger Csp2-H blue-shift compared to the electron-withdrawing ones. Notably, the stronger Csp2-H blue-shift turns out to involve a less polarized Csp2-H bond and a decrease in the occupation at the σ*(Csp2-H) antibonding orbital in the isolated monomer.

Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond.

Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.

Indicuen, a new hopane from Parmotrema indicum Hale growing in Vietnam.

One new hopane-type triterpene, indicuen (1), along with eight known compounds (2-9) were isolated from the n-hexane extract of the lichen Parmotrema indicum Hale. The chemical structures of isolated compounds were identified by interpretation of their spectroscopic data (1D, 2D NMR and HRESIMS) combined with DFT-NMR chemical shift calculations and subsequent assignment of DP4+ probabilities and by comparison with the literature. Indicuen represents for a rare hopane bearing a 1-carboxyethyl substituent at C-21 in lichens. Compounds 1-3 and 5-8 were evaluated for α-glucosidase inhibition and cytotoxicity against K562 and HepG2 cancer cell lines. Compounds 1, 5 and 7 exhibited moderate α-glucosidase inhibition with IC50 values of 201.1, 156.3 and 187.4 µM, respectively. Compound 1 also showed weak cytotoxicity toward K562 cell line while others showed no activity.

Role of O-H⋯O/S conventional hydrogen bonds in considerable Csp2 -H blue-shift in the binary systems of acetaldehyde and thioacetaldehyde with substituted carboxylic and thiocarboxylic acids.

Stable binary complexes of RCZOH⋯CH3CHZ (R = CH3, H, F; Z = O, S) are due to contributions from the O-H⋯O/S and Csp2 -H⋯O/S hydrogen bonds. The strength of Csp2 /O-H⋯O is 1.5 to 2 times greater than that of the Csp2 /O-H⋯S bond. The substitution of H(Csp2 ) of HCZOH by CH3 causes a decrease in complex stability, while the opposite trend occurs for the F atom. A very large red shift of the O-H stretching frequency in O-H⋯O/S bonds was observed. A surprising Csp2 -H blue shift up to 104.5 cm-1 was observed for the first time. It is found that the presence of O-H⋯O/S hydrogen bonds and a decisive role of intramolecular hyperconjugation interactions in the complex cause a significant blue shift of the Csp2 -H covalent bonds. A striking role of O compared to the S atom in determining the blue shift of Csp2 -H stretching vibration and stability of binary complexes is proposed. The obtained results show that the ratio of deprotonation enthalpy and proton affinity could be considered as an index for the classification of the non-conventional hydrogen bond. SAPT2+ results show that the strength of RCSOH⋯CH3CHS complexes is dominated by electrostatic and induction energies, while a larger contribution to the stability of remaining complexes is detected for the electrostatic component.

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones.

Substituted 4-acetyl-3-hydroxy-3-pyrroline-2-ones have been prepared via three-component reactions and the tautomerism of these 3-pyrroline-2-ones is due to the slight difference of energy, and the significantly large rate constant of transformation between two tautomers. 1,4,5-Trisubstituted pyrrolidine-2,3-dione derivatives were prepared from the above mentioned 2-pyrrolidinone derivatives and aliphatic amines, which exist in enamine form and are stabilized by an intramolecular hydrogen bond. A possible reaction mechanism between 3-pyrroline-2-one and aliphatic amine (CH3NH2) was proposed based on computational results and the main product is formed favorably following the PES via the lowest ΔG # pathway in both the gas-phase and an ethanol solvent model. DFT calculations showed that kinetic selectivity is more significant than thermodynamic selectivity for forming main products.

Importance of water and intramolecular interaction governs substantial blue shift of Csp2 -H stretching frequency in complexes between chalcogenoaldehydes and water.

Geometrical structure, stability and cooperativity, and contribution of hydrogen bonds to the stability of complexes between chalcogenoaldehydes and water were thoroughly investigated using quantum chemical methods. The stability of the complexes increases significantly when one or more H2O molecules are added to the binary system, whereas it decreases sharply going from O to S, Se, or Te substitution. The O-H⋯O H-bond is twice as stable as Csp2 -H⋯O and O-H⋯S/Se/Te H-bonds. It is found that a considerable blue-shift of Csp2 -H stretching frequency in the Csp2 -H⋯O H-bond is mainly determined by an addition of water into the complexes along with the low polarity of the Csp2 -H covalent bond in formaldehyde and acetaldehyde. The Csp2 -H stretching frequency shift as a function of net second hyperconjugative energy for the σ*(Csp2 -H) antibonding orbital is observed. Remarkably, a considerable Csp2 -H blue shift of 109 cm-1 has been reported for the first time. Upon the addition of H2O into the binary systems, halogenated complexes witness a decreasing magnitude of the Csp2 -H stretching frequency blue-shift in the Csp2 -H⋯O H-bond, whereas CH3-substituted complexes experience the opposite trend.

