A new model for the simulation of electron transport through duplex DNA is developed and applied to DNA segments of varying lengths consisting of a thymine and complementary adenine strand. The model for electron transport involves moving an excess electron from the 5' to the 3' end of the thymine strand by means of the fluctuating geometry of the thymines, using the molecular dynamics method coupled with N1-methylthymine vertical electron affinities calculated at the B3LYP/6-31+G* level of theory. The electron transport lifetimes calculated using this model follow the distance dependence of Jortner's incoherent multistep hopping theory (Jortner. J.; Bixon, M.: Langenbacher, T. Proc. Natl. Aad. Sci U.S.A. 1998. 95, 12759) and were found to decrease with temperature.

Theoretical abinitio calculations have been performed to determine the stability of covalent and dipole-bound anions of cytosine. The work is related to the recent anion spectroscopy experiments performed on some nucleic acid bases including cytosine by Schiedt et al. [Chem, Phys. 239 (1998) 511], where two anion states attributed to dipole-bound anions of the amino-hydroxy (A-H) and amino-oxo (A-O) tautomers were detected. The present calculations reveal that (i) the A-O isomer and two rotamers of the A-H isomer have sufficient dipole moments to bind sigma excess electrons in stationary dipole-bound states. The calculated adiabatic electron affinities are 58, 22, and 6 meV for the A-O cytosine and the two rotamers of the A-H cytosine, respectively. These values are considerably smaller than the two experimentally determined values of 85 +/- 8 and 230 +/- 8 meV; (ii) our calculations also describe covalent anions of the A-O and A-H tautomers. In both systems, the six-member ring is noticeably distorted from planarity. According to the calculations only, the A-O covalent anion is vertically stable with respect to the electron attachment, and the corresponding vertical electron detachment energy is 102 meV. However, both A-O and A-H cytosine anions are predicted to be unstable with respect to the adiabatic electron detachment. This finding is consistent with the lack of a covalent anion feature in the experimental spectrum. (C) 2000 Elsevier Science B.V. All rights reserved.

Rydberg electron transfer spectroscopy (RET) has been used to determine the dipole-bound electron affinity of the indole molecule, and the value of 3 meV was obtained. RET has also been employed to study [indole–(water)N]− cluster anions and the results have been interpreted with the help of ab initio calculations. It has been shown that for N=1 and 2 only dipole-bound anions are formed and that the electron attachment induces large amplitude motions in these systems. [Indole–(water)N]− anions with N=3 and 4 have not been observed. This finding for N=3 is consistent with a low theoretically predicted dipole moment of the neutral indole–(water)3 complex, which is insufficient for the formation of a stable dipole-bound anion. Above N=5, RET experiments showed formation of valence [indole–(water)N]− anions. From the observed size threshold for the formation of these anions, the negative value of the valence electron affinity of indole equal to −1.03±0.05 meV was deduced.

The influence of N-methylation on the dipole-bound electron affinities of pyrimidine nucleic acid bases, uracil and thymine, has been investigated theoretically using ab initio quantum mechanical calculations, and experimentally using Rydberg electron transfer spectroscopy. Both experiment and theory are consistent in showing that replacement of hydrogen atoms by methyl groups reduces electron affinities corresponding to formation of dipole-bound anions of these systems. Also, the distortion of the anion geometries with respect to the geometries of the neutral parents are reduced with the methylation.

Results of ab initio calculations of the (H2O)5/(H2O)5− systems are presented. The main conclusions of the study are as follows: Based on the calculations we predict that water pentamer anions are metastable systems in agreement with their weak spectral manifestation in the gas-phase experiments of Bowen and co-workers; the excess electrons in all five structural isomers of the water pentamer anion found in the calculations are attached to the clusters by virtue of a dipole–electron interaction; the (H2O)5− anions found in the calculations are close in energy but have different vertical electron detachment energies ranging from 143 to 395 meV.

The influence of methylation upon adiabatic electron affinities of formamide (F), N- methylformamide (NMF), and N,N-dimethylformamide (DMF) is experimentally investigated by means of Rydberg electron transfer spectroscopy and calculated with the use of high-level ab initio methods. In the anions of these systems the excess electrons are captured in diffuse dipole-bound states. The methylation of formamide results in a slight increase of the dipole moment and in an increased molecular size. The two factors have opposite effects on the electron affinity. Both experimental data and theoretical results are in agreement, showing that the molecular size effect dominates and that the electron affinity noticeably decreases with the methylation.

