Electronic spectroscopy and computational studies of glutathionylco(III)balamin

We have studied glutathionylcobalamin (GS-Cbl) by optical spectroscopy and with density functional theory (DFT) and time-dependent DFT (TD-DFT) electronic structure methods of truncated geometric models. We examined the geometric structure of the models by comparison of DFT calculations with recent high-resolution experimental X-ray structure data ( Hannibal, L. et al. Inorg. Chem. 2010, 49, 9921) for GS-Cbl, and we examined the TD-DFT excitation simulations by comparison of the models with measured optical spectra. The calculations employed the B3LYP hybrid functional and the nonhybrid BP86 functional in both vacuum and water (conductor polarized continuum model (cpcm)) with the 6-311G(d,p) basis set. The optimized geometric structure calculations for six truncated models were made by varying the chemical structure, solvent model, and the two DFT functionals. All showed similar geometry. Charge decomposition analysis (CDA) and extended charge decomposition analysis (ECDA), especially with BP86 shows the similar charge transfer nature of the Co-S bond in GS-Cbl and the Co-C bond in CH(3)Cbl. Mayer and Wiberg bond orders illustrate the similar covalent nature of the two bonds. Finally, absolute optical spectral simulation calculations were compared with the experimental UV-visible extinction spectrum and the electronic circular dichroism (ECD) differential extinction spectrum. The BP86 method shows more spectral features, and the best fit was found for a GS-Cbl model with 5,6-dimethylbenzimidazole at the BP86/6-311G(d,p) level with a water cpcm solvent model. The excited state transitions were investigated with Martin's natural transition orbitals (NTOs). The BP86 calculations also showed π bonding interactions between Co and the axial S of the GS- ligand in the molecular orbitals (MOs) and NTOs.     

Density Functional Study of Tetraphenylporphyrin Long-Range Exciton Coupling

The performance of time-dependent density functional theory (TDDFT) for calculations of long-range exciton circular dichroism (CD) is investigated. Tetraphenylporphyrin (TPP) is used as a representative of a class of strongly absorbing chromophores for which exciton CD with chromophore separations of 50 Å and even beyond has been observed experimentally. A dimer model for TPP is set up to reproduce long-range exciton CD previously observed for a brevetoxin derivative. The calculated CD intensity is consistent with TPP separations of over 40 Å. It is found that a hybrid functional with fully long-range corrected range-separated exchange performs best for full TDDFT calculations of the dimer. The range-separation parameter is optimally tuned for TPP, resulting in a good quality TPP absorption spectrum and small DFT delocalization error (measured by the curvature of the energy calculated as a function of fractional electron numbers). Calculated TDDFT data for the absorption spectra of TPP are also used as input for a ‘matrix method’ (MM) model of the exciton CD. For long-range exciton CD, comparison of MM spectra with full TDDFT CD spectra for the dimer shows that the matrix method is capable of producing very accurate results. A MM spectrum obtained from TPP absorption data calculated with the nonhybrid Becke88–Perdew86 (BP) functional is shown to match the experimental brevetoxin spectrum ‘best’, but for the wrong reasons.     

Accurate Structure and Bonding Description of the Transition Metal‐Disulfur Monoxide Complexes [(PMe3)2M(S2O)] (M = Ni,Pd, Pt): Grimme Dispersion Corrected DFT Study

Geometry and bonding energy analysis of M–S₂O bonds in the metal‐disulfur monoxide complexes [(PMe₃)₂M(S₂O)] of nickel, palladium, and platinum were investigated at DFT, DFT‐D3, and DFT‐D3(BJ) methods using three different functionals (BP86, PBE, and TPSS). The TPSS/DFT‐D3(BJ) yields better geometry, while the BP86 geometry is least accurate for studied complexes. The geometry of platinum complex optimized at TPSS/DFT‐D3(BJ) level is in excellent agreement with the available experimental values. The M–S bonds are shorter than the M–S(O) bonds. The Mayer bond orders suggest the presence of M–S and M–S(O) single bonds. Both the M–S and M–S(O) bond lengths vary with the density functionals as TPSS‐D3(BJ) < TPSS < PBE < BP86. The Hirshfeld charge distribution indicates that the overall charge flows from metal fragment to [S₂O]. The Ni–S₂O bond has greater degree of covalent character than the ionic. The contribution of dispersion interactions is large in computing accurate bond dissociation energies between the interacting fragments. The BDEs are largest for the functional TPSS and smallest for the functional BP86. The DFT‐D3 dispersion corrections to the BDEs between the metal fragments [(PMe₃)₂M] and ligand fragment [(S₂O)] for the TPSS functional are in the range 7.1–7.3 kcal · mol^–1, which are smaller than the corresponding DFT‐D3(BJ) dispersion corrections (9.4–10.6 kcal · mol^–1).     

