Diversification of Nucleophile-Intercepted Beckmann Fragmentation Products and Related Density Functional Theory Studies.
Ontology highlight
ABSTRACT: The nucleophile-intercepted Beckmann fragmentation (NuBFr) has the potential to be broadly applicable to the synthesis of indoline alkaloid-based natural products. However, the reaction has not been widely adopted, in part, because of limitations associated with the availability of appropriate promoter-Nu reagents. We have devised a stereospecific Ag(I)-promoted reaction for functionalizing NuBFr products to give novel compositions of matter that may be useful in synthesis and medicinal chemistry. With unhindered amine nucleophiles, structurally unique [2.2.2]-bicycloamidines are generated. We also disclose for the first time detailed density functional theory studies, which shed light on the mechanism of the NuBFr and Ag-promoted substitution reaction that supports an unusual aziridinium ion as a key intermediate.
Project description:We describe the first examples of nucleophile-intercepted Beckmann fragmentations of indoline oximes. This reaction uses MsCl as a promoter to give cyano chlorides and is believed to proceed through an aziridinium intermediate via a double stereoinvertive process. Mechanistic insights have led to the further discovery that oxygen, nitrogen, and bromide nucleophiles can be employed for this fragmentation by the use of other promoters. We envision that these products may be useful in the syntheses of members of the akuammiline and koumine families of indoline alkaloids.
Project description:Within the framework of the density functional theory (DFT) and the hybrid functional B3LYP by means of the CRYSTAL17 program code, the wavenumbers and intensities of normal oscillations of MgCO3, CaCO3, ZnCO3, CdCO3 in the structure of calcite; CaMg(CO3)2, CdMg(CO3)2, CaMn(CO3)2, CaZn(CO3)2 in the structure of dolomite; BaMg(CO3)2 in the structure of the norsethite type; and CaCO3, SrCO3, BaCO3, and PbCO3 in the structure of aragonite were calculated. Infrared absorption and Raman spectra were compared with the known experimental data of synthetic and natural crystals. For lattice and intramolecular modes, linear dependences on the radius and mass of the metal cation are established. The obtained dependences have predictive power and can be used to study solid carbonate solutions. For trigonal and orthorhombic carbonates, the linear dependence of wavenumbers on the cation radius RM (or M-O distance) is established for the infrared in-plane bending mode: 786.2-65.88·RM and Raman in-plane stretching mode: 768.5-53.24·RM, with a correlation coefficient of 0.87.
Project description:Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-? basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ?0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.
Project description:Following recent developments in multilevel embedding methods, we introduce a novel density matrix-based multilevel approach within the framework of density functional theory (DFT). In this multilevel DFT, the system is partitioned in an active and an inactive fragment, and all interactions are retained between the two parts. The decomposition of the total system is performed upon the density matrix. The orthogonality between the two parts is maintained by solving the Kohn-Sham equations in the MO basis for the active part only, while keeping the inactive density matrix frozen. This results in the reduction of computational cost. We outline the theory and implementation and discuss the differences and similarities with state-of-the-art DFT embedding methods. We present applications to aqueous solutions of methyloxirane and glycidol.
Project description:Fullerenes, boron nitride nanotubes (BNNTs), and carbon nanotubes (CNTs) have all been extensively explored for biomedical purposes. This work describes the use of BNNTs and CNTs as mycolactone inhibitors. Density functional theory (DFT) has been used to investigate the chemical properties and interaction mechanisms of mycolactone with armchair BNNTs (5,5) and armchair CNTs (5,5). By examining the optimized structure and interaction energy, the intermolecular interactions between mycolactone and nanotubes were investigated. The findings indicate that mycolactone can be physically adsorbed on armchair CNTs in a stable condition, implying that armchair CNTs can be potential inhibitors of mycolactone. According to DOS plots and HOMO-LUMO orbital studies, the electronic characteristics of pure CNTs are not modified following mycolactone adsorption on the nanotubes. Because of mycolactone's large π-π interactions with CNTs, the estimated interaction energies indicate that mycolactone adsorption on CNTs is preferable to that on BNNTs. CNTs can be explored as potentially excellent inhibitors of mycolactone toxins in biological systems.
Project description:Thiamin diphosphate (ThDP) is a key coenzyme in sugar metabolism. The 4'-aminopyrimidine ring of ThDP cycles through several ionization and tautomeric states during enzyme catalysis, but it is not fully understood which states are adopted during the individual steps of the catalytic cycle. Thiamin has been synthesized with labels selectively inserted into the C2 and C6' positions, as well as into the amino group, creating [C2, C6'-(13)C(2)] thiamin and [N4'-(15)N] thiamin. Magic-angle spinning (MAS) NMR spectroscopy has been employed to record the (13)C and (15)N chemical shift anisotropy (CSA) tensors for C2, C6', and N4' atoms. Our results indicate that the isotropic chemical shifts as well as the principal components of the (13)C and (15)N CSA tensors are very sensitive to the protonation states in these compounds and, therefore, permit differentiating between the two ionization states, 4-aminopyrimidine and 4-aminopyrimidinium. Using density functional theory (DFT), we have calculated the magnetic shielding anisotropy tensors of C2, C6', and N4' and found excellent agreement between the computed and the experimental tensors. Our findings indicate that MAS NMR spectroscopy in conjunction with DFT calculations is a sensitive probe of ionization states in the thiamin cofactor. The results of this study will serve as a guide for characterization of ionization and tautomeric states of thiamin in complexes with thiamin-dependent enzymes.