Ab initio calculations have been performed to determine structures and electron detachment energies of the hydrogen fluoride hydrogen-bonded polymers, (HF)(n)(-), n = 5-9. In these systems, the excess electron is bound by virtue of the dipole-electron interaction. It was found that, unlike the neutral complexes which form cyclic structures, the equilibrium geometries of the anions have "zig-zag" linear shapes. For all the five complexes, the predicted vertical detachment energies are positive (307, 363, 405, 437, and 461 meV for (HF)(5)(-) (HF)(6)(-), (HF)(7)(-), (HF)(9)(-), and (HF)(9)(-), respectively). These results were obtained at the Moller-Plesset second-order level of theory at the geometries of the anions calculated at the Hartree-Fock level. The calculations also indicate that up to n = 8, the (HF)(n)(-) anions are metastable systems with respect to electron detachment and simultaneous transformation of the cluster to the most stable cyclic configurations. However, calculations predict that starting from (HF)(9)(-) the linear HF cluster anions are adiabatically stable systems. (C) 1999 Elsevier Science B.V. All rights reserved.

Ab initio calculations were performed on gas-phase calcium and magnesium dications chelated with various anionic pyrophosphate species: H2P2O72-, HP2O73-, and P2O74-. The cleavage of the pyrophosphate into a metaphosphate and an orthophosphate complexed to either calcium or magnesium was also investigated. The studied isomerization reaction of the metal-pyrophosphate complexes can be written as [M . HNP2O7](N-2) --> [PO3. M . HNPO4](N-2) where M = Mg, Ca, and N = 0, 1, 2. Geometries for the complexes were optimized with the self-consistent-field (SCF) level of theory, and the total energy for each system was subsequently calculated with the second-order Moller-Plesset perturbation (MP2) method using 6-31+G** basis functions for the H, 0, and P atoms and valence double-zeta basis functions polarization augmented with a diffuse function (pVDZ+) for the Mg and Ca atoms. Zero-point energies (ZPE) and entropies were calculated with the SCF harmonic frequencies from which enthalpies and Gibbs free energies were also estimated. The nb initio isomerization energies of all of the calcium-containing complexes were positive and had a large contribution of correlation, while those of the magnesium-containing complexes were negative and had a significantly lower contribution of correlation. These calculated gas-phase isomerization energies may provide an explanation to the observation that pyrophosphatases utilize magnesium complexes as substrates for the hydrolysis of pyrophosphates but do not utilize calcium complexes.

The infrared spectrum of 3-hydroxy-2-methyl-4-pyrone reveals an O-H stretching frequency roughly 200 cm−1 lower than that of a typical alcohol group. The frequency lowering results from intramolecular hydrogen bonding between the alcohol and ketone groups. In this work, the stretching and bending vibrations of the O-H group in 3-hydroxy-2-methyl-4-pyrone are studied with a theoretical methodology more rigorous than the conventional harmonic approximation. A two-dimensional potential energy surface in internal coordinates corresponding to different hydrogen positions in the plane of the molecule is calculated with the use of the second order Mo/ller-Plesset perturbation theory. To include all possible variations in kinetic energy in a large amplitude vibrational mode, g-matrix elements with variable values are employed. The analytical expression for the Hamiltonian matrix elements of the two-dimensional vibrational problem in a basis of shifted Gaussian functions is derived. Expectation values for the O-H stretch nuclear states are variationally determined with the use of shifted Gaussian functions as the basis set. The results of the calculations are compared with the recent matrix-isolation infrared (IR) spectroscopic results. The calculated transition frequency corresponding to the in-plane O-H stretching is found to be in good agreement with the experimental value.

Ab initio calculations have been performed to determine structures and adiabatic electron affinities of water complexes of hydrogen cyanide. In these systems the excess electron is bound by the dipole field of the complex. Based on the calculations we determined that, as for the neutral complexes, there are two equilibrium anion structures, [HCN⋯H2O]− and [H2O⋯HCN]−. Upon electron attachment to the neutral H2O⋯HCN complex, which the only system detected in the gas phase, its stability with respect to the HCN⋯H2O complex increases even further, from 1.4 kcal/mol to 3.0 kcal/mol. The adiabatic electron affinities of H2O⋯HCN and HCN⋯H2O complexes are predicted to be 86 and 17 meV, respectively.