Ricicomin A, a new alkaloid from the leaves of Ricinus communis Linn.

From the leaves of Ricinus communis Linn., one new alkaloid, named ricicomin A (1) together with three known ones, ricinine (2), N-demethylricinine (3) and 4-[2-formyl-5-(methoxymethyl)-1H-pyrrol-1-yl]butanoic acid (4) were justified by repeated chromatographic methods. Their structures were determined by comprehensive IR, HR-ESI-MS and NMR analyses. Compound 4 was identified for the first time from the genus Ricinus. DFT-NMR chemical shift calculations and subsequent DP4+ probability methods were applied to confirm the chemical structure of 1. Compounds 1-3 did not display cytotoxic effect against three human cancer cell lines (MCF-7, HepG2 and HeLa) using SRB assay.

A new 26-norlanostane from Phlogacanthus turgidus growing in Vietnam.

Chemical investigation on chloroform extract of Phlogacanthus turgidus led to the isolation of one new compound namely turgidol, together with five known triterpenoids, lupeol, lupenone, betulin, betulinic acid, and taraxerol. Their structures and stereochemistry have been determined by 1 D and 2 D NMR analysis, high resolution mass spectrometry, and compared with those in literatures. The relative configuration of turgidol was defined using DFT-NMR chemical shift calculations and subsequent DP4+ probability method. Turgidol, betulin, and betulinic acid were evaluated for cytotoxic activity toward K562 cancer cell line and the alpha-glucosidase inhibition.

A new diterpenoid from the leaves of Phyllanthus acidus.

A new diterpenoid, phyllane C (1), along with three known compounds, ovoideal E (2), spruceanol (3), and fluacinoid B (4) were isolated from the leaves of Phyllanthus acidus growing in Thailand. The structures were determined by analysis of their MS and NMR data as well as by comparison with literature values. DFT-NMR chemical shift calculations and subsequent DP4/DP4+ probability methods were applied to define the relative configuration of 1. Compound 3 showed a weak cytotoxicity against K562 cell line (IC50 41.9 ± 2.31 µg/mL).

Rukamtenol, a new spiro compound isolated from Flacourtia rukam Zoll. & Moritzi growing in Vietnam.

Chemical investigation of chloroform extract of Flacourtia rukam Zoll. & Moritzi stems led to the isolation of one new compound namely rukamtenol together with four known compounds, viz., chaulmooric acid, flacourtin, 3,4,5-trimethoxyphenyl ß-D-glucopyranoside, and daucosterol. Their structures and relative stereochemistry have been determined by 1D and 2D NMR analysis, high resolution mass spectroscopy, and compared with those in literatures. Rukamtenol represented the first 2-oxaspiro[4.4]non-8-en-3-one in nature. The relative configuration of rukamtinol was defined using DFT-NMR chemical shift calculations and subsequent DP4 probability method. Rukamtenol, flacourtin, and 3,4,5-trimethoxyphenyl ß-D-glucopyranoside were tested for cytotoxic activity toward three MDA-MB-231, HepG2, and RD cancer cell lines. However, they failed to reveal any activity (IC50 > 100 µM) on these cell lines.

Theoretical Aspects of Nonconventional Hydrogen Bonds in the Complexes of Aldehydes and Hydrogen Chalcogenides.

Hydrogen bonds (H-bonds) in the complexes between aldehydes and hydrogen chalcogenides, XCHO...nH2Z with X = H, F, Cl, Br, and CH3, Z = O, S, Se, and Te, and n = 1,2, were investigated using high-level ab initio calculations. The Csp2-H...O H-bonds are found to be about twice as strong as the Csp2-H...S/Se/Te counterparts. Remarkably, the S/Se/Te-H...S/Se/Te H-bonds are 4.5 times as weak as the O-H...O ones. The addition of the second H2Z molecule into binary systems induces stronger complexes and causes a positive cooperative effect in ternary complexes. The blue shift of Csp2-H stretching frequency involving the Csp2-H...Z H-bond sharply increases when replacing one H atom in HCHO by a CH3 group. In contrast, when one H atom in HCHO is substituted with a halogen, the magnitude of blue-shifting of the Csp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm-1 of Csp2-H stretching frequency in Csp2-H...O H-bond in CH3CHO...2H2O has rarely been observed and is much greater than that in the cases of the Csp2-H...S/Se/Te ones. The Csp2-H blue shift of Csp2-H...Z bonds in the halogenated aldehydes is converted into a red shift when H2O is replaced by a heavier analogue, such as H2S, H2Se, or H2Te. The stability and classification of nonconventional H-bonds including Csp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

SERS Chemical Enhancement of 2,4,5-Trichlorophenoxyacetic Acid Adsorbed on Silver Substrate.

