A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.     

Survey of the proton affinities of adenine, cytosine, thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides

The kinetic method was applied to the determination of the proton affinities (PAs) of modified deoxy- and dideoxyribonucleosides. A correlation between the measured PAs and the replacement of one of the three hydroxyl groups of the ribose unit is presented. A PA scale was obtained which shows that the replacement of the primary or of one or both secondary hydroxyl groups of a ribonucleoside with a hydrogen atom induces the lowering or the enhancement of the nucleoside PA, respectively. The scale extends over a very narrow range of approximately 2 kcal mol(-1), thus demonstrating the sensitivity of the kinetic method in the evaluation of small differences in thermodynamic parameters.     

Fragmentation mechanisms of protonated benzylamines. Electrospray ionisation-tandem mass spectrometry study and ab initio molecular orbital calculations

Our research into neurotransmitters in a biological fluid presented an opportunity to investigate the fragmentations under low collision energy characterising benzyl-amines protonated under electrospray ionisation (ESI) conditions in a triple quadrupole mass spectrometer. In this work we present the breakdown graphs of protonated 3,4-dihydroxybenzylamine, DHBAH(+), and 3-methoxy, 4-hydroxybenzylamine, HMBAH(+), at various source temperatures and various pressures in the collision cell, the collision energy varying from 0 to 46 eV in the laboratory frame. Both parent ions eliminate first NH(3) at very low collision energy. The fragmentations of [MH - NH(3)](+) occur at high collision energy and are quite different for DHBAH(+) and HMBAH(+): formation of [MH - NH(3) - H(2)O - CO](+) for the former; formation of the radical cation [MH - NH(3) - CH(3)](+.) for the latter. These fragmentations are interpreted by means of ab initio calculations up to the B3LYP/6-311+G(2d,2p) level of theory. The successive losses of H(2)O and CO involve first the rearrangement in two steps of benzylic ions formed by loss of NH(3) into tropylium ions. The transition states associated with this rearrangement are very high in energy (about 400 kJ mol(-1) above MH(+)) explaining (i). the absence of an ion corresponding to [DHBAH - NH(3) - H(2)O](+). The determining steps associated with the losses of H(2)O and with H(2)O + CO are located lower in energy than the transition states associated with the isomerisation of benzylic ions into tropylium ions; explaining (ii). the formation of the radical cation [MH - NH(3) - CH(3)](+.). The homolytic cleavage of CH(3)-O requires less energy than does the rearrangement.     

The molecular electrostatic potentials for the nucleic acid bases: Adenine,thymine, and cytosine

The electrostatic potentials arising from ab initio MO LCAO GTO SCF wave functions for adenine, thymine and cytosine are given and discussed.Well defined characteristic regions of immediate chemical significance are found. The analysis of such results aims at comparing different protonation sites in the same molecule as well as in different ones. Differences among the proton affinities of the nitrogen atoms (pyridine-like, amine and imine) are evidenced, as well as the distinction between oxygen and nitrogen atoms.

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Zusammenfassung Die mit Hilfe von ab initio MO LCAO GTO SCF Wellenfunktionen berechneten elektrostatischen Potentiale von Adenin, Thymin und Cytosin werden angegeben und diskutiert.Man findet genau bestimmte charakteristische Zonen von klarer chemischer Bedeutung. Durch die Analyse solcher Resultate können verschiedene Protonierungsplätze sowohl in ein und demselben Molekül als auch in verschiedenen Molekülen verglichen werden. Deutlich zeigen sich Unterschiede der Protonenaffinitäten der unterschiedlich chemisch gebundenen Stickstoffatome (pyridinartiger, Amin- und Iminstickstoff) und der Unterschied zwischen Stickstoff- und Sauerstoffatomen.

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Résumé Les potentiels electrostatiques moléculaires calculés à partir de fonctions d'onde ab initio MO SCF LCAO GTO sont donnés et discutés pour l'adénine, la thymine et la cytosine.Des régions bien définies sont obtenues dont la signification chimique apparait clairement. L'analyse de l'ensemble des résultats permet la comparaison des differents sites de protonation dans une même molécule ainsi que dans differentes molécules, ainsi que la distinction entre oxygene et azote d'une part, azotes de differents types d'autre part.

