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In this work, the difference between pH-induced isomerization and urea-induced unfolding, and the urea- and thermal-induced unfolding processes in different isomeric forms of Bovine serum albumin (BSA) are studied experimentally. Our results show that urea-induced unfolding is a two-step, three-state transition in both the N-form and the B-form, but a single-step, two-state transition in both the E-form and the F-form. At the same time, thermal-induced unfolding shows a two-state transition in all isomeric forms, but the cooperativity of unfolding is different.

Nonlinear refraction in a new polymer material based on diglycidylether of bisphenol-A and containing 4-aminoazobenzene covalently attached to the polymer chains have been studied. The material was shown to exhibit fast nonlinear response (relaxation time about 20 ns, χ⁽³⁾= 5 × 10^{- 8} esu) together with slow one (relaxation time of the order of tens of hours). This makes it possible to record fast and long life (quasi stationary) phase holograms. An analysis of possible mechanisms for the refractive index nonlinear behavior in the new structure is presented. In particular, a role of electronic, thermal, orientation, and isomerization processes is discussed. It was for the first time shown that the rotational and inversion mechanisms of the cis → trans isomerization of the azo-compounds have determinative effect upon kinetics of the nonlinear refractive index relaxation. For the rotational mechanism the relaxation time was found to be 10^-4 s meanwhile for the inversion mechanism it was 10⁵ s.

New global ab initio potential energy surfaces (PES) are presented for the low-lying 1¹A′, 1¹A′′ and 2¹A′ electronic states which are correlated to O(¹D) + HCl. These potential energy surfaces are computed by using the multi-reference configuration interaction method with the Davidson correction (MRCI+Q). The reference functions are constructed by the complete active space self-consistent field (CASSCF) calculations using the quadruple zeta + polarization basis set augmented with diffuse functions. The computations are carried out at about 5000 molecular conformations on each three-dimensional potential energy surface. The high accuracy of the computations is confirmed by a comparison with the available most accurate data for the ground state 1¹A′; thus the present work is the first report of the accurate potential energy surfaces for the two excited states. Three low-lying transition states on the excited surfaces, two (TS2 and TS4) on 1¹A′′ and one (TS3) on 2¹A′, are found. Since TS2 and TS3 are as low as 0.07 eV and 0.28 eV, respectively, and correlate to the OH(²Π) + Cl(²P) product, these excited surfaces are expected to play quite important roles in the reaction dynamics. Possible effects of nonadiabatic couplings among the three PESs are also briefy discussed, although the nonadiabatic couplings have not yet been estimated. The quantum reaction dynamics on these three PESs are discussed in the second accompanying paper, Paper II.