Surface-enhanced Raman spectroscopy (SERS) was employed to gain an understanding of the chemical enhancement mechanism of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), an Agent Orange, adsorbed on a silver substrate surface. Experimental measurements were performed using a micro-Raman spectrophotometer with an excitation wavelength of 532 nm and successfully detected 2,4,5-T at a relatively low concentration of 0.4 nM. Density functional theory (DFT) calculations on the interactions of the 2,4,5-T molecule with some small silver clusters, Agn with n = 4, 8, and 20, as well as with extended Ag surfaces, demonstrate that the most stable adsorption configuration is formed via coordination of Cl9 sites and carbonyl C═O group on the 2,4,5-T ligand to the Ag atoms on surfaces. Analyses of charge transfer mechanism and frontier orbitals distributions show an electron transfer from 2,4,5-T to the cluster in the ground state, and an inversed trend occurs for the excited singlet state process, consequently leading to a chemical enhancement of SERS signals. The obtained results are of importance for subsequent work in guiding the design of mobile sensors specifically used for services of rapid screening and detection of these toxic compounds present in the environment, as well as agricultural and food products. Extensive computations pointed out that small silver clusters, in particular of Ag20 size, can be used as appropriate models for a metal nanoparticle surface.

Manilkzapotane, a novel dimeric alkylresorcinol derivative from the stem bark of Manilkara zapota.

A novel dimeric alkylresorcinol derivative, manilkzapotane (1), along with seven known compounds, lupeol acetate (2), lupeol (3), arjunolic acid (4), ergosterol peroxide (5), taraxerol (6), hederagonic acid (7), and glochidiol (8) were isolated from the stem bark of Manilkara zapota. Their structures were determined on the basis of spectroscopic data. DFT-NMR chemical shift calculations and a modified probability (DP4+) method were applied to define the relative configuration of 1. To the best of our knowledge, this represents the first isolation of a dimeric alkylresorcinol derivative from the Sapotaceae family.

In-Depth Investigation of a Donor-Acceptor Interaction on the Heavy-Group-14@Group-13-Diyls in Transition-Metal Tetrylone Complexes: Structure, Bonding, and Property.

Stabilization for tetrylone complexes, which carry ylidone(0) ligands [(CO)5W-X (YCp*)2] (X = Ge, Sn, Pb; Y = B-Tl), has become an active theoretical research because of their promising application. Structure, bonding, and quantum properties of the transition-metal donor-acceptor complexes were theoretically investigated at the level of theory BP86 with several types of basis sets including SVP, TZVPP, and TZ2P+. The optimized structures reveal that all ligands X (YCp*)2 are strongly bonded in tilted modes to the metal fragment W(CO)5, and Cp* rings are mainly η5-bonded to atom X. DFT-based bonding analysis results in an implication that the stability of W-X bond strength primarily stems from the donation (CO)5W ← X(YCp*)2 formed by both σ- and π-bondings and the electrostatic interaction ΔE elstat. The W-X bond possesses a considerable polarizability toward atom X, and analysis on its hybridization is either sp2-characteristic or mainly p-characteristic. EDA-NOCV-based results further imply that the ligands XY perform as significant σ-donors but minor π-donors. The visual simulations of NOCV pairs and the deformation densities assemble a comprehensive summary on different components of the chemical bond via σ- and π-types in the complexes. This work contributes to the literature as an in-depth overview on predicted molecular structures and quantum parameters of the complexes [(CO)5W-X(YCp*)2] (X = Ge, Sn, Pb; Y = B-Tl), conducive to either further theoretical reference or extending experimental research.

Correction to Investigation into SARS-CoV-2 Resistance of Compounds in Garlic Essential Oil.

[This corrects the article DOI: 10.1021/acsomega.0c00772.].

Evaluation of the Inhibitory Activities of COVID-19 of Melaleuca cajuputi Oil Using Docking Simulation.

GC-MS was applied to identify 24 main substances in Melaleuca cajuputi essential oil (TA) extracted from fresh cajeput leaves through steam distilling. The inhibitory capability of active compounds in the TA from Thua Thien Hue, Vietnam over the Angiotensin-Converting Enzyme 2 (ACE2) protein in human body - the host receptor for SARS-CoV-2 and the main protease (PDB6LU7) of the SARS-CoV-2 using docking simulation has been studied herein. The results indicate that the ACE2 and PDB6LU7 proteins were strongly inhibited by 10 out of 24 compounds accounting for 70.9% in the TA. The most powerful anticoronavirus activity is expressed in the order: Terpineol (TA2) ≈ Guaiol (TA5) ≈ Linalool (TA19) > Cineol (TA1) > ß-Selinenol (TA3) > α-Eudesmol (TA4) > γ-Eudesmol (TA7). Interestingly, the synergistic interactions of these 10 substances of the TA exhibit excellent inhibition into the ACE2 and PDB6LU7 proteins. The docking results orient that the natural Melaleuca cajuputi essential oil is considered as a valuable resource for preventing SARS-CoV-2 invasion into human body.