Control of the Helical Chirality of Enantiopure Sulfinyl (Z)‐Azobenzene‐Based Photoswitches

A new class of enantiopure ortho,ortho‐disubstituted azobenzene photoswitches has been synthesized from (S)‐2‐(p‐tolylsulfinyl)benzoquinone and arylhydrazines. The sulfoxide acts as a unidirectional controller of the helical chirality that arises in the Z isomer after photoisomerization. Highly congested E‐azobenzenes 5 c showed two atropisomeric diastereoconformers in the solid state that converged upon irradiation into a unique Z isomer with defined helicity (M), as evident in the X‐ray structure. The chiroptical properties of this three‐state enantiopure switch can be externally tuned both photochemically and/or thermally. Theoretical CD spectra calculated by using time‐dependent DFT methods support the existence of two atropoisomeric E isomers and only one Z isomer with (M) helicity. Complementary to the classical azobenzene‐based switches, the photoswiching event is promoted under green/blue light and do not occur under UV irradiation.     

Assignment of Phosphorus NMR Parameters to Absolute Configurations in Chiral Phosphorus Sulfide Cage Compounds,using Ab Initio Methods

The closo cage molecules α‐ and β‐P₄S₃(μ‐NCH(Me)Ph) were modelled at the RHF/3‐21G* and MPW1PW91/DZVP levels. For each, the conformational space corresponding to rotation about the C–N bond was explored, and relative average electronic energies were calculated. The β‐isomer was more stable than the α‐isomer by 10.7 kJ mol^?1, according to the DFT calculations, in contrast to the unsubstituted model compounds α‐ and β‐P₄S₃(μ‐NH), where the α‐isomer was more stable. GIAO calculations of phosphorus isotropic NMR shieldings, in the rotamers, led to relative average chemical shifts in the diastereomers. Comparison with experimental chemical shift differences gave an assignment to absolute configuration for α‐P₄S₃(μ‐NCH(Me)Ph), which agreed with the assignment obtained by comparing calculated relative diastereomer stability with observations. For β‐P₄S₃(μ‐NCH(Me)Ph), the GIAO calculations allowed relative assignment of observed chemical shifts to the nitrogen bridgehead phosphorus atoms.     

Asymmetric Synthesis of the cis‐ and trans‐3,4‐Dihydro‐2,4,8‐trihydroxynaphthalen‐1(2H)‐ones

A short and efficient protocol for the asymmetric synthesis of cis‐ and trans‐3,4‐dihydro‐2,4,8‐trihydroxynaphthalen‐1(2H)‐one ( 1 and 2 , resp.) is described, with a phthalide annulation as the key step. Introduction of a OH substituent at position 2 was performed by Sharpless dihydroxylation of a silyl enol ether or by means of an N‐sulfonyloxaziridine. The absolute configuration of each isomer was determined via Mosher‐ester derivatives. By comparison with previously recorded CD spectra of our natural sample, we established that the natural trans‐ and cis‐isomers from Ceratocystis fimbriata sp. platani were the (?)‐(2S,4S)‐isomer (?)‐ 2 and the (+)‐(2S,4R)‐isomer (+)‐ 1 , respectively.     

Mechanism of the Thermal Z⇌E Isomerization of a Stable Silene; Experiment and Theory

The E and Z geometric isomers of a stable silene (tBu₂MeSi)(tBuMe₂Si)Si=CH(1‐Ad) ( 1 ) were synthesized and characterized spectroscopically. The thermal Z to E isomerization of 1 was studied both experimentally and computationally using DFT methods. The measured activation parameters for the 1Z ? 1E isomerization are: E_a=24.4 kcal mol^?1, ΔH^≠=23.7 kcal mol^?1, ΔS^≠=?13.2 e.u. Based on comparison of the experimental and DFT calculated (at BP86‐D3BJ/def2‐TZVP(‐f)//BP86‐D3BJ/def2‐TZVP(‐f)) activation parameters, the Z?E isomerization of 1 proceeds through an unusual (unprecedented for alkenes) migration–rotation–migration mechanism (via a silylene intermediate), rather than through the classic rotation mechanism common for alkenes.     