Tropane alkaloids are generally known as anticholinergics. Radiolabeled tropane compounds could be brain imaging agents used in biomedical imaging technique positron emission tomography (PET). A novel entry to aryltropane analogs of cocaine was developed based on the conjugate addition reaction of Grignard reagents phenylmagnesium (10), (4'-isopropenylphenyl)magnesium (11), or 2-naphthylmagnesium bromide (12) to α,β-unsaturated esters anhydroecgonine methyl ester (9) or t-butyl ester (13) which gave several aryltropanes (1–8) with high binding affinities for dopamine and serotonin transporters. Basic conditions are frequently employed in the radiolabeling chemistry of many aryltropane cocaine analogs (1–8b, 14–24b). However, isomerization at C-2 position can also occur under basic conditions, resulting in loss of the biologically potent 2β-isomers (1–8b, 14–24b) by conversion to the much less active 2α-isomer (1–8a, 14–24a). Tropinone (25) could be envisaged as a convenient starting material for the synthesis of diverse tropane alkaloids. A novel entry into tropane alkaloid intermediates was developed based on the ring-opening reaction of tropinone. In this reaction, the enolate of tropinone, resulting from deprotonation with lithium diisopropylamide [LDA,LiN(CHMe₂)₂] or sodium bis(trimethylsilyl)amide [NaN(SiMe₃)₂] was treated with alkyl chloroformate to give a novel, structurally unique class of tropane alkaloid intermediates 6-N-carboalkyoxy-N-methyl-2-cycloheptenone (26), 1-alkyoxycarboxy-6-N-carboalkoxy-N-methyl-2,7-cyclohept-dien (27) and 6-N-carboalkyoxy-N-methyl-7-carboalkoxy-2,7-cyclohept-dien-ol (28). In this paper we study the conjugate addition reaction of Grignard reagents to α,β-unsaturated esters, the isomerization of aryltropane cocaine analogs, and the ring-opening reaction of tropinone by ab initio MO calculation at the Hartree–Fock (HF) level. The calculation results solely in terms of energetics indicate that the 2α-isomers (equatorial configurations) of aryltropane cocaine analogs are more stable than their 2β-isomers (axial configurations), at the AM1, STO-3G and 3-21G(*) levels, and the Grignard 1,4- and then 1,2-addition (double addition) products (2, 4, 5 and 7) are likely more stable than the Grignard 1,4-addition (single addition) products (1, 3, 6 and 8), respectively, at the STO-3G and 3-21G(*) levels except at the AM1 level. Therefore the tendency of Grignard addition toward double addition is competitive with single addition, and the isomerization tends to the formation of more stable 2α-isomers. Likewise, the calculation results solely in terms of energetics indicate that the stability of the reaction product forms is 28>27>26, at the AM1, STO-3G and 3-21G(*) levels, and the tendency of alkyl chloroformate addition toward double addition to the products 27 and 28 is competitive with single addition to the products 26. Ab initio MO calculations provide a theoretical rationalization for the chemoselectivity of the conjugate addition reaction and the ring-opening reaction, the most stable configurations of reaction products (1–8, 14–24, 26–28), and the isomerization between 1–8b, 14–24b and 1–8a, 14–24a, and between 27 and 28.

The mechanism of DNA damage caused by the isomerization of purine base is studied with density functional theory calculations at the B3LYP/6-311+G(d,p) level. The transition states of all the isomerizations are obtained, and the intrinsic reaction coordinate (IRC) analyses are performed to identify these transition states further. The isomerizations of purine bases can be classified into two types. The first is the hydrogen transfer between atoms, whose transition state includes a four-member ring. The second is the bond N–H rotation about the double bond N=C, and the plane CNH is perpendicular to the molecular plane in its transition state. The hydrogen transfer has higher reaction potential barrier, larger tunnel effect, and smaller equilibrium constant and rate constant than that of the N–H rotation. Effects of the hydration are considered in the framework of the polarizable continuum model (PCM) in SCRF method at the B3LYP/6-311+G(d,p) level. The isomerizations which result in the configuration changes of purine base and bring directly the DNA damage are endothermic and thermodynamic nonspontaneous processes. The probability of DNA damage caused by the guanine isomerization is larger than that by adenine.

The structures of the germylenoid H₂GeFMgF and its insertion reactions with RH (R = F, OH, NH₂) were studied using the DFT B3LYP and QCISD approaches for the first time. The geometries of all of the stationary points were optimized at the B3LYP/6-311+G (d, p) level of theory. And then the QCISD/6-311++G (d, p) single-point energies were calculated. The solvent effects on the geometries and insertion reactions were also computed using the PCM model. The calculated results suggested that H₂GeFMgF had three equilibrium configurations, in which the p-complex structure had the lowest energy and was the most stable structure. The isomerization reactions among the three complexes had been studied. For the insertion reactions of H₂GeFMgF with RH (R = F, OH, NH₂), along the potential energy surface, there were one transition state and one intermediate which connected the reactants and the products. For the three insertion reactions the mechanisms are identical. However, under the same conditions the insertion reactions should occur easily in the order of H-F > H-OH > H-NH₂. The solvent effect calculations suggested the larger the solvent polarity is, the easier the reaction will be.

