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.

Synchronous rectal adenocarcinoma and intestinal mantle cell lymphoma: A case report

BACKGROUND

Mantle cell lymphoma (MCL) of the gastrointestinal tract is a rare malignancy, accounting for about 0.2% of malignant colorectal tumors. MCL synchronous with rectal adenocarcinoma is extremely rare. We know of only a few cases reported in the literature. We describe the case of a patient with synchronous rectal adenocarcinoma and intestinal MCL.

CASE SUMMARY

A 63-year-old man was admitted to our hospital due to abdominal pain and hematochezia over the past month. The patient was diagnosed with middle rectal cancer cT2N0M0 and underwent surgery. However, we found a large tumor in the small intestine during surgery. The patient underwent total mesorectal excision for rectal cancer and resectioning of the ileal segment containing the large mass. Pathology and immunohistochemistry revealed the presence of both rectal adenocarcinoma and pathognomonic MCL stage IIE presenting as multiple lymphomatous polyposis. The patient subsequently underwent RDHAP/RCHOP chemotherapy and was maintained with rituximab. A Positron Emission Tomography and Computed Tomography (PET/CT) scan showed that the disease responded well to treatment without tumor-increased metabolism in the gastrointestinal tract.

CONCLUSION

Synchronous rectal adenocarcinoma and intestinal MCL presenting as multiple lymphomatous polyposis are extremely rare. MCL is often discovered fortuitously when rectal cancer is diagnosed. The coexistence of these tumors poses treatment challenges.

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.

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.

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.

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 C_sp²–H⋯O and O–H⋯S/Se/Te H-bonds. It is found that a considerable blue-shift of C_sp²–H stretching frequency in the C_sp²–H⋯O H-bond is mainly determined by an addition of water into the complexes along with the low polarity of the C_sp²–H covalent bond in formaldehyde and acetaldehyde. The C_sp²–H stretching frequency shift as a function of net second hyperconjugative energy for the σ*(C_sp²–H) antibonding orbital is observed. Remarkably, a considerable C_sp²–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 C_sp²–H stretching frequency blue-shift in the C_sp²–H⋯O H-bond, whereas CH₃-substituted complexes experience the opposite trend.

The considerable blue shift of C_sp²–H stretching frequency.

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

The presence of O–H⋯O/S conventional hydrogen bonds in the complex governs a significant blue shift of Csp2–H bonds.

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 C_sp2-H...O H-bonds are found to be about twice as strong as the C_sp2-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 C_sp2-H stretching frequency involving the C_sp2-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 C_sp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm^-1 of C_sp2-H stretching frequency in C_sp2-H...O H-bond in CH₃CHO...2H₂O has rarely been observed and is much greater than that in the cases of the C_sp2-H...S/Se/Te ones. The C_sp2-H blue shift of C_sp2-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 C_sp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

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.

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, Ag_n 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.

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 β-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 β-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.

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.

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.

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

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

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.

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) > β-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.

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.

Transformation between Hexagonal Prism and Antiprism of the Singly and Doubly Cr-Doped Ge12 Clusters

Structural transformation is a unique characteristic of atomic clusters, but it turns out very different from cluster to cluster. This theoretical study proves that the isomeric transformation between hexagonal prism and hexagonal antiprism is found for the doubly doped Cr₂Ge₁₂ cluster but not for singly doped CrGe₁₂ cluster. We confirm that the ground state of CrGe₁₂ is the distorted hexagonal prism C_2h at the ³B_g triplet state instead of various shapes predicted in the previous studies. Upon comparison between the estimation at the B3P86/6-311+G(d) level of theory and the detachment energies measured by photoelectron spectroscopy, hexagonal antiprismatic shape is identified as the most stable isomer of the Cr₂Ge₁₂ cluster and it is easy to transform to the hexagonal prism-a less stable isomer by the rotation of the hexagonal rings. That is the first evidence for the structural transformation between a hexagonal prism and an antiprism of the germanium clusters, referring to the ability of Ge-based clusters in the formation of tubular geometry by doping Cr atoms. All the low-energy isomers of both Cr-doped germanium clusters have high magnetic moments. Interestingly, there is a tuning in magnetic properties of Cr₂Ge₁₂ from the ferromagnetism of the lowest-lying hexagonal antiprism to the ferrimagnetism of the higher-energy hexagonal prism. The stronger Cr-Cr bond and stronger interaction between the Cr₂ moiety and the antiprism cage are accounted for by the higher stability of the hexagonal antiprismatic isomer.