CIRCULAR DICHROISM AND ELECTRONIC ABSORPTION OF RHODIUM(III) EDTA-TYPE COMPLEXES: Ethylenediamine-N,N′-diacetato-N,N′-di-3-propionatorhodate(III) and (S,S)-Ethylenediamine-N,N′-disuccinatorhodate(III) Ions

Abstract

Electronic absorption and CD spectra are reported for the sexidentate complexes, trans(O₅)-Rh(EDDDA)^?, trans(O₅ O₆)-Rh(EDDDA)^?, and trans(O₅)-Rh(S,S-EDDS)^? (EDDDA)=ethylenediamine-N,N′-di-3-propionate; S,S-EDDS=(S,S)-ethylenediamine-N,N′-disuccinate). Because of the sterospecific coordination of the S,S-EDDS ligand the absolute configuration of (+)_D-trans(O₅)-Rh(S,S-EDDS)^? is known to be Λ. By comparison of their CD spectra to that of the (+)_D isomer of trans(O₅)-Rh(S,S-EDDS)^?, the absolute configurations of the (?)_DEDDDA complexes are assigned tentatively.     

Circular dichroism spectra of trans-chalcone epoxides

The electronic absorption and CD spectra of (−)-trans-chalcone epoxide and its derivatives with methyl and alkoxy substituents at the ortho-positions of the aromatic rings have been measured. The spectra have been assigned with help of the energies, oscillatory strengths, and rotatory strengths of the singlet transitions obtained from DFT calculations. The features of the CD spectra, indicative of the absolute configuration, are the carbonyl n–π¹ band and two further strong bands assigned to the overlapping signals of π–π¹ and n_epoxy–π¹ excitations.     

Chromatographic Resolution,Circular Dichroism Spectra,Absolute Configurations,and Crystal Structures of Bridged Biphenyls,Containing Sulfide,Sulfoxide, and Sulfone Groups in the Bridge

Four chiral 1,1′‐biphenyls with one or two sulfur‐containing bridges in 2,2′‐ or 2,2′‐ and 6,6′‐positions, viz. 1,11‐dimethyl‐5,7‐dihydrodibenzo[c,e]thiepin ( 1 ), its S‐oxide ( 2 ) and S,S‐dioxide ( 3 ), and the doubly bridged 10,12‐dihydro‐4H,6H‐[2]benzothiepino[6,5,4‐def][2]benzothiepin ( 4 ) have been studied by chromatography, CD spectroscopy, X‐ray crystallography, and empirical force‐field and CNDO/S calculations. The structures obtained by force‐field calculations showed good agreement with the crystal structures determined for 2 and 3 . Compounds 2 , 3 , and 4 , but not 1 , could be resolved into enantiomers by chromatography on swollen microcrystalline triacetylcellulose. The barrier for biphenyl inversion in 2 was found to be higher than 167 kJ⋅mol⁻¹ by an attempted thermal racemization. The CD spectra of the enantiomers of 2 – 4 were recorded and resolved into individual bands, and the corresponding rotational strengths were calculated. The transitions showed considerable similarity to those of a 1,1′‐biphenyl with hydrocarbon bridge (cf. 5 ), albeit with bathochromic shifts, which permitted the assignment of the absolute configurations of the enantiomers of 2 – 4 . The assignments were supported by comparison of the experimental CD spectra with spectra calculated by the CNDO/S method. All first‐eluted enantiomers were found to have the (S)‐configuration.     

1H-NMR.-, 13C-NMR.-, UV.- und CD.-Daten von synthetischem (3S, 3′S)-Astaxanthin,seinem 15-cis-Isomeren und einigen analogen Verbindungen

¹H-NMR., ¹³C-NMR., UV. and CD. spectral data of synthetic (3S, 3′S)-astaxanthin, its 15-cis isomer, and some related compounds ¹H-NMR., ¹³C-NMR., UV. and CD. spectra are reported for synthetic (3S, 3′S)-astaxanthin ( 1 ), its 15-cis isomer ( 2 ), its diacetate ( 3 ), and the 15, 15′-didehydro compound ( 5 ). These data prove the identity of the synthetic and the naturally occuring compound 1 . A full interpretation of the ¹H- and ¹³C-NMR. spectra is given and confirms the configuration of all the double bonds. The conformation of the cyclohexene end group of all the compounds is shown to be identical. The signs of the different CD. maxima of 15-cis-astaxanthin are found to be opposite to those of the all-trans compound.     