Project description:A variety of benzimidazole by the heterocyclization of orthophenylenediamine were synthesized in 69-86% yields. The synthesized compounds 3a-f and 6a-f were characterized and further investigated as jack bean urease inhibitors. Density functional theory (DFT) studies were performed utilizing the basis set B3LYP/6-31G (d, p) to acquire perception into their structural properties. Frontier molecular orbital (FMO) analysis of all compounds 3a-f and 6a-f was computed at the same level of theory to get a notion about their chemical reactivity and stability. The mapping of the molecular electrostatic potential (MEP) over the entire stabilized molecular geometry indicated the reactive centers. They exhibited urease inhibition activity with IC50 between 22 and 99 μM. Compounds containing withdrawing groups on the benzene ring (3d, 6d) were not showing significant urease inhibition. The value obtained for 3a, 3b, 3f had shown their significant urease inhibition for both theoretical and experimental. Notably, the compound having S-configuration (3a) (22.26 ± 6.2 μM) was good as compared to its R enantiomer 3f (31.42 ± 23.3 μM). Despite this, we elaborated the computational studies of the corresponding compounds, to highlight electronic effect which include HOMO, LUMO, Molecular electrostatic potential (MEP) and molecular docking.
Project description:Oleic acid oxidation is one of the main sources of food flavor compounds. Volatile profiling was investigated using thermal desorption cryo-trapping combined with gas chromatography-mass spectrometry to analyze the volatile composition of oleic acid oxidation. A total of 43 volatile compounds, including aldehydes (11), ketones (2), alcohols (5), furans (2), acids (8), ester (12) and alkane (3) were identified from oleic acid during heating. Then, density functional theory (DFT) was applied to analyze the oxidative mechanism of oleic acid during heating. A total of 30 reactions were obtained and grouped into the peroxide (ROOH), alkoxy radical (RO•), and peroxide radical (ROO•) pathways. The structures of intermediates, transition states (TS), and products in each reaction were also determined. Results show that the branch chemical reactions were the key reactions in different reaction pathway. Moreover, the reaction priority of the thermal oxidation reaction of oleic acid was the peroxide radical mechanism > the peroxide mechanism > the alkoxy radical mechanism.
Project description:Orbital-free density functional theory (OF-DFT) is an electronic structure method with a low computational cost that scales linearly with the number of simulated atoms, making it suitable for large-scale material simulations. It is generally considered that OF-DFT strictly requires the use of local pseudopotentials, rather than orbital-dependent nonlocal pseudopotentials, for the calculation of electron-ion interaction energies, as no orbitals are available. This is unfortunate situation since the nonlocal pseudopotentials are known to give much better transferability and calculation accuracy than local ones. We report here the development of a theoretical scheme that allows the direct use of nonlocal pseudopotentials in OF-DFT. In this scheme, a nonlocal pseudopotential energy density functional is derived by the projection of nonlocal pseudopotential onto the non-interacting density matrix (instead of "orbitals") that can be approximated explicitly as a functional of electron density. Our development defies the belief that nonlocal pseudopotentials are not applicable to OF-DFT, leading to the creation for an alternate theoretical framework of OF-DFT that works superior to the traditional approach.
Project description:To induce double-proton transfer (DPT) with guanine in a biological environment, 12 cytosine analogues (Ca) were formed by atomic substitution. The DPT reactions in the Watson-Crick cytosine-guanine model complex (Ca0G) and 12 modified cytosine-guanine complexes (Ca1-12G) were investigated using density functional theory methods at the M06-2X/def2svp level. The intramolecular proton transfers within the analogues are not facile due to high energy barriers. The hydrogen bond lengths of the Ca1-12G complexes are shorter than those in the Ca0G complex, which are conducive to DPT reactions. The DPT energy barriers of Ca1-12G complexes are also lower than that of the Ca0G complex, in particular, the barriers in the Ca7G and Ca11G complexes were reduced to -1.33 and -2.02?kcal/mol, respectively, indicating they are significantly more prone to DPT reactions. The DPT equilibrium constants of Ca1-12G complexes range from 1.60 × 100 to 1.28 × 107, among which the equilibrium constants of Ca7G and Ca11G are over 1.0 × 105, so their DPT reactions may be adequate. The results demonstrate that those cytosine analogues, especially Ca7 and Ca11, are capable of inducing DPT with guanine, and then the guanine tautomer will form mismatches with thymine during DNA replication, which may provide new strategies for gene therapy.