     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

Vacuum-ultraviolet photoionization studies of the microhydration of DNA bases (guanine, cytosine, adenine, and thymine)

In this work, we report on a photoionization study of the microhydration of the four DNA bases. Gas-phase clusters of water with DNA bases [guanine (G), cytosine (C), adenine (A), and thymine (T)] are generated via thermal vaporization of the bases and expansion of the resultant vapor in a continuous supersonic jet expansion of water seeded in Ar. The resulting clusters are investigated by single-photon ionization with tunable vacuum-ultraviolet synchrotron radiation and mass analyzed using reflectron mass spectrometry. Photoionization efficiency (PIE) curves are recorded for the DNA bases and the following water (W) clusters: G, GWn (n = 1-3); C, CWn (n = 1-3); A, AWn (n = 1,2); and T, TWn (n = 1-3). Appearance energies (AE) are derived from the onset of these PIE curves (all energies in eV): G (8.1 +/- 0.1), GW (8.0 +/- 0.1), GW2 (8.0 +/- 0.1), and GW3 (8.0); C (8.65 +/- 0.05), CW (8.45 +/- 0.05), CW2 (8.4 +/- 0.1), and CW3 (8.3 +/- 0.1); A (8.30 +/- 0.05), AW (8.20 +/- 0.05), and AW2 (8.1 +/- 0.1); T (8.90 +/- 0.05); and TW (8.75 +/- 0.05), TW2 (8.6 +/- 0.1), and TW3 (8.6 +/- 0.1). The AEs of the DNA bases decrease slightly with the addition of water molecules (up to three) but do not converge to values found for photoinduced electron removal from DNA bases in solution.     

Study of NH stretching vibrations in small ammonia clusters by infrared spectroscopy in He droplets and ab initio calculations

Infrared spectra of the NH stretching vibrations of (NH3)n clusters (n = 2-4) have been obtained using the helium droplet isolation technique and first principles electronic structure anharmonic calculations. The measured spectra exhibit well-resolved bands, which have been assigned to the nu1, nu3, and 2nu4 modes of the ammonia fragments in the clusters. The formation of a hydrogen bond in ammonia dimers leads to an increase of the infrared intensity by about a factor of 4. In the larger clusters the infrared intensity per hydrogen bond is close to that found in dimers and approaches the value in the NH3 crystal. The intensity of the 2nu4 overtone band in the trimer and tetramer increases by a factor of 10 relative to that in the monomer and dimer, and is comparable to the intensity of the nu1 and nu3 fundamental bands in larger clusters. This indicates the onset of the strong anharmonic coupling of the 2nu4 and nu1 modes in larger clusters. The experimental assignments are compared to the ones obtained from first principles electronic structure anharmonic calculations for the dimer and trimer clusters. The anharmonic calculations were performed at the M?ller-Plesset (MP2) level of electronic structure theory and were based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structures. In general, there is excellent (<20 cm(-1)) agreement between the experimentally measured band origins for the N-H stretching frequencies and the calculated anharmonic vibrational frequencies. However, the calculations were found to overestimate the infrared intensities in clusters by about a factor of 4.     

Confirmation of the "long-lived" tetra-nitrogen (N4) molecule using neutralization-reionization mass spectrometry and ab initio calculations

Tetra-nitrogen (N(4)), which has been the subject of recent controversy [Cacace, d. Petris, and Troiani, Science 295, 480 (2002); Cacace, Chem. Eur. J. 8, 3839 (2002); Nguyen et al., J. Phys. Chem. A 107, 5452 (2003); Nguyen, Coord. Chem. Rev. 244, 93 (2003)] as well as of great theoretical interest, has been prepared from the N(4) (+) cation and then detected as a reionized gaseous metastable molecule with a lifetime exceeding 0.8 micros in experiments based on neutralization-reionization mass spectrometry. Moreover, we have used the nature of the charge-transfer reaction which occurs between a beam of fast N(4) (+) ions (8 keV translational energy) and various stationary gas targets to identify the vertical neutralization energy of the N(4) (+) ion. The measured value, 10.3+/-0.5, most closely matches that of the lowest energy azidonitrene (4)N(4) (+)C(s)((4)A(')) ion, resulting in the formation of the neutral bound azidonitrene (3)N(4)C(s)((3)A(")). Neutralization of the global minimum (2)N(4) (+)D( infinity h)((2)Sigma(u) (+)) ion leads to a structure 166 kJ mol(-1) above the dissociation products [N(2)((1)Sigma(g) (+))+N(2)((1)Sigma(g) (+))]; moreover, it was not possible to find a minimum on the (1)N(4) neutral potential energy surface for a covalently bonded structure. Ab initio calculations at the G3, QCISD/6-31G(d), and MP2/AUG-cc-pVTZ levels of theory have been used to determine geometries and both vertical neutralization energies of ions (doublet and quartet) and ionization energies of neutrals (singlet and triplet). In addition, we have also described in detail the EI ion source for the Ottawa VG ZAB mass spectrometer [Holmes and Mayer, J. Phys. Chem. A 99, 1366 (1995)] which was modified for high-pressure use, i.e., for the production of dimer and higher number cluster ions.     