Chemical properties of marine terpenoids. 1. Some reactions of (6S,10R)-10-bromo-3,11,11-trimethyl-7-methylidenespiro[5,5]undec-2-en-4-one,a sesquiterpenoid from the sea hare Aplysia dactylomela

The structures of products obtained by reductive debromination and CF₃COOH- and KOH-induced transformations of natural chamigrane-type sesquiterpenoid (6S,10R)-10-bromo-3,11,11-trimethyl-7-methylidenespiro[5,5]undec-2-en-4-one (dactylone) isolated from the sea hare Aplysia dactylomela were analyzed. The absolute configurations of the reaction products were established by CD spectra taking into account the configuration of the starting dactylone.     

Spectroscopic characteristics of dimethylsulfoxide molecules coordinated to Mg2+ cation. structure of complexes [Mg(DMSO)i(CH3CN)6-i]2+ from the data of quantum-chemical calculations and IR spectra of Mg(ClO4)2-DMSO-CH3CN Solutions

By the DFT B3LYP/6-31G** method the geometry was optimized and IR spectra were calculated of complexes [Mg(DMSO) _i (CH₃CN)_6-i ]²⁺ (i = 1–6). The values of free energy ΔG in the reaction of ligands substitution in the coordination sphere of the cation were determined. A satisfactory agreement between experimental and calculated values of structural parameters and infrared spectra of free molecules and coordinated to the cation DMSO was obtained. The regularities in the changes of the spectroscopic and structural characteristics of [Mg(DMSO) _i (CH₃CN)_6-i ]²⁺ complexes at varying their composition were revealed. The frequencies and absolute integral intensities of DMSO bands in the IR spectra of pure liquid, solutions in acetonitrile, and in three-component solutions Mg(ClO₄)₂-DMSO-CH₃CN were measured. A correspondence between the calculated change of the frequency and absolute intensity of the IR bands v(C≡N), v(C-C), v(S=O), and v(SC) of the complexes and the corresponding values in the IR spectra of the solutions with different content of components of binary solvent was found.     

Stereochemical effects in mass spectrometry. 7. Determination of absolute configuration of some organic molecules by reaction mass spectrometry

It was found that in the chemical ionization (isobutane) mass spectra of some asymmetric secondary alcohols and α-amino acids, when a pair of enantiomers (such as R- and S-2-phenyIbutyric anhydride, R- and S-mandelic acid, R- and S-2-methylbutanoic acid or R- and S-α-phenyl ethyl amine) were used as reaction reagents, the relative abundances of characteristic ions formed by the stereoselective reaction between sample and reagent of the same configuration were much higher than those ions formed by the sample and a reagent of a different configuration. The absolute configuration of the sample molecule may be predicted by examination of mass spectra of the sample measured with R- and S-reagent respectively. This approach proved to be a convenient way for determination of the absolute configurations of organic molecules on a micromole level by mass Spectrometry.     

Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree–Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.     

Molecular Structure, Vibrational Spectrum and Ionization Energy of m-Dimethoxybenzene

The optimized molecular geometries of the three rotamers of m-dimethoxybenzene in the ground So and electronically excited Sl states were predicted by ab initio and density functional theory （DFF） calculations. Their vibrational spectra in the St state were studied by one color resonant two photon ionization （1C-R2PI） method, and their ionization energies were measured by two color resonant two photon ionization （2C-R2PI） experiment. The optimized molecular geometries showed that the total energy of conformer a was the lowest in the So state. Most of the active vibrations assigned from the 1C-R2PI spectrum were found to be of the in-plane ring modes. The ionization energies （IE） of conformers a, b and c were determined to be 63521, 64487 and 63755 cm^-1, respectively.     

Synthesis and Absolute Configuration of Novel Mono- and Dinuclear Cobalt(III) Complexes Containing S-Phenylalanine

Two diastereomers of bis(1,3-diaminopropane)(S-phenylalaninato)cobalt(III) were prepared by reaction of S-phenylalanine with carbonatobis(1,3-diaminopropane)cobalt(III). The diastereomers were separated on an optically active Sephadex QAE column and their absolute configurations assigned by means of circular dichroism. In addition, ¹HNMR spectra of the diastereomers were analyzed in terms of the population of the three predominant rotamers of the coordinated S-phenylalaninato ligand. One out of 24 theoretically possible diastereomers of the dinuclear species di- µ -hydroxo- tetrakis(S-phenylalaninato)dicobalt(III) was obtained by direct synthesis and its absolute configuration deduced from CD spectra.     