The misfolding and aggregation of amyloid-$\beta$ (A$\beta )$ peptides into amyloid fibrils is regarded as one of the possible causes of Alzheimer’s disease (AD). Aromatic interactions (i.e. $\pi$–$\pi$ interactions) between tanshinone drugs extracted from Chinese herb Salvia Miltiorrhiza (SM) and aromatic residues of A$\beta$ peptides have been shown to prevent further growth of amyloid aggregates. In this work, the effects of isomerization, complexation and polarity of environment on the strength of $\pi$–$\pi$ stacking interactions of tanshinone I (TS1) and isotanshinone I (IS1), as the two diterpenoid quinones in the SM herb, and their complexes with Mg${}^{2+}$ cation, IS1-Mg${}^{2+}$ and TS1-Mg${}^{2+}$, with phenylalanine (PHE), as an aromatic amino acid in A$\beta$ structure have been investigated using the quantum mechanical calculations in the gas-phase, ether, acetone, DMSO, and water solvent. Molecular electrostatic potential (MEP), which are used to predict the nucleophile active sites, electron densities calculated at the bond critical points (${\rho }_{\mathrm{\text{BCP}}})$ and ring critical points (${\rho }_{\mathrm{\text{RCP}}})$ by the atoms in molecules (AIM) method and the donor–acceptor interaction energies ($E^2)$ calculated using the natural bond orbital (NBO) method were used to investigate the interplay between $\pi$–$\pi$ stacking and complexation. The results show that the IS1/TS1-Mg${}^{2+}$ compounds have a more protective role compared to TS1/IS1-Mg${}^{2+}$ compounds due to the stronger interaction with PHE of A$\beta$ in antiaggregation for further development of A$\beta$ inhibitors to prevent and disaggregate amyloid formation. Complexation with Mg${}^{2+}$ increases the interaction diterpenoid drugs with PHE and makes notable changes in structural and electronic properties of diterpenoids. Also, the interactions between diterpenoid and PHE in less polar environment are more than other environments. Low-polarity environments have the best mimics of the A$\beta$ binding site.

We present a quasiclassical trajectory study of the photodissociation of CD₃CHO based on a global ab initio-based potential energy surface. Calculations are performed at the total energy corresponding to the photolysis wavelength of 280nm. In addition to the major radical and molecular products, CD${}_3+\mathrm{\text{HCO}}$ and CD₃H $+$ CO, respectively, this paper focuses on the unusual radical channel CD₂H $+$ DCO, which requires a D/H exchange process before the conventional C–C bond cleavage. Five D/H exchange mechanisms are reported, which are related to the isomerizations from acetaldehyde to vinyl alcohol and back, to oxirane and back, and to the intermediate (CD–CHD–OD) and back. These D/H exchange mechanisms are in good agreement with the experimental findings [Heazlewood BR, Maccarone AT, Andrews DU, Osborn DL, Harding LB, Klippenstein SJ, Jordan MJT, Kable SH, Nat Chem3:443, 2011].

1,19,21,24-tetrahydro-1,19-bilindione is the framework of pigments frequently found in nature, which includes biliverdin IX α, phytochromobilin and phycocyanobilin. 1,19-bilindiones have unique features such as (1) photochemical and thermal cis-trans isomerization, (2) excited energy transfer, (3) chiroptical properties due to the cyclic helical conformation, (4) redox activity, (5) coordination to various metals, and (6) reconstitution to proteins. 1,19-bilindione can adopt a number of conformations since it has exocyclic three double bonds and three single bonds that are rotatable thermally and photochemically. In solution, biliverdin and phycocyanobilin adopt a cyclic helical ZZZ, syn, syn, syn conformation, but other conformations are stabilized depending on the experimental conditions and substituents on the bilin framework. The conformational changes in 1,19-bilindiones are related to the biological functions of a photoreceptor protein, phytochrome. Structural and conformational studies of bilindiones are summarized both in solution and in protein. The conformational changes of bilins can be used for other functions such as a chirality sensor. The bilindiones and the zinc complexes of bilindiones can be employed as a chirality sensor due to the helically chiral structure and the dynamics of racemization of enantiomers. In this paper, we discuss the conformational equilibria and dynamics of bilindiones and its implications in photobiology and materials science.

We saw (Section 4.4) that CO₂ (carbon dioxide) reacts with quicklime (calcium oxide) in water at 25°C, under 1 atm generating calcium carbonate or limestone (CaCO₃). The process is a sequence of two reactions (4.14) and (6.1):