Jiande Gu

Homoleptic Carbonyls of the Second-Row Transition Metals: Evaluation of Hartree−Fock and Density Functional Theory Methods†

The homoleptic mono- and multinuclear carbonyls for Mo, Tc, Ru, and Rh, namely, Mo(CO)6, Ru(CO)5, Tc2(CO)10, Ru3(CO)12, Rh4(CO)12, and Rh6(CO)16, are investigated theoretically by the Hartree-Fock method and three density functional theory (DFT) methods, i.e., BP86, B3LYP, and MPW1PW91, along with the SDD ECP basis sets. The results predicted by all the methods are basically in agreement with each other. The MPW1PW91 and BP86 methods predict geometric parameters and vibrational spectra, respectively, closest to the experimental values. For Ru3(CO)12 the relative energies of the D3h isomer with only terminal CO groups and the C2v isomer with two bridging CO groups are within 3 kcal/mol of each other with the lower energy isomer depending upon the computational method used. For Rh4(CO)12 the global minimum is predicted to have C3v symmetry, with three bridging and nine terminal carbonyls, in accord with experiment. The Rh6(CO)16 structure has Td symmetry and satisfies the Wade-Mingos rules for an octahedral cluster. Using the MPW1PW91 method the Rh-Rh distances in Rh4(CO)12 are found to be 2.692 Å and 2.750 Å and those in Rh6(CO)16 to be 2.785 Å.

Electron attachment to DNA single strands: gas phase and aqueous solution

The 2′-deoxyguanosine-3′,5′-diphosphate, 2′-deoxyadenosine-3′,5′-diphosphate, 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate systems are the smallest units of a DNA single strand. Exploring these comprehensive subunits with reliable density functional methods enables one to approach reasonable predictions of the properties of DNA single strands. With these models, DNA single strands are found to have a strong tendency to capture low-energy electrons. The vertical attachment energies (VEAs) predicted for 3′,5′-dTDP (0.17 eV) and 3′,5′-dGDP (0.14 eV) indicate that both the thymine-rich and the guanine-rich DNA single strands have the ability to capture electrons. The adiabatic electron affinities (AEAs) of the nucleotides considered here range from 0.22 to 0.52 eV and follow the order 3′,5′-dTDP > 3′,5′-dCDP > 3′,5′-dGDP > 3′,5′-dADP. A substantial increase in the AEA is observed compared to that of the corresponding nucleic acid bases and the corresponding nucleosides. Furthermore, aqueous solution simulations dramatically increase the electron attracting properties of the DNA single strands. The present investigation illustrates that in the gas phase, the excess electron is situated both on the nucleobase and on the phosphate moiety for DNA single strands. However, the distribution of the extra negative charge is uneven. The attached electron favors the base moiety for the pyrimidine, while it prefers the 3′-phosphate subunit for the purine DNA single strands. In contrast, the attached electron is tightly bound to the base fragment for the cytidine, thymidine and adenosine nucleotides, while it almost exclusively resides in the vicinity of the 3′-phosphate group for the guanosine nucleotides due to the solvent effects. The comparatively low vertical detachment energies (VDEs) predicted for 3′,5′-dADP− (0.26 eV) and 3′,5′-dGDP− (0.32 eV) indicate that electron detachment might compete with reactions having high activation barriers such as glycosidic bond breakage. However, the radical anions of the pyrimidine nucleotides with high VDE are expected to be electronically stable. Thus the base-centered radical anions of the pyrimidine nucleotides might be the possible intermediates for DNA single-strand breakage.

Electron attachment induced proton transfer in a DNA nucleoside pair: 2 '-deoxyguanosine-2 '-deoxycytidine