In this work we investigate the ability of the uracil·water complex to form stable anionic systems. As the experimental evidence and theoretical calculations have indicated, the isolated uracil molecule can only attach an excess electron into a diffuse dipole-bound state, while some recent experiments suggest that the uracil· water complex can form a more stable valence-type anion. In this work we demonstrate that it is possible to converge ab initio calculations of uracil·(H2O)3- to an equilibrium structure that is significantly different from the structure of the neutral cluster and that has a positive and remarkably significant vertical ionization potential. Apart from the valence anion, the uracil·(H2O)3 complex can form a stable dipolebound anion, but as the present calculations indicate the electron affinity, which corresponds to this attachment, is very small (13 meV). The structure of the dipole-bound anion is virtually identical with the structure of the neutral complex.

Ab initio calculations have been performed to determine the electron affinity of the hydrogen fluoride dimer, (HF)2. Although, a single hydrogen fluoride molecule does not form a stable stationary state with an excess electron, the hydrogen fluoride dimer has a positive electron affinity. In this system the excess electron is bound by the dipole field of the complex. The present theoretical calculations render the value of adiabatic electron affinity equal to 52 meV. The calculated value is in a good agreement with experimental result of 63 ± 6 meV of Bowen and coworkers.

Matrix isolation IR spectroscopy and high-level ab initio calculations were applied to investigate the structure and vibrational spectra of quinone-pyrimidine heterodimers formed in low-temperature Ar matrices. A specially developed experimental technique was used to separate bands of quinone-pyrimidine dimer from bands of quinone and pyrimidine monomers and homodimers in the IR spectra. As a result, nine bands assigned to the quinone-pyrimidine heterodimer were identified. Ab initio calculations at the MP2/6-31+G*, MP2/6-31++G** and SCF/6-31++G** levels of theory have been carried out to determine the relative energies and vibrational spectra of three stable configurations of the quinone-pyrimidine dimer found theoretically. These configurations are two planar complexes with two weak C-H ... O and C-H ... N hydrogen bonds and one stacked complex stabilized by dispersion forces. The effect of basis set superposition error (BSSE) on the relative stabilities and the vibrational spectra of the dimers was also investigated. The non-BSSE-corrected calculations at the MP2/6-31+G* and MP2/6-31++G** levels of theory predict the stacked dimer to be the most stable conformer, but accounting for BSSE resulted in a reverse stability ordering of the stacked and the planar dimers. The comparison of the observed frequency shifts with the theoretically predicted shifts has shown that the planar configuration is responsible for the experimentally observed bands. This is in agreement with the stability ordering derived from the BSSE-corrected relative energies. To account for the matrix effects on the stability of the planar and stacked dimers, additional calculations were carried out using the Onsager's reaction field model and the MP2/6-31++G** level of theory. These calculations confirm that the planar H-bonded dimer is the most stable configuration.

Ab initio calculations have been performed to determine structures and vertical electron detachment energy (VDE) of the hydrogen fluoride trimer and tetramer anions, (HF)3− and (HF)4−. In these systems the excess electron is bound by the dipole field of the complex. It was determined that, unlike the neutral complexes which prefer the cyclic structures, the equilibrium geometries of the anions have “zig–zag” shapes. For both complexes the predicted VDEs are positive [210 meV and 363 meV for (HF)3− and (HF)4−, respectively], indicating that the anions are stable systems with respect to the vertical electron detachment. These results were obtained at the coupled-cluster level of theory with single, double and triple excitations [CCSD(T) method; the triple-excitation contribution in this method is calculated approximately using the perturbation approach] with the anion geometries obtained using the second-order Mo/ller–Plesset perturbation theory (MP2) method. The same approach was also used to determine the adiabatic electron affinities (AEA) of (HF)3 and (HF)4. In addition to the electronic contribution, we also calculated the contributions (using the harmonic approximation) resulting from different zero-point vibration energies of the neutral and anionic clusters. The calculations predicted that while the AEA of (HF)3 is positive (44 meV), the AEA for (HF)4 is marginally negative (−16 meV). This suggests that the (HF)3− anion should be a stable system, while the (HF)4− is probably metastable.

Following the experimental characterization of the N,N-dimethylated uracil anion by Bowen and co-workers, we have undertaken an investigation of the influence of the methylation on the electron affinity of the uracil molecule. Both experiment and theory agree that, as it is in the case of the isolated uracil molecule, the methylated uracils can only attach excess electrons into diffuse dipole-bound states. The corresponding electron affinities are very small (several MeV). The bonding effect in the dipole-bound state depends on the magnitude of the molecular dipole and on the size of the molecule. Selective methylation of the uracil molecule can be used to reduce or increase the dipole value and to change the electron affinity of the molecule. The present calculated results are consistent with the experimental determination that N,N-dimethylation of uracil results in reduction of the electron affinity.