Growth Pattern, Stability, and Properties of Complexes of C2H5OH and nCO2 (n = 1-5) Molecules: A Theoretical Study.

This work is dedicated to theoretically investigate the formation process of C2H5OH···nCO2 (n = 1-5) complexes and to shed light on the nature of interactions formed under the variation of CO2 concentration. It is found that CO2 molecules tend to locate around the polarized -OH group to interact with the lone pairs of the O atom. The interaction of ethanol with three CO2 molecules (C2H5OH···3CO2) induces the most stable structure in the sequence considered. The atoms in molecules (AIM), NCIplot, and natural bond orbital (NBO) analyses point out that the Oethanol···CCO2 tetrel bond overcomes hydrogen, chalcogen, and CO2···CO2 tetrel-bonded interactions and mainly contributes to the strength of C2H5OH···nCO2 (n = 1-5) complexes. All intermolecular interactions in the examined complexes are weakly noncovalent, and their positive cooperativity is evaluated to be slightly weaker than that of CO2 pure systems. SAPT2+ and molecular electrostatic potential (MEP) calculations indicate that the electrostatic force is the main factor underlying the attractive interplay in the complexes of C2H5OH and CO2.

Investigation into SARS-CoV-2 Resistance of Compounds in Garlic Essential Oil.

Eighteen active substances, including 17 organosulfur compounds found in garlic essential oil (T), were identified by GC-MS analysis. For the first time, using the molecular docking technique, we report the inhibitory effect of the considered compounds on the host receptor angiotensin-converting enzyme 2 (ACE2) protein in the human body that leads to a crucial foundation about coronavirus resistance of individual compounds on the main protease (PDB6LU7) protein of SARS-CoV-2. The results show that the 17 organosulfur compounds, accounting for 99.4% contents of the garlic essential oil, have strong interactions with the amino acids of the ACE2 protein and the main protease PDB6LU7 of SARS-CoV-2. The strongest anticoronavirus activity is expressed in allyl disulfide and allyl trisulfide, which account for the highest content in the garlic essential oil (51.3%). Interestingly, docking results indicate the synergistic interactions of the 17 substances, which exhibit good inhibition of the ACE2 and PDB6LU7 proteins. The results suggest that the garlic essential oil is a valuable natural antivirus source, which contributes to preventing the invasion of coronavirus into the human body.

A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation.

Ribavirin and remdesivir have been preclinically reported as potential drugs for the treatment of SARS-CoV-2 infection, while light silver tetrylene complexes (NHEPh-AgCl and (NHEPh-AgCl)2 with E = C, Si, and Ge) have gained significant interest due to their promising applicability on the cytological scale. Firstly, the structures and bonding states of silver-tetrylene complexes (NHE-Ag) and bis-silver-tetrylene complexes (NHE-Ag-bis) were investigated using density functional theory (DFT) at the BP86 level with the def2-SVP and def2-TZVPP basis sets. Secondly, the inhibitory capabilities of the carbene complexes (NHC-Ag and NHC-Ag-bis) and the two potential drugs (ribavirin and remdesivir) on human-protein ACE2 and SARS-CoV-2 protease PDB6LU7 were evaluated using molecular docking simulation. The carbene ligand NHC bonds in a head-on configuration with AgCl and (AgCl)2, whereas, the other NHE (E = Si and Ge) tetrylene ligands bond in a side-on mode to the metal fragments. The bond dissociation energy (BDE) of the NHE-Ag bond in the complex families follows the order of NHC-Ag > NHSi-Ag > NHGe-Ag and NHSi-Ag-bis > NHGe-Ag-bis > NHC-Ag-bis. The natural bond orbital analysis implies that the [NHEPh→AgCl] and [(NHEPh)2→(AgCl)2] donations are derived mainly from the σ- and π-contributions of the ligands. The docking results indicate that both the ACE2 and PDB6LU7 proteins are strongly inhibited by silver-carbene NHC-Ag, bis-silver-carbene NHC-Ag-bis, ribavirin, and remdesivir with the docking score energy values varying from -17.5 to -16.5 kcal mol-1 and -16.9 to -16.6 kcal mol-1, respectively. The root-mean-square deviation values were recorded to be less than 2 Å in all the calculated systems. Thus, the present study suggests that silver-carbene NHC-Ag and bis-silver-carbene NHC-Ag-bis complexes are potential candidates to inhibit ACE2 and PDB6LU7, and thus potentially conducive to prevent infection caused by the SARS-CoV-2 virus.