To elucidate electron attachment induced damage in the DNA double helix, electron attachment to the 2-deoxyribonucleoside pair dG:dC has been studied with the reliably calibrated B3LYP/DZP++ theoretical approach. The exploration of the potential energy surface of the neutral and anionic dG:dC pairs predicts a positive electron affinity for dG:dC [0.83 eV for adiabatic electron affinity (EAad) and 0.16 eV for vertical electron affinity (VEA)]. The substantial increases in the electron affinity of dG:dC (by 0.50 eV for EAad and 0.23 eV for VEA) compared to those of the dC nucleoside suggest that electron attachment to DNA double helices should be energetically favored with respect to the single strands. Most importantly, electron attachment to the dC moiety in the dG:dC pair is found to be able to trigger the proton transfer in the dG:dC- pair, surprisingly resulting in the lower energy distonic anionic complex d(G-H)-:d(C+H).. The negative charge for the latter system is located on the base of dC in the dG:dC- pair, while it is transferred to d(G-H) in d(G-H)-:d(C+H)., accompanied by the proton transfer from N1(dG) to N3(dC). The low energy barrier (2.4 kcal/mol) for proton transfer from dG to dC- suggests that the distonic d(G-H)-:d(C+H). pair should be one of the important intermediates in the process of electron attachment to DNA double helices. The formation of the neutral nucleoside radical d(C+H). is predicted to be the direct result of electron attachment to the DNA double helices. Since the neutral radical d(C+H). nucleotide is the key element in the formation of this DNA lesion, electron attachment might be one of the important factors that trigger the formation of abasic sites in DNA double helices.

Electron attachment to PCl3 and POCl3, 296–552 K

Rate constants for electron attachment to PCl3 and POCl3 have been measured over the temperature range 296–552 K in 135 Pa of helium gas, using a flowing-afterglow Langmuir-probe apparatus. Electron attachment to PCl3 is dissociative, producing only Cl− ions in this temperature range. The rate constant is 6.4±1.6×10−8u2009cm3u2009s−1 at 296 K and increases with temperature in a way that may be described by an activation energy of 43±10u2009meV. Electron attachment to POCl3 is a richer process in which a nondissociative channel (POCl3−) competes with two dissociative ones (POCl2− and Cl−). The rate constant for electron attachment to POCl3 is 1.8±0.4×10−7u2009cm3u2009s−1 at 296 K and is relatively temperature independent in our temperature range. POCl2− is the major product over the entire temperature range. Ab initio MP2 and MP4 calculations have been carried out on ground-state neutral and anionic PCln and POCln for n=1–3. The calculated adiabatic electron affinities agree with experimental estimates where available. The ca...

The barrier height for decomposition of HN2

The barrier height and exothermicity for the HN2→H+N2 reaction are predicted by high level ab initio quantum mechanical methods. The classical barrier is predicted to be 10.0±1.0u2009kcal/mol, and the reaction exothermicity is predicted to be 3.8±0.5u2009kcal/mol. The importance of these parameters to the thermal De–NOx process is discussed. The apparent conflict between the theoretical potential energy surface for HN2 and recent kinetic modeling studies is seen to persist.

The electron affinities of PF and PF2

Theoretical investigations of the adiabatic electron affinities of PF and PF2 have been carried out. Large basis sets were used in this research, ranging from TZ2Pf+diff up to aug-cc-pVQZ. The theoretical methods applied here were Hartree–Fock self-consistent-field (SCF) theory, single and double excitation configuration interaction (CISD), single and double excitation coupled cluster (CCSD), and the CCSD(T) method, which adds perturbatively the connected triple excitations to the CCSD method. The results of this investigation show that three theoretical methods, DZP++ BHLYP, G2, and aug-cc-pVQZ CCSD(T) provide excellent agreement with each other for the adiabatic electron affinities of PF and PF2. The high level of theory used in this research suggests that the adiabatic electron affinity of PF is about 0.75 eV, and that of PF2 is about 0.76 eV. These predictions are in contrast to the experimental values of 3.4 eV (for PF) and 1.4–1.6 eV (for PF2).

Stability and Structures of the DNA Base Tetrads: A Role of Metal Ions

Nucleic acids can form complex structures that consist of multi-strands, which play a vital role in many biological processes. Quantum chemistry studies of the polyads of the nucleic acid bases (NABs) strongly suggest that all of them (NABs) can form stable tetrad structure in cyclic form through the H-bonding between the neighboring bases. All of the cyclic form tetrads possess the strong cooperativity of the hydrogen bonds. The cooperative effects should play a key role in the formation of stable tetraplexes. The existence of cation in the cavity of the tetrads greatly improves the stability of the tetraplexes. Metals can also replace the protons in the bases to form tetrads. This phenomenon could be extremely important in the construction of variety of newly designed nanomaterials. DNA bases are also able to form larger species. The studies of isoG quintet reveal that metal ions are crucial for regulating the strand association.