scholarly journals New Sulfur-Containing Polyarsenicals from the New Caledonian Sponge Echinochalina bargibanti

Marine Drugs ◽  
2018 ◽  
Vol 16 (10) ◽  
pp. 382 ◽  
Author(s):  
Petri Tähtinen ◽  
Graziano Guella ◽  
Giacomo Saielli ◽  
Cécile Debitus ◽  
Edouard Hnawia ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Density Functional ◽  
Antimicrobial Activities ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Combined Use ◽  
Computational Testing ◽  
Td Dft ◽  
Sulfur Containing ◽  
Structural Definition

Arsenicin A (C3H6As4O3) was isolated from the New Caledonian poecilosclerid sponge Echinochalina bargibanti, and described as the first natural organic polyarsenic compound. Further bioguided fractionation of the extracts of this sponge led us to isolate the first sulfur-containing organic polyarsenicals ever found in Nature. These metabolites, called arsenicin B and arsenicin C, are built on a noradamantane-type framework that is characterized by an unusual As–As bonding. Extensive NMR measurements, in combination with mass spectra, enabled the assignment of the structure for arsenicin B (C3H6As4S2) as 2. The scarcity of arsenicin C and its intrinsic chemical instability only allowed the collection of partial spectral data, which prevented the full structural definition. After the extensive computational testing of several putative structures, structure 3 was inferred for arsenicin C (C3H6As4OS) by comparing the experimental and density functional theory (DFT)-calculated 1H and 13C NMR spectra. Finally, the absolute configurations of 2 and 3 were determined with a combined use of experimental and time-dependent (TD)-DFT calculated electronic circular dichroism (ECD) spectra and observed specific rotations. These findings pose great challenges for the investigation of the biosynthesis of these metabolites and the cycle of arsenic in Nature. Arsenicins B and C showed strong antimicrobial activities, especially against S. aureus, which is comparable to the reference compound gentamycin.

scholarly journals New Sulfur-Containing Polyarsenicals from the New Caledonian sponge Echinochalina bargibanti

2018 ◽  
Author(s):  
Petri Tähtinen ◽  
Graziano Guella ◽  
Giacomo Saielli ◽  
Cécile Debitus ◽  
Edouard Hnawia ◽  
...  
Keyword(s):  
2D Nmr ◽  
Antibacterial Activities ◽  
The Novel ◽  
1H And 13C Nmr ◽  
Combined Use ◽  
Computational Testing ◽  
Td Dft ◽  
Bioassay Guided Fractionation ◽  
Sulfur Containing ◽  
Structural Definition

Isolated from a New Caledonian collection of the poecilosclerid sponge Echinochalina bargibanti, arsenicin A (C3H6As4O3) was described as the first natural organic polyarsenic compound. Continuing on bioassay guided fractionation of the organic extracts of this sponge, we describe here the isolation and structural elucidation of the first sulfur-containing organic polyarsenicals ever found in nature. The novel metabolites, called arsenicin B and arsenicin C, are built on a noradamantane type framework and they further distinguish from the adamantane type framework of arsenicin A by a different heteroatom composition and by the presence of an unusual As-As bonding. Extensive 1D and 2D-NMR measurements, in combination with tandem APCI mass spectra, allowed to establish the structure of arsenicin B (C3H6As4S2) as 2. The scarcity of arsenicin C and and its intrinsic chemical instability, only allowed to collect partial spectral data which prevented the full structural definition. After extensive computational testing of several putative structures, structure 3 for arsenicin C (C3H6As4OS) was inferred by comparing experimental with DFT-calculated 1H and 13C NMR spectra. Finally, the absolute configuration of 2 and 3 were determined with a combined use of experimental and TD-DFT calculated ECD spectra and observed specific rotations. These findings pose great challenges for both the biosynthesis of these metabolites and the cycle of Arsenic in nature. Arsenicin B and arsenicin C showed strong antifungal and antibacterial activities, especially against S. aureus comparable to the antibiotic gentamycin.