Antioxidant Motifs in Flavonoids: O-H versus C-H Bond Dissociation

Flavonoids provide potential health benefits due to their antioxidant properties. The antioxidant activity of natural flavonoids is primarily exerted by phenolic hydroxyl groups; however, C-H bonds also contribute to these properties. In this study, the contributions of phenolic groups and C-H bonds to the antioxidant properties of 13 flavonoids were investigated by using the (RO)B3LYP/6-311++G(2df,2p)//B3LYP/6-311G(d,p) model chemistry in the gas phase and water and ethanol solvents. It was found that the C-H bonds have lower bond dissociation energies than O-H bonds in the 4-carbonyl and/or 3-hydroxyl group containing flavonoids and hence define antioxidant activity. The HOO· radical scavenging of the selected flavonoids is also investigated in detail through the potential energy surface, natural bond orbitals, and kinetic calculations. It was found that the favored radical scavenging mechanism of the flavonoids is hydrogen atom transfer, with the gas phase rate constants in the range of 7.23 × 103-2.07 × 109 L·mol-1·s-1. The results suggest that the flavonoids, isomelacacidin, isoteracacidin, melacacidin, and teracacidin, have antioxidant properties as high as typical phenolic compounds such as quercetin, trans-resveratrol, trolox, and ascorbic acid.

Remarkable shifts of Csp2 -H and O-H stretching frequencies and stability of complexes of formic acid with formaldehydes and thioformaldehydes

Thirty-six stable complexes of formic acid with formaldehydes and thioformaldehydes were determined on the potential energy surface, in which the XCHO···HCOOH complexes are found to be more stable than the XCHS···HCOOH counterparts, with X = H, F, Cl, Br, CH₃ , NH₂ . All complexes are stabilized by hydrogen bonds, and their contribution to the total stabilization energy of the complexes increases in going from C-H···S to C-H···O to O-H···S and finally to O-H···O. Remarkably, a significant blueshift of C_sp2 -H bond by 81-96 cm^-1 in the C_sp2 -H···O hydrogen bond has hardly ever been reported, and a considerable redshift of O-H stretching frequency by 206-544 cm^-1 in the O-H···O/S hydrogen bonds is also predicted. The obtained results in our present work and previous literatures support that a distance contraction and a stretching frequency blueshift of C-H bond involving hydrogen bond depend mainly on its polarity and gas phase basicity of proton acceptor, besides the rearrangement of electron density due to complex formation. Markedly, we suggest the ratio of deprotonation enthalpy to proton affinity (R _c ) as an indicator to prospect for classification of hydrogen bonds. The symmetry adapted perturbation theory results show a larger role of attractive electrostatic term in XO-n as compared to that in XS-n and the electrostatic interaction is overwhelming dispersion or induction counterparts in stabilizing XO-n and XS-n, with n = 1, 2, 3. © 2019 Wiley Periodicals, Inc.

An insight into Csp–H⋯π hydrogen bonds and stability of complexes formed by acetylene and its substituted derivatives with benzene and borazine

Theoretical calculations at the MP2/aug-cc-pVDZ level are used to investigate the C_sp–H⋯π interactions of C₂HX (X = H, F, Cl, Br, CH₃, NH₂) with C₆H₆ and B₃N₃H₆ molecules.

Complexes of carbon dioxide with dihalogenated ethylenes: structure, stability and interaction

Interactions of ethylene and its 1,2-dihalogenated derivatives with CO₂ induce twenty four molecular complexes with stabilization energies in the range of 1.1 to 7.5 kJ mol⁻¹ as computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level of theory.

Remarkable effects of substitution on stability of complexes and origin of the C–H⋯O(N) hydrogen bonds formed between acetone's derivative and CO2, XCN (X = F, Cl, Br)

What are the important factors affecting C–H bond length changes in C–H⋯O and C–H⋯N hydrogen bonds?

Decomposition pathways of the neutral and protonated formamide in some lower-lying excited states

Unimolecular decompositions of neutral (NH2CHO) and protonated (NH3CHO(+)) formamide, an active precursor of biomolecules in prebiotic chemistry, are investigated in the ground (S0) and first triplet (T1) and singlet (S1) excited states. Different decomposition channels including the homolytic bond dissociations, dehydration, decarbonylation, dehydrogenation, etc., are explored using coupled-cluster theory (CCSD(T)/CBS method) for both S0 and T1 states and RASPT2(18,15)/6-31G(d,p) computations for the S1 state. On S1 and T1 energy surfaces, formamide preferentially follows C-N homolytic bond cleavages forming NH2 + HCO radical pairs. Formation of HCN and HNC from dehydration of neutral and protonated formamide via formimic acid and aminohydroxymethylene isomers has higher energy barriers. A strong stabilization upon triplet excitation of the two latter isomers significantly facilitates the interconversions between isomers, and thus considerably reduces the energy barriers for dehydration pathways. The most probable pathways for HCN and HNC generation are found to be dehydration of formamide in the T1 state. Dehydration pathways from the neutral S1 and protonated T1 forms lead to stable complexes of HCN and HNC with water but are associated with large energy barriers. Overall, in the lower-lying excited states of either neutral or protonated formamide, dehydration is not competitive with homolytic C-N bond cleavages, which finally lead to formation of CO.