Structure and dissociation characteristics of metal chloride anion clusters containing redox-active metal ions studied by laser desorption and electrospray ionization mass spectrometry and ab initio calculations

Copper chloride anion clusters with both copper oxidation states can be made by laser desorption of CuCl(2) crystals. We have used this method to study the dissociation characteristics of such cluster ions. The stability and the structure of the observed complexes were probed by ab initio calculations. These calculations show that many of these complexes are bridged structures. Thus, for the Cu(2)Cl(4) dimer anion, formally [ClCu-Cl-CuCl(2)](-) , with putative mixed copper oxidation states, the two copper ions become equivalent through bridging. Such bridging does not occur when redox inactive metal ions are present as in [ClCu-Cl-CaCl(2)](-) . By observing the dissociation characteristics of a variety of metal chloride cluster anions produced from binary mixtures, the following Cl(-) affinity order is obtained: FeCl(3) > CuCl > CaCl(2) > FeCl(2) > AgCl ≈ CuCl(2) ≈ ZnCl(2) > LiCl. Ab initio calculations on the Cl(-) affinity of selected chlorides confirm this order as do Cl(-) affinity estimates from the experimentally known vertical electron detachment energies of the superhalogens CaCl(3)(-) and LiCl(2)(-) . An equimolar mixture of CuCl(2) and FeCl(3) produces an intense cluster ion, which, from (65)Cu labeling experiments, is best described as FeCl(4)(-)···Cu(+)···(-)Cl(4) Fe, a Cu(+) bound superhalogen FeCl(4)(-) dimer. The Cu(+) ion can be replaced by the redox inactive alkali cations and by Ag(+) but these metal ion bound FeCl(4)(-) dimers show an entirely different fragmentation behavior which is attributed to the absence of bridging. Electrospray ionization (ESI) of CuCl(2) produces an extended series of (CuCl(2))(n) Cl(-) anions (n = 1-11) and so in ESI very limited reduction of Cu(2+) takes place. The (CuCl(2))(n) Cl(-) anions show an abundant dissociation via loss of neutral Cu(2)Cl(4) which according to our ab initio calculations is 9 kcal/mol more stable than two CuCl(2).     

Aspects of the electron distribution in adenine,thymine and cytosine as given by probability density curves from nonempirical calculations

The electron probability density curves of adenine, thymine and cytosine are given and discussed.     

Pyrrolidinium-based ionic liquids. 1-Butyl-1-methyl pyrrolidinium dicyanoamide: thermochemical measurement, mass spectrometry, and ab initio calculations

The standard molar enthalpy of formation of the ionic liquid 1-butyl-1-methylpyrrolidinium dicyanamide has been determined at 298 K by means of combustion calorimetry, while the enthalpy of vaporization and the mass spectrum of the vapor (ion pairs) have been determined by temperature-programmed desorption and line of sight mass spectrometry. Ab initio calculations for 1-butyl-1-methylpyrrolidinium dicyanamide have been performed using the G3MP2 and CBS-QB3 theory, and the results from homodesmic reactions are in excellent agreement with the experiments.     

Positive ion chemistry of SiH4/GeF4 gaseous mixtures studied by ion trap mass spectrometry and ab initio calculations

The positive ion chemistry occurring in SiH(4)/GeF(4) gaseous mixtures was investigated by ion trap mass spectrometry and ab initio theoretical calculations. The GeF(3)(+) cation, the only fragment obtained from ionized GeF(4), was unreactive towards SiH(4). All the primary ions SiH(n)(+) (n = 0-3) react instead with GeF(4) so to form SiF(+) or SiH(2)F(+). The latter species reacts in turn with SiH(4) and GeF(4) so to form SiH(3)(+) and SiHF(2)(+), respectively. The potential energy profiles conceivably involved in these reactions were investigated by ab initio calculations performed at the MP2 and coupled cluster (CCSD(T)) level of theory.     

