Docking, triggering, and biological activity of dynemicin A in DNA: a computational study

The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.     

Some thoughts about the stability and reliability of commonly used exchange–correlation functionals – coverage of dynamic and nondynamic correlation effects

 The self-interaction error (SIE) of commonly used density functional theory (DFT) exchange functionals mimics long-range (nondynamic) pair correlation effects in an unspecified way. Slater exchange suffers from a larger SIE and, therefore, covers more nondynamic correlation effects than Becke exchange, which is the reason why exchange–correlation (XC) functionals based on Slater exchange lead to stabler restricted DFT solutions than those based on Becke exchange. However, the stability of an XC functional does not guarantee higher accuracy. On the contrary, if system-specific nondynamic correlation effects have to be introduced via the form of the wave function, these will be suppressed by nondynamic correlation effects already covered by the exchange functional. Hybrid functionals suffer less from the SIE and, therefore, cover a smaller number of nondynamic electron correlation effects. Accordingly, they are better suited when nondynamic electron correlation has to be introduced by the form of the wave function. It is shown that, for example, broken-symmetry unrestricted DFT calculations are more accurate when carried out with B3LYP than BLYP contrary to claims made in the literature. Received: 8 November 2001 / Accepted: 30 January 2002 / Published online: 8 April 2002     

Trishomocyclopropenylium Cations. Structure, Stability, Magnetic Properties, and Rearrangement Possibilities

Potentially trishomoaromatic cations possessing the 6-X-bicyclo[3.1.0]hex-3-yl (X = CH(2), BH, NH, O) or bicyclo[3.2.0]hept-3-yl unit have been investigated at the Hartree-Fock, second-order, third-order, and fourth-order (single, double, quadruple excitations) M?ller-Plesset perturbation level employing the 6-31G(d) basis set. IGLO/6-31G(d) chemical shift calculations have been carried out at optimized geometries. Through-space interactions between the symmetric Walsh orbital of the three-membered ring and ppi(C3) orbital have been analyzed as a function of orbital energies and orbital overlap. The best indicators for trishomoaromaticity are NMR chemical shifts and magnetic susceptibility. There is a simple relationship between the conformation of the trishomocyclopropenylium cation, its charge distribution, and delta(13)C3, which can be used to determine the conformation or the C1C3 interaction distance from NMR measurements. Trishomocyclopropylium cations investigated can rearrange to an envelope form of higher energy where the height of the inversion barrier and the chair-envelope energy difference are a measure for the homoaromatic stabilization energy. The bicyclo[3.1.0]hex-3-yl cation in its envelope form can rearrange with a barrier of just 1 kcal/mol to the bicyclo[3.1.0]hept-2-yl cation. In the case of the bicyclo[3.2.0]hept-3-yl cation, there exists just the envelope form, which can rearrange to a ethano-bridged center-protonated spirocyclopentyl cation. The later cation should be an interesting target of chemical synthesis since it contains a pentacoordinated carbon atom and possesses unusual properties.     

Zur konfigurativen stabilität syn/anti-isomerer überbrückter [14]annulene mit anthracen-perimeter

The existence of a thermal equilibrium between aromatic syn-1,6:8,13-bisoxido[14]annulene and its olefinic anti-isomer is deduced from stereochemical and theoretical studies.     

Nearly Degenerate Isomers of C(BH)2: Cumulene,Carbene, or Carbone?

The ground electronic state of C(BH)₂ exhibits both a linear minimum and a peculiar angle‐deformation isomer with a central B‐C‐B angle near 90°. Definitive computations on these species and the intervening transition state have been executed by means of coupled‐cluster theory including single and double excitations (CCSD), perturbative triples (CCSD(T)), and full triples with perturbative quadruples (CCSDT(Q)), in concert with series of correlation‐consistent basis sets (cc‐pVXZ, X=D, T, Q, 5, 6; cc‐pCVXZ, X=T, Q). Final energies were pinpointed by focal‐point analyses (FPA) targeting the complete basis‐set limit of CCSDT(Q) theory with auxiliary core correlation, relativistic, and non‐Born–Oppenheimer corrections. Isomerization of the linear species to the bent form has a minuscule FPA reaction energy of 0.02 kcal mol^?1 and a corresponding barrier of only 1.89 kcal mol^?1. Quantum tunneling computations reveal interconversion of the two isomers on a timescale much less than 1 s even at 0 K. Highly accurate CCSD(T)/cc‐pVTZ and composite c～CCSDT(Q)/cc‐pCVQZ anharmonic vibrational frequencies confirm matrix‐isolation infrared bands previously assigned to linear C(BH)₂ and provide excellent predictions for the heretofore unobserved bent isomer. Chemical bonding in the C(BH)₂ species was exhaustively investigated by the atoms‐in‐molecules (AIM) approach, molecular orbital plots, various population analyses, local mode vibrations and force constants, unified reaction valley analysis (URVA), and other methods. Linear C(BH)₂ is a cumulene, whereas bent C(BH)₂ is best characterized as a carbene with little carbone character. Weak B–B attraction is clearly present in the unusual bent isomer, but its strength is insufficient to form a CB₂ ring with a genuine boron–boron bond and attendant AIM bond path.     

Diabatic ordering of vibrational normal modes in reaction valley studies

Diabatic ordering of the normal model of a reaction complex along the reaction path has several advantages with regard to adiabatic ordering. The method is based on rotations of the vibrational normal modes at one point, s, of the reaction path to maximize overlap with the vibrational modes at a neighboring point. Global rotations precede the rotations of degenerate modes so that changes in the direction of the reaction path and changes in the force constant matrix, which represent the two major effects for changes in mode ordering, can be separated. Overlap criteria identify resolved and unresolved avoided crossings of normal modes of the same symmetry. Diabatic mode ordering (DMO) can be used to resolve the latter by reducing the step size, thus guaranteeing correct ordering of normal modes in dependence of s. DMO is generally applicable to properties of the reaction complex that depend on s such as normal mode frequencies, orbital energies, the energy of excited states, etc. Additional applications are possible using a generalized reaction path vector, which may describe the change in atom masses, geometrical parameters, and/or the force constant matrix. In this way, the vibrational spectra of isotopomers can be investigated or the vibrational frequencies of different molecules correlated. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1282–1294, 1997