Theoretical analysis of the (HNO)2, (HNO···HNS), and (HNS)2 dimers — A case of red and blue shifts of N–H stretching frequency

The hydrogen-bonded interactions in the simple (HNZ)2 dimers, with Z = O and S, were investigated using quantum chemical calculations with the second-order Møller–Plesset perturbation (MP2), coupled-cluster with single, double (CCSD), and triple excitations (CCSD(T)) methods in conjunction with the 6-311++G(2d,2p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets. Six-membered cyclic structures were found to be stable complexes for the dimers (HNO)2, (HNS)2, and (HNO–HNS). The pair (HNS)2 has the largest complexation energy (–11 kJ/mol), and (HNO)2 the smallest one (–9 kJ/mol). A bond length contraction and a frequency blue shift of the N–H bond simultaneously occur upon hydrogen bond formation of the N–H···S type, which has rarely been observed before. The stronger the intramolecular hyperconjugation and the lower the polarization of the X–H bond involved as proton donor in the hydrogen bond, the more predominant is the formation of a blue-shifting hydrogen bond.

Hydrolysis of aspartic acid phosphoramidate nucleotides: a comparative quantum chemical study

L-Aspartic acid has recently been found to be a good leaving group during HIV reverse transcriptase catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. This showed that L-Asp is a good mimic for the pyrophosphate moiety of deoxyadenosine triphosphate. The present work explores the thermochemistry and mechanism for hydrolysis of several models for L-aspartic-dAMP using B3LYP/DGDZVP, MP2/6-311++G** and G3MP2 level of theory. The effect of the new compound is gradually investigated: starting from a simple methyl amine leaving group up to the aspartic acid leaving group. The enzymatic environment was mimicked by involving two Mg(2+) ions and some important active site residues in the reaction. All reactions are compared to the corresponding O-coupled leaving group, which is methanol for methyl amine and malic acid for aspartic acid. With methyl amine as a leaving group a tautomeric associative or tautomeric dissociative mechanism is preferred and the barrier is lower than the comparable mechanism with methanol as a leaving group. The calculations on the aspartic acid in the enzymatic environment show that qualitatively the mechanism is the same as for triphosphate but the barrier for hydrolysis by the associative mechanism is higher for L-aspartic-dAMP than for L-malic-dAMP and pyrophosphate.

Remarkable blue shifts of C-H and N-H stretching frequencies in the interaction of monosubstituted formaldehyde and thioformaldehyde with nitrosyl hydride

Weak interactions of monosubstituted formaldehydes and thioformaldehydes with nitrosyl hydride were investigated by using ab initio MO calculations at the MP2/aug-cc-pVTZ level. Thirty two equilibrium structures having different complex forms were located on the corresponding potential energy surfaces (all having C(s) symmetry). Obtained binding energies, which include both ZPE and BSSE corrections, range from 7 to 14 kJ x mol(-1) and 6 to 12 kJ x mol(-1) for complexes of substituted formaldehydes and thioformaldehydes, respectively. In each geometrical structure, the (XCHO,HNO) complex is consistently more stable than the (XCHS,HNO) complex. The H-bond strength significantly increases when one H atom is replaced by a methyl group in both formaldehyde and thioformaldehyde. When replacing H by a halogen atom, the binding energy tends to decrease. It is remarkable that all the C-H and N-H bonds are shortened upon complexation, resulting in an increase of their stretching frequencies. Furthermore, the blue shifts are consistently observed for the interacting N-H bonds in N-H...X, Z, with X = F, Cl, Br, and Z = O, S; such contraction of a covalent N-H bond is extremely rare. In addition, the N-H bond length contraction and its frequency blue shift in the N-H...S complex have been revealed for the first time.

PCR detection and analysis of Pasteurella multocida from the tonsils of slaughtered pigs in Vietnam

A total of 36 tonsil swab samples were collected from healthy swine prior to slaughter at the abattoirs in Can tho and Tien giang provinces of Southern Vietnam. The presence of Pasteurella multocida in these samples was detected by the combination of direct cultivation and isolation, mouse inoculation and the polymerase chain reaction (PM-PCR). P. multocida was detected in 16 samples by PCR, with 17 strains ultimately isolated. All samples were negative for serogroup B by HSB-PCR and conventional serotyping, with isolates identified as A:3, D:1 or D:3. In addition, all samples were determined to be negative for the P. multocida toxin (PMT). Characterisation of isolated P. multocida by REP-PCR and biotyping revealed nine distinct REP profiles and seven biotypes among the 17 isolates. Some correlation was seen with P. multocida isolated from a previous Australian outbreak of acute swine pasteurellosis, and those isolated from fowl cholera outbreaks in Vietnamese poultry.

Acute septicaemic pasteurellosis in Vietnamese pigs

Sixteen isolates of Pasteurella multocida were cultured from cases diagnosed as acute septicaemic pasteurellosis in Vietnamese pigs. The HSB-PCR assay provided rapid presumptive determination of 10 isolates of P. multocida identified as haemorrhagic septicaemia (HS) causing type B cultures (B:2, B:5, B:2,5). Serological designation using the Carter and Heddleston typing systems confirmed these findings, and identified the six HSB-PCR negative cultures as either A:1, A:3 or D:3,4. Biochemical fermentation and REP-PCR revealed phenotypic and genotypic identity between P. multocida type A:1 isolated from Vietnamese pigs and poultry. Marked homogeneity was also demonstrated among HSB-PCR positive swine isolates, which were shown to possess genotypic identity with P. multocida type B:2 from buffaloes diagnosed with HS.