Infrared spectra and ab initio calculations for the Cl--(CH4)n (n = 1-10) anion clusters

In an effort to elucidate their structures, mass-selected Cl--(CH4)n (n = 1-10) clusters are probed using infrared spectroscopy in the CH stretch region (2800-3100 cm(-1)). Accompanying ab initio calculations at the MP2/6-311++G(2df,2p) level for the n = 1-3 clusters suggest that methane molecules prefer to attach to the chloride anion by single linear H-bonds and sit adjacent to one another. These conclusions are supported by the agreement between experimental and calculated vibrational band frequencies and intensities. Infrared spectra in the CH stretch region for Cl--(CH4)n clusters containing up to ten CH4 ligands are remarkably simple, each being dominated by a single narrow peak associated with stretching motion of hydrogen-bonded CH groups. The observations are consistent with cluster structures in which at least ten equivalent methane molecules can be accommodated in the first solvation shell about a chloride anion.     

Infrared spectra and ab initio calculations for the F- -(CH4)n (n = 1-8) anion clusters

Infrared spectra of mass-selected F- -(CH4)n (n = 1-8) clusters are recorded in the CH stretching region (2500-3100 cm-1). Spectra for the n = 1-3 clusters are interpreted with the aid of ab initio calculations at the MP2/6-311++G(2df 2p) level, which suggest that the CH4 ligands bind to F- by equivalent, linear hydrogen bonds. Anharmonic frequencies for CH4 and F--CH4 are determined using the vibrational self-consistent field method with second-order perturbation theory correction. The n = 1 complex is predicted to have a C3v structure with a single CH group hydrogen bonded to F-. Its spectrum exhibits a parallel band associated with a stretching vibration of the hydrogen-bonded CH group that is red-shifted by 380 cm-1 from the nu1 band of free CH4 and a perpendicular band associated with the asymmetric stretching motion of the nonbonded CH groups, slightly red-shifted from the nu3 band of free CH4. As n increases, additional vibrational bands appear as a result of Fermi resonances between the hydrogen-bonded CH stretching vibrational mode and the 2nu4 overtone and nu2+nu4 combination levels of the methane solvent molecules. For clusters with n < or = 8, it appears that the CH4 molecules are accommodated in the first solvation shell, each being attached to the F- anion by equivalent hydrogen bonds.     

Conformational preferences of modified nucleic acid bases N6-(Δ2-isopentenyl) adenine and 2-methylthio-N6-(Δ2-isopentenyl) adenine by the quantum chemical PCILO calculations

Conformational preferences of the hypermodified nucleic acid bases N⁶-(Δ²-isopentenyl) adenine, (i⁶Ade) and its 2-methylthio derivative (ms²i⁶Ade) have been investigated theoretically by the quantum chemical perturbative configuration interaction using localized orbitals (PCILO ) method. The predicted most stable conformation of i⁶Ade and ms²i⁶Ade are such that the isopentenyl substituent is oriented away from the imidazole moiety of the adenine ring. The atoms N(6), C(10), and C(11) remain coplanar with the adenine ring for both molecules. However, in contrast to the predicted cis orientation of the C(10)? C(11) bond with respect to the C(6)? N(6) bond in i⁶Ade, the trans orientation is favored for ms²i⁶Ade. The plane of the isopentenyl group is rotated by 120° from that of the purine base in i⁶Ade, whereas rotation by 60° is favored in ms²i⁶Ade. The favored orientation of the methylthio group with respect to the C(2)? N(3) bond is trans; however, the alternative cis arrangement is also quite probable. The conformational implications of the methylthiolation of the isopentenyladenine are brought out in the context of the considerably large range of accessible (β,γ) and χ orientations. The compatible roles of i⁶Ade and ms²i⁶Ade in tRNA are thus understood, besides their distinguishing features.     

Gas phase infrared spectrum and ab initio calculations of phosphorus(III) thiocyanide, SPCN

An attempt has been made to record the gas phase infrared spectrum of phosphorus(III) thiocyanide, SPCN, for the first time. The molecule was generated by an on-line process