Nancy A. Richardson

The deprotonated guanine-cytosine base pair

Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26–27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine–cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal·mol−1, vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal·mol−1 lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H···O2 distance dramatically reduced from 1.88 to 1.58 Å, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a “reverse wobble” incorporating two N-H···N hydrogen bonds. Three different types of relaxation energies (4.3–54 kcal·mol−1) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.

Investigating the Effects of Basis Set on Metal–Metal and Metal–Ligand Bond Distances in Stable Transition Metal Carbonyls: Performance of Correlation Consistent Basis Sets with 35 Density Functionals

Density functional theory (DFT) is a widely used method for predicting equilibrium geometries of organometallic compounds involving transition metals, with a wide choice of functional and basis set combinations. A study of the role of basis set size in predicting the structural parameters can be insightful with respect to the effectiveness of using small basis sets to optimize larger molecular systems. For many organometallic systems, the metal-metal and metal-carbon distances are the most important structural features. In this study, we compare the equilibrium metal-ligand and metal-metal distances of six transition metal carbonyl compounds predicted by the Hood-Pitzer double-ζ polarization (DZP) basis set, against those predicted employing the standard correlation consistent cc-pVXZ (X = D,T,Q) basis sets, for 35 different DFT methods. The effects of systematically increasing the basis set size on the structural parameters are carefully investigated. The Mn-Mn bond distance in Mn2(CO)10 shows a greater dependence on basis set size compared to the other M-M bonds. However, the DZP predictions for re(Mn-Mn) are closer to experiment than those obtained with the much larger cc-pVQZ basis set. Our results show that, in general, DZP basis sets predict structural parameters with an accuracy comparable to the triple and quadruple-ζ basis sets. This finding is very significant, because the quadruple-ζ basis set for Mn2(CO)10 includes 1308 basis functions, while the equally effective double-ζ set (DZP) includes only 366 basis functions. Overall, the DZP M06-L method predicts structures that are very consistent with experiment.

The rule breaking Cr2(CO)10. A 17 electron Cr system or a Cr=Cr double bond?

Density functional theory (DFT) has been used to investigate the conformations and thermochemistry on the singlet and triplet potential energy surfaces (PES) of Cr2(CO)10. The global minimum energy structure for the lowest singlet state of C2h symmetry is consistent with a model of two interacting Cr(CO)5 fragments in which one carbonyl in each fragment acts as an asymmetric four-electron donor bridging carbonyl, with chromium-chromium distances of 2.93 A (B3LYP) or 2.83 A (BP86). Avoiding a Cr...Cr bond by incorporating four-electron donor CO groups in this way allows each chromium atom in singlet Cr(CO)10 to attain the favored 18-electron configuration by using, in a simple picture of the bonding, only the six octahedral sp3d2 hybrids. The dissociation energy to two Cr(CO)5 fragments or to Cr(CO)6 + Cr(CO)4 fragments is predicted to be 10 kcal mol(-1). The lowest triplet state of Cr2(CO)10 is predicted to lie approximately 10 kcal mol(-1) above the singlet global minimum. In the case of triplet Cr2(CO)10 the lowest energy minima were found to be of C2 and C2h symmetry, with similar energies. The chromium-chromium distances in triplet Cr2(CO)10 were found to be shorter than those in the corresponding singlet structures, namely 2.81 (B3LYP) or 2.68 A (BP86) suggesting a sigma + 2(1/2) pi Cr=Cr double bond similar to the O=O bond in O2 or the Fe=Fe bond in the experimentally observed triplet state (Me5C5)2Fe2(mu-CO)3.

Characterization of the and electronic states of CH2

Abstract The X 2 A 1 and a 4 A 2 electronic states of the methylene cation, CH 2 + , were investigated using the coupled cluster method with singles, doubles, and perturbatively applied triples [CCSD(T)] with Dunnings correlation consistent polarized valence basis set series (cc-pVXZ, where X=T, Q, and 5), core-valence basis sets (cc-pCVXZ, where X=T and Q), and augmented basis sets (aug-cc-pVXZ, where X=Q and 5). Explicit computation of the full set of triples (CCSDT) was also performed with the cc-pVTZ basis set. The most reliable equilibrium structures of r e =1.094 A and θ e =140.4° ( X 2 A 1 ) and r e =1.190 A and θ e =77.1° ( a 4 A 2 ) were obtained at the CCSD(T)/aug-cc-pV5Z level. The X 2 A 1 – a 4 A 2 classical energy separation is predicted to be 86.9 kcal/mol ( 30 400 cm −1 , 3.77 eV) at the CCSD(T)/cc-pCVQZ level of theory, and the zero-point vibrational energy corrected value is 84.5 kcal/mol ( 29 500 cm −1 , 3.66 eV).

CHARACTERIZATION OF THE

The electronic ground state and first excited state (A2Σ+) of phosphaethyne cation (HCP+) have been systematically investigated using ab initio electronic structure theory. The total energies, geometries, rotational constants, dipole moments, harmonic vibrational frequencies, and parameters for Renner–Teller splittings were determined using self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), coupled cluster (CC) with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], CC with single, double, and iterative partial triple excitations (CCSDT-3), and CC with single, double, and full triple excitations (CCSDT) methods and eight different basis sets. Some of the largest full triples coupled cluster computations to date are reported. Degenerate bending frequencies for the A2Σ+ state were determined using the equation-of-motion (EOM)-CCSD technique. The two states have been confirmed to have linear equilibrium structures. At the full CCSDT level of theory with the correlation-consistent polarized valence quadruple zeta (cc-pVQZ) basis set, the classical splitting (Te value) is predicted to be 47.7 kcal/mol (2.07 eV, 16,700 cm-1) and the quantum mechanical splitting (T0 value) to be 48.1 kcal/mol (2.08 eV, 16,800 cm-1), which are in excellent agreement with the experimental values of Te = 47.77 kcal/mol (2.072 eV, 16,708 cm-1) and T0 = 47.94 kcal/mol (2.079 eV, 16,766 cm-1). The excitation energies predicted by the CCSDT-3 and CCSD(T) methods differ from the full triples CCSDT result by 0.38 and 0.45 kcal/mol, respectively. With the aug-cc-pVQZ CCSDT-3 method the Renner parameter and the averaged harmonic bending vibrational frequency are determined to be ∊= -0.0390 and for the ground state of HCP+, which are reasonably consistent with the experimental values of ∊=-0.0415 and . The predicted dipole moments are 1.30 Debye ( state, polarity-hydrogen atom positive) and 0.06 Debye (A2Σ+ state, polarity-phosphorus atom positive).