Four-component assembly of chiral N-B heterocycles with a natural product-like framework

The dative N-B bond was used to simply assemble heterocycles with a skeleton akin to the 5-oxofuro[2,3-b]furan motif. Twenty-five new N-B heterocycles were prepared via a highly efficient one-pot four-component reaction in yields and diastereoselectivities up to 95% and >97%, respectively. Several reaction intermediates were discovered using electrospray ionization mass spectroscopy which set the basis for the mechanism elucidation using DFT calculations.     

Exploring Superacid-Promoted Skeletal Reorganization of Aliphatic Nitrogen-Containing Compounds

Here we report a method to reorganize the core structure of aliphatic unsaturated nitrogen-containing substrates exploiting polyprotonation in superacid solutions. The superelectrophilic activation of N-isopropyl systems allows for the selective formal C_sp3−H activation/cyclization or homologation / functionalization of nitrogen-containing substrates. This study also reveals that this skeletal reorganization can be controlled through protonation interplay. The mechanism of this process involves an original sequence of C−N bond cleavage, isopropyl cation generation and subsequent C−N bond and C−C bond formation. This was demonstrated through in situ NMR analysis and labelling experiments, also confirmed by DFT calculations.     

Quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts in the stereochemical determination of conicasterol F, a nuclear receptor ligand from Theonella swinhoei

Here we report the first application of combined accurate ROE-distance analysis with DFT calculations of NMR chemical shifts to achieve the relative configuration assignment of a marine natural product, conicasterol F, a new polyhydroxylated steroid isolated from the marine sponge Theonella swinhoei. We demonstrate the substantial advantages of this combined approach as a tool for structural studies of natural products, providing a powerful alternative to, or information to underpin, total synthesis when more classical NMR data analysis fails to provide unequivocal results. In this paper, we also describe the isolation and structure elucidation of conicasterol F and its 24-ethyl derivative, theonellasterol I, and their pharmacological evaluation as human nuclear receptor modulators.     

Noncovalent control of absorption and fluorescence spectra

Perylene dyes with N-tert-alkyl substituents were prepared in which noncovalent interactions of the crowded substituent cause a variation of the geometry of the core and induce hypsochromic shifts in absorption and fluorescence. The interpretation of the shifts was supported by means of DFT calculations and an X-ray crystal structure analysis.     

Coverage‐Dependent Variation of Adsorption Configurations of Methionine on Ge(100)

The adsorption configurations of methionine molecules on the Ge(100) surface have been studied by using DFT calculations, core‐level photoemission spectroscopy (CLPES), and low‐energy electron diffraction (LEED) to scrutinize the adsorption structure as a function of coverage. At first, we obtained two important and stable structures. One is the most stable structure between these structures described as an “O H dissociated‐N dative‐S dative‐bonded structure” and the other is a less stable adsorption structure of these indicating an “O H dissociated‐S dative‐bonded structure” by using DFT calculations. We also performed CLPES to clarify our DFT calculation results. Through the spectral analysis of the S 2p, C 1s, N 1s, and O 1s core‐level spectra, we acquired the reasonable results that also revealed quite different bonding configurations depending on the methionine coverage. At low coverage (ca. 0.30 ML), a single type of sulfur and charged nitrogen peaks, which indicate an “O H dissociated‐N dative‐S dative‐bonded structure”, were observed. On the other hand, two types of sulfur peaks with thiol formation and two nitrogen peaks with neutralized and charged characteristics were monitored at a higher coverage (0.60 ML and above), which can be described as an “O H dissociated‐S dative‐bonded structure”. Hence, we can clearly demonstrate that our results obtained from CLPES spectra and DFT calculations are matched well with each other. Moreover, we additionally confirmed that the relative population of the two types of thiols and amines being included in methionine in between half monolayer induces a surface reorientation in the ordering from 2×1 to 1×1 employing LEED. This interesting variation of the methionine adsorbed on the Ge(100) surface by coverage dependence will be precisely discussed by using DFT calculations, CLPES, and LEED.     

Reaction of the 4-biphenylnitrenium ion with 4-biphenyl azide to produce a 4,4'-azobisbiphenyl stable product: a time-resolved resonance Raman and density functional theory study

A time-resolved resonance Raman (TR(3)) and density functional theory (DFT) study of the reaction of the 4-biphenylnitrenium ion with 4-biphenyl azide in a mixed aqueous solution is reported. The reaction of the 4-biphenylnitrenium ion with its unphotolyzed precursor 4-biphenyl azide in a mixed aqueous solution generates a 4,4'-azobisbiphenyl stable product via an intermediate species. With the aid of DFT calculations for likely transient species, this intermediate was tentatively assigned to a 4,4'-azobisbiphenyl cation. The DFT calculations predict this reaction can take place via two pathways that compete with one another to produce the trans and cis 4,4'-azobisbiphenyl product. The observation of the 4,4'-azobisbiphenyl cation intermediate demonstrates that the reaction of the arylnitrenium ion with its aryl azide to produce a stable azo product occurs via a stepwise mechanism.     

Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RKKM study

Theoretical model calculations were performed to investigate the degree of validity of the mobile proton model of protonated peptides. The structures and energies of the most important minima corresponding to different structural isomers of protonated diglycine and their conformers, as well as the barriers separating them, were determined by DFT calculations. The rate coefficients of the proton transfer reactions between the isomers were calculated using the RRKM method in order to obtain a quantitative measure of the time scale of these processes. The proton transfer reactions were found to be very fast already at and above the threshold to the lowest energy decomposition pathway. Two possible mechanisms of b2+-ion formation via water loss from the dipeptide are also discussed. The rate-determining step of the proton migration along a peptide chain is also investigated using the model compound N-formylglycylglycinamide. The investigations revealed that this process very possibly occurs via the protonation of the carbonyl oxygens of the amide bonds, and its rate-determining step is an internal rotation-type transition of the protonated C=O-H group between two adjacent C=O-HellipsisO=C bridges.     

Atoms-in-molecules analysis for planewave DFT calculations--a numerical approach on a successively interpolated charge density grid

We used a successive charge interpolation scheme and Ridders method for differentiation, to acquire accurate charge densities and their higher derivatives in electronic structure calculations. This enables us to search bond critical points using arbitrary charge density grids. We applied the planewave-DFT code, VASP, to generate the charge density of selected benchmark molecules. The properties of bond critical points are in good agreement with those obtained by complementary implementations. We validated our GRID implementation by performing electronic structure calculations using the Gaussian 03 program package and various tools for analysis of the charge density provided by the AIMPAC package. In particular, we carefully investigate the influence of effective core potentials on the location of bond critical points, especially for a short chemical bond, which is crucial in the present pseudopotential-based planewave DFT calculations. We expect our generic implementation will not only be useful for the analysis of chemical bonding in molecules, but will particularly provide a microscopic understanding of extended systems including periodic boundary conditions.     

Structural and spectroscopic characterization of a diruthenium o-dioxolene complex possessing a singly occupied molecular orbital delocalized over the entire molecule, [Ru2(3,6-DTBDiox)4]-

Chemical oxidation of [Ru2(6+)(3,6-DTBCat)4]2- affords [n-Bu4N][Ru2(3,6-DTBDiox)4].acetone (2.acetone). The oxidized species was characterized by X-ray crystallographic analysis and EPR, and the delocalization of the unpaired electron over the entire molecule was indicated. This example showed that the utilization of redox-active ligands into a Ru2 complex expanded the degree of freedom in the electronic structure. DFT calculations support this view, and the spin population was estimated to be approximately 18% and 82% for the Ru2 core and the four dioxolene ligands, respectively.     

Spectroscopic and DFT study of tungstic acid peroxocomplexes

The catalytic system formed by tungstic acid and its complexes with H2O2 and phenylphosphonic acid has been analyzed from the experimental and theoretical points of view. Previous structural studies by XRD proved the validity of the DFT proposed models and methodology. Hydrogen peroxide reacts with tungstic acid to form a peroxo complex. Vibrational and electronic spectra showed significant changes upon interaction with H2O2. The DFT and TD-DFT for IR and UV-vis calculations not only are in agreement with experimental data but also allow for a deeper characterization of the species formed in in situ conditions. A SCRF/PCM methodology was chosen to account for the solvent effect. The solvent effect of water was considered for geometry re-optimization of the structure and for the TD-DFT calculations.     

Self-assembly of iron TCPP (meso-tetra(4-carboxyphenyl)porphyrin) into a chiral 2D coordination polymer

Synthetic metalloporphyrin complexes are often used as analogues of natural systems, and they can be used for the preparation of high-dimensional coordination polymers. In this work, a new chiral Fe-TCPP (TCPP is meso-tetra-(4-carboxyphenyl)porphyrin) coordination compound has been synthesized and structurally characterized. The compound is 2D via coordination bonds, and it exhibits strong hydrogen bonds that connect the planar arrays forming the 3D framework. The oxidation of the original Fe^II ions to Fe^III accounts for the formation of this array, in which the topological analysis reveals a very high connectivity based on a simple extension fashion of the structure. DFT calculations have been also carried out to study the stabilization of the Fe^III-compound. This is the third example of a 2D coordination compound based on TCPP in which the dimensionality refers just to coordination bonds, and no other ligands are present in the structure.     

A first-principles DFT study of UN bulk and (001) surface: comparative LCAO and PW calculations

LCAO and PW DFT calculations of the lattice constant, bulk modulus, cohesive energy, charge distribution, band structure, and DOS for UN single crystal are analyzed. It is demonstrated that a choice of the uranium atom relativistic effective core potentials considerably affects the band structure and magnetic structure at low temperatures. All calculations indicate mixed metallic-covalent chemical bonding in UN crystal with U5f states near the Fermi level. On the basis of the experience accumulated in UN bulk simulations, we compare the atomic and electronic structure as well as the formation energy for UN(001) surface calculated on slabs of different thickness using both DFT approaches.     