An Unexpected Atropisomerically Stable 1,1‐Biphenyl at Ambient Temperature in Solution,Elucidated by Vibrational Circular Dichroism (VCD)

Biphenyls with only two substituents at the ‘peri'‐position normally show rotation about their chiral axis at room temperature. Using vibrational circular dichroism (VCD), we found no evidence for rotation of (P)‐2′‐[(4S)‐4,5‐dihydro‐4‐(1‐methylethyl)oxazol‐2‐yl][1,1′‐biphenyl]‐2‐methanol ((P,S)‐ 1 ) in CDCl₃ about its chiral axis due to stabilization by intramolecular H‐bonding. All rotamers of 1 were calculated at the DFT level, and, from these optimized structures, the VCD spectra were calculated and compared to the measured VCD spectra. The best agreement between calculated and measured spectra is obtained when two rotamers are present in solution. These rotamers differ primarily in their intramolecular H‐bonding interactions, having either OH???N (the form present in the solid state) or OH???O H‐bonds, i.e., a rotation of the heterocycle in 1 takes place in solution.     

Enantiomer resolution of intrinsically chiral C21-alkylated N-confused porphyrin complexes

The resolution of stereoisomers of C21‐alkylated nickel(II) complexes of N‐confused porphyrin (NCP) was performed by means of chiral‐phase HPLC with an effectiveness of above 90 % molar ratio for each isomer. The reverse signs of the Cotton effects in the circular dichroism (CD) spectra of the separated fractions are indicative of the pair of enantiomers. The application of low‐temperature 2D NMR methods to the separated diastereomers of the system comprising a chiral 2‐(S)‐methylbutyl substituent, in connection with the CD spectra and relative HPLC migration rates, allowed the assignment of the absolute configuration of the chiral C21‐substituted complexes of NCP. The assignment was confirmed by time‐dependent DFT (TDDFT) calculations of CD spectra for the C21‐methylated nickel(II) complex. The system remains chiral after removal of the metal ion from the macrocyclic crevice, despite the fact that this demetalation is connected with a change of the C21 hybridization from pyramidal to trigonal. The retention of chirality was established by means of CD spectra and confirmed by TDDFT calculations for a C21‐methylated NCP free base. Stereoisomers were also separated for three covalently linked bis(NCP) systems with bridges involving one or two C21 carbon atoms. The occurrence of a pair of enantiomers was established for nonsymmetrical dimers comprising only one stereogenic center. In the case of the 21,21′‐(o‐xylene)‐linked dimer, three stereoisomers, that is, a pair of enantiomers and an optically inactive meso‐form, were separated and analyzed by CD and ¹H NMR spectroscopy. The stereoisomers of a diastereoselectively formed nonsymmetrical chloroplatinum(II)‐linked dimer, consisting of heterochiral C21‐alkylated NCP nickel(II) subunits, after separation displayed a strong optical activity, which can be ascribed to the rigid helical structure of the complex.     

Absolute configuration reassignment of two chromanes from Peperomia obtusifolia (Piperaceae) using VCD and DFT calculations

Previous analysis of the ECD spectra of two prenylated benzopyrans isolated from Peperomia obtusifolia, by means of the helicity rule for the chromane chromophore, resulted in the incorrect assignment of their absolute configuration, (S) instead of (R) for a deduced P-helicity of the chromane ring for the (+)-enantiomers. This was discovered by the application of DFT calculations and VCD spectroscopy. Experimental and calculated (B3LYP/6-31G(d)) VCD and IR spectra were compared, and a definitive absolute configuration of (+)-1 and (+)-2 is reassigned directly in solution as (R). The assumption of equatorial positioning of bulky groups, shown here to be invalid for the title molecules, is the underlying cause of the previous incorrect assignment of absolute configuration. Moreover, TDDFT (B3LYP/6-311++G(2d,2p)//B3LYP/6-31G(d)) calculations of ECD spectra have shown that both P- and M-helicity of the heterocyclic ring, for a given absolute configuration, lead to the same sign for the ¹L_b ECD band, thus bringing into question the validity of the empirical ECD helicity rule for chromane molecules.