The Nature of S-N Bonding in Sulfonamides and Related Compounds: Insights into π-Bonding Contributions from Sulfur K-Edge XAS

2020 ◽  
Author(s):  
Tulin Okbinoglu ◽  
Pierre Kennepohl
Keyword(s):  
Density Functional ◽  
Chemical Properties ◽  
Functional Theory ◽  
Rotational Barriers ◽  
Td Dft ◽  
Nitrogen Bonds ◽  
X Ray Absorption ◽  
Related Compounds ◽  
And Chemical Properties

Molecules containing sulfur-nitrogen bonds, like sulfonamides, have long been of interest due to their many uses and chemical properties. Understanding the factors that cause sulfonamide reactivity is important, yet their continues to be controversy regarding the relevance of S-N π bonding in describing these species. In this paper, we use sulfur K-edge x-ray absorption spectroscopy (XAS) in conjunction with density functional theory (DFT) to explore the role of S<sub>3p</sub> contributions to π-bonding in sulfonamides, sulfinamides and sulfenamides. We explore the nature of electron distribution of the sulfur atom and its nearest neighbors and extend the scope to explore the effects on rotational barriers along the sulfur-nitrogen axis. The experimental XAS data together with TD-DFT calculations confirm that sulfonamides, and the other sulfinated amides in this series, have essentially no S-N π bonding involving S<sub>3p</sub> contributions and that electron repulsion and is the dominant force that affect rotational barriers.

scholarly journals Exo⇔Endo Isomerism, MEP/DFT, XRD/HSA-Interactions of 2,5-Dimethoxybenzaldehyde: Thermal, 1BNA-Docking, Optical, and TD-DFT Studies

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5970
Author(s):  
Nabil Al-Zaqri ◽  
Mohammed Suleiman ◽  
Anas Al-Ali ◽  
Khaled Alkanad ◽  
Karthik Kumara ◽  
...  
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Structural Parameters ◽  
Population Analysis ◽  
Xrd Analysis ◽  
X Ray Diffraction ◽  
Optical Energy Gap ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Td Dft

The exo⇔endo isomerization of 2,5-dimethoxybenzaldehyde was theoretically studied by density functional theory (DFT) to examine its favored conformers via sp2–sp2 single rotation. Both isomers were docked against 1BNA DNA to elucidate their binding ability, and the DFT-computed structural parameters results were matched with the X-ray diffraction (XRD) crystallographic parameters. XRD analysis showed that the exo-isomer was structurally favored and was also considered as the kinetically preferred isomer, while several hydrogen-bonding interactions detected in the crystal lattice by XRD were in good agreement with the Hirshfeld surface analysis calculations. The molecular electrostatic potential, Mulliken and natural population analysis charges, frontier molecular orbitals (HOMO/LUMO), and global reactivity descriptors quantum parameters were also determined at the B3LYP/6-311G(d,p) level of theory. The computed electronic calculations, i.e., TD-SCF/DFT, B3LYP-IR, NMR-DB, and GIAO-NMR, were compared to the experimental UV–Vis., optical energy gap, FTIR, and 1H-NMR, respectively. The thermal behavior of 2,5-dimethoxybenzaldehyde was also evaluated in an open atmosphere by a thermogravimetric–derivative thermogravimetric analysis, indicating its stability up to 95 °C.

Photophysical Properties of N-Methyl and N-Acetyl Substituted Alloxazine: A Theoretical Investigation

2021 ◽  
Author(s):  
Huimin Guo ◽  
Xiaolin Ma ◽  
Zhiwen Lei ◽  
Yang Qiu ◽  
Bernhard Dick ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Theoretical Investigation ◽  
Density Functional ◽  
Photophysical Properties ◽  
Time Dependent ◽  
Functional Theory ◽  
Td Dft ◽  
Dependent Density

The electronic structure and photophysical properties of a series of N-Methyl and N-Acetyl substituted alloxazine (AZs) were investigated with extensive density functional theory (DFT) and time-dependent density functional theory (TD-DFT)...

Density functional theory investigation of the effect of axial coordination and annelation on the absorption spectroscopy of nickel(II) and vanadyl porphyrins relevant to bitumen and crude oils

2013 ◽  
Vol 91 (9) ◽  
pp. 872-878 ◽  
Author(s):  
Stanislav R. Stoyanov ◽  
Cindy-Xing Yin ◽  
Murray R. Gray ◽  
Jeffrey M. Stryker ◽  
Sergey Gusarov ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Polyaromatic Hydrocarbons ◽  
Geometry Optimization ◽  
Soret Band ◽  
Heavy Oils ◽  
Visible Absorption ◽  
Functional Theory ◽  
Axial Coordination ◽  
Td Dft

The vanadium and nickel components in heavy oils and bitumen are important impurities in catalytic processing and form aggregates with other asphaltene components. Metalloporphyrins are commonly analyzed using the characteristic Soret band in the UV–vis absorption spectrum. However, the Soret band of metalloporphyrins in petroleum is broadened and weaker than expected based on the concentration of Ni and V in heavy oils and the extinction coefficients of isolated porphyrins. We hypothesize that the low intensity and broadening of the Soret band could be due to axial coordination of the metal center or fusion (annelation) of aromatic rings on the porphyrin π-system. This hypothesis is examined using the density functional theory for geometry optimization and time-dependent density functional theory (TD-DFT) for calculation of excited states of nickel(II) and vanadyl porphyrins with axially coordinated ligands and annelated polyaromatic hydrocarbons. Predictions of the excited electronic states performed using the tandem of TD-DFT and conductor-like polarizable continuum model of solvation support this hypothesis and provide insight into the extent of Soret band broadening and intensity decrease due to coordination and annelation. These computational results, validated with respect to visible absorption spectra, are important for understanding asphaltene aggregation and spectroscopic characterization and suggest methods for removal of transition metals from heavy oil.

scholarly journals Experimental and Computational Studies on N-alkylation Reaction of N-Benzoyl 5-(Aminomethyl)Tetrazole

Chemistry ◽  
2021 ◽  
Vol 3 (3) ◽  
pp. 704-713
Author(s):  
Younas Aouine ◽  
Aaziz Jmiai ◽  
Anouar Alami ◽  
Abdallah El Asri ◽  
Souad El Issami ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nmr Spectroscopy ◽  
Density Functional ◽  
Computational Study ◽  
Benzyl Bromide ◽  
13C Nmr Spectroscopy ◽  
Alkylation Reaction ◽  
Computational Studies ◽  
Functional Theory ◽  
1H And 13C Nmr

The N-alkylation reaction of N-benzoyl 5-(aminomethyl)tetrazole (5-AMT) with benzyl bromide was carried out in the presence of K2CO3 as a base. Two separable regioisomers were obtained, thus their purification led to determine the proportion of each of them, and their structures were attributed essentially based on 1H and 13C NMR spectroscopy in addition to the elemental analysis and MS data. In order to confirm the results obtained at the synthesis level, a computational study was carried out by application of density functional theory (DFT) using the Becke three-parameter hybrid exchange functional and the Lee-Yang-Parr correlation functional (B3LYP).

Spectroscopic trends in a series of Re(I) α-diimine complexes as a function of the antenna/photoisomerizable ligands: a TD-DFT and MS-CASPT2 study

2014 ◽  
Vol 92 (10) ◽  
pp. 979-986 ◽  
Author(s):  
Megumi Kayanuma ◽  
Chantal Daniel ◽  
Etienne Gindensperger
Keyword(s):  
Excited States ◽  
Electronic Structures ◽  
Density Functional ◽  
Time Dependent ◽  
Functional Theory ◽  
B3lyp Level ◽  
Ligand Charge Transfer ◽  
Td Dft ◽  
Energy Domain ◽  
Diimine Complexes

The absorption spectra of 11 rhenium(I) complexes with photoisomerizable stilbene-like ligands have been investigated by means of density functional theory (DFT). The electronic structures of the ground and excited states were determined for [Re(CO)3(N,N)(L)]+ (N,N = bpy (2,2′-bipyridine), phen (1,10-phenanthroline), Me4phen (3,4,7,8-tetramethyl-1,10-phenanthroline), ph2phen (4,7-diphenyl-1,10-phenanthroline), or Clphen (5-chloro-1,10-phenanthroline); L = bpe (1,2-bis(4-pyrydil)ethylene), stpy (4-styrylpyridine), or CNstpy (4-(4-cyano)styrylpyridine)) at the time–dependent (TD) DFT/CAM-B3LYP level of theory in vacuum and acetonitrile to highlight the effects of both antenna N,N and isomerizable L ligands. The TD-DFT spectra of two representative complexes, namely [Re(CO)3(bpy)(stpy)]+ and [Re(CO)3(phen)(bpe)]+, have been compared with MS-CASPT2 spectra. The TD-DFT spectra obtained in vacuum and acetonitrile agree rather well both with the ab initio and experimental spectra. The absorption spectroscopy of this series of molecules is characterized by the presence of three low-lying metal to ligand charge transfer (MLCT) states absorbing in the visible energy domain. The nature of the isomerizable ligands (bpe, stpy, or CNstpy) and the type of antenna ligands (bpy, phen, and substituted phen) control the degree of mixing between the MLCT and intraligand excited states, their relative energies, as well as their intensities.

scholarly journals Predicting the UV–vis spectra of oxazine dyes

2011 ◽  
Vol 7 ◽  
pp. 432-441 ◽  
Author(s):  
Scott Fleming ◽  
Andrew Mills ◽  
Tell Tuttle
Keyword(s):  
Excitation Energy ◽  
Density Functional ◽  
Polarizable Continuum Model ◽  
Implicit Solvent ◽  
Continuum Approach ◽  
Excitation Energies ◽  
Functional Theory ◽  
Partial Charges ◽  
Td Dft ◽  
Polarizable Continuum

In the current work we have investigated the ability of time-dependent density functional theory (TD-DFT) to predict the absorption spectra of a series of oxazine dyes and the effect of solvent on the accuracy of these predictions. Based on the results of this study, it is clear that for the series of oxazine dyes an accurate prediction of the excitation energy requires the inclusion of solvent. Implicit solvent included via a polarizable continuum approach was found to be sufficient in reproducing the excitation energies accurately in the majority of cases. Moreover, we found that the SMD solvent model, which is dependent on the full electron density of the solute without partitioning into partial charges, gave more reliable results for our systems relative to the conductor-like polarizable continuum model (CPCM), as implemented in Gaussian 09. In all cases the inclusion of solvent reduces the error in the predicted excitation energy to <0.3 eV and in the majority of cases to <0.1 eV.

scholarly journals Structural and spectroscopic characterization and DFT studies of 2-amino-1,10-phenanthrolin-1-ium chloride

2019 ◽  
Vol 10 (2) ◽  
pp. 95-101
Author(s):  
Sebile Işık Büyükekşi ◽  
Namık Özdemir ◽  
Abdurrahman Şengül
Keyword(s):  
Density Functional Theory ◽  
Electronic Absorption ◽  
13C Nmr ◽  
Density Functional ◽  
Electronic Absorption Spectra ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Basis Set ◽  
Functional Theory ◽  
1H And 13C Nmr

A versatile synthetic building block, 2-amino-1,10-phenanthrolin-1-ium chloride (L∙HCl) was synthesized and characterized by IR, 1H and 13C NMR DEPT analysis, UV/Vis and single-crystal X-ray diffraction technique. The molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO), 1H and 13C NMR chemical shifts values of the title compound in the ground state were obtained by using density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set and compared with the experimental data. Electronic absorption spectrum of the salt was determined using the time-dependent density functional theory (TD-DFT) method at the same level. In the NMR and electronic absorption spectra calculations, the effect of solvent on the theoretical parameters was included using the default model with DMSO as solvent. The obtained theoretical parameters agree well with the experimental findings.

scholarly journals Radical-Scavenging and UV-Radiation Absorption Activities of Aaptamine Derivatives: DFT and TD-DFT Studies

2021 ◽  
Author(s):  
Thi Hoai Nam Doan ◽  
Thi Le Anh Nguyen ◽  
Nguyen Thi Ai Nhung ◽  
Duong Tuan Quang ◽  
Duy Quang Dao
Keyword(s):  
Density Functional ◽  
Antioxidant Activities ◽  
Radical Scavenging Activity ◽  
Radical Scavenging ◽  
Hydrogen Atom Transfer ◽  
Radiation Absorption ◽  
Functional Theory ◽  
Radical Adduct ◽  
Td Dft ◽  
Potential Applications

Antioxidant and UV absorption activities of three aaptamine derivatives including piperidine[3,2-b]demethyl(oxy)aaptamine (C1), 9-amino-2-ethoxy-8-methoxy-3H-benzo[de][1,6]naphthyridine-3-one (C2), and 2-(sec-butyl)-7,8-dimethoxybenzo[de]imidazo[4,5,1-ij][1,6]-naphthyridin-10(9H)-one (C3) were theoretically studied by density functional theory (DFT). Optimized geometries of C1C3 and theirs intrinsic thermochemical properties such as bond dissociation energy, proton affinity, and ionization potential were calculated at DFT/M05-2X/6-311++G(d,p) level of theory in vacuo and in water. The results show that C1C3 exhibited similar potent antioxidant activities, which are comparable to well-known antioxidants such as Trolox or cembrene. The radical scavenging activity of the antioxidants were then investigated by evaluation the Gibbs free energy (ΔrG0) of the reaction between C1C3 and the HOO●/HO● radicals via four mechanisms, including: hydrogen atom transfer (HAT), single electron transfer (SET), proton loss (PL) and radical adduct formation (RAF). Kinetic calculation reveals that HOO● scavenging in water is occurred via HAT mechanism with C1@C19 while RAF is more dominant with C2 and C3. Antioxidant activity of aaptamine derivatives can be classified as C1 > C3 > C2. In addition, all compounds are active in UV-Vis absorption; the excitations of which are determined as π-π* transition. Overall, the results suggest the potential applications of the aaptamines in pharmaceutics and cosmetics, i.e. as sunscreen and antioxidant ingredient<br>

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