Original phenyl-P(O) bond cleavage at palladium(0): a combined experimental and computational study

The reaction of the diphosphine-phosphine oxide ligand {[o-iPr(2)P-(C(6)H(4))](2)P(O)Ph} with Pd(PtBu(3))(2) proceeds with cleavage of the Ph-P(O) bond to give an original κ(P,P(O),P)-pincer complex. According to DFT calculations, this oxidative addition occurs via a three-center P,C(ipso),Pd transition state.     

Dithizone and its oxidation products: a DFT, spectroscopic, and X-ray structural study

Air oxidation of ortho-fluorodithizone resulted in the first X-ray resolved structure of a disulfide of dithizone, validating the last outstanding X-ray structure in the oxidation of dithizone, H(2)Dz, which proceeds via the disulfide, (HDz)(2), to the deprotonated dehydrodithizone tetrazolium salt, Dz. Density functional theory calculations established the energetically favored tautomers along the entire pathway; in gas phase and in polar as well as nonpolar solvent environments. DFT calculations using the classic pure OLYP and PW91, or the newer B3LYP hybrid functional, as well as MP2 calculations, yielded the lowest energy structures in agreement with corresponding experimental X-ray crystallographic results. Atomic charge distribution patterns confirmed the cyclization reaction pathway and crystal packing of Dz. Time dependent DFT for the first time gave satisfactory explanation for the solvatochromic properties of dithizone, pointing to different tautomers that give rise to the observed orange color in methanol and green in dichloromethane. Concentratochromism of H(2)Dz was observed in methanol. Computed orbitals and oscillators are in close agreement with UV-visible spectroscopic experimental results.     

DFT‐EPR study of radiation‐induced radicals in α‐D‐glucose

The structures of two radiation‐induced radicals in solid‐state α‐D ‐glucose have been identified by means of single‐molecule density function theory (DFT) calculations. Using the original crystalline structure as input, several radical models were created and their geometries optimized. Subsequently, electron paramagnetic resonance (EPR) parameters were calculated. During these calculations, the global orientation of the radical structure was kept fixed with respect to the crystal axes reference frame. This was essential to allow for an easy analysis of the hyperfine tensor principal directions, besides the isotropic and anisotropic coupling constants. By comparing these calculated EPR parameters with their experimentally determined counterparts, a plausible identification of two carbon‐centered glucose radicals was possible. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Spiroleucettadine: synthetic studies and investigations towards structural revision

Synthetic efforts towards spiroleucettadine are described, including the enantioselective synthesis of the presumed biosynthetic precursor. High level density functional theory calculations were used to predict the ¹³C NMR shifts of possible alternative structures and, along with a re-evaluation of the available NMR data, allow the proposal of revised structures for this spirocyclic alkaloid.     

Catalytic activity tuning of a biomimetic HO-FeV=O oxidant for methane hydroxylation by substituents on aromatic rings: theoretical study

HO-(TPA)FeV=O (TPA = tris(2-pyridylmethyl)amine) has been proposed in the literature as the key high-valent iron-oxo intermediate involved in alkane hydroxylation. Here the structure of this species is investigated theoretically in the framework of density functional theory (DFT). A detailed electronic structure analysis leads to the presumption that the properties of the FeV=O bond can be modified by introducing substituents to the aromatic rings of TPA and thus the reactivity of HO-(TPA)FeV=O for the hydrogen atom abstraction of methane hydroxylation can be tuned on the quartet potential energy surface. The validity of our presumption is verified by DFT calculations. According to the rebound mechanism, the H-abstraction step is examined by using five complexes with TPA and TPA-derivative ligands and the corresponding reaction energies and energy barriers are obtained and compared with each other. The results are fully in agreement with our qualitative model, showing that electron-withdrawing groups are able to lower the barrier and facilitate the reaction, whereas the electron-donating groups increase the barrier and reduce the reactivity.     

Anti-Markovnikov additions to N-allylic derivatives involving ammonium-carbenium superelectrophiles

Anti-Markovnikov additions to non-conjugated unsaturated amines in superacid are reported. In situ NMR studies, DFT calculations and labelled substrates reactions support the involvement of new ammonium-carbenium superelectrophiles in this original process.     

Redox‐Dependent Transformation of a Hydrazinobuckybowl between Curved and Planar Geometries

A red‐fluorescent heterobuckybowl with an embedded hydrazine structure was synthesized from a cyclobiphenothiazine derivative via a strained cyclobicarbazole. The hydrazinobuckybowl was found to possess bowl and twist structures in the neutral state, a shallow bowl structure in the monocation state, and a planar structure in the dication state by means of X‐ray crystallographic analysis, DFT calculations, and a comparison of experimental and calculated ¹³C NMR chemical shifts. The hydrazinobuckybowl is the first buckybowl that changes its geometry between curved bowl/twist structures and a planar structure depending on the oxidation state. The drastic geometrical change was possible as a result of the presence of two heteroatoms in the bowl skeleton and the multiple reversible redox reactions of the compound. Owing to the two kinds of bowl and twist conformations, the bowl‐inversion dynamics of the hydrazinobuckybowl were found to follow a triple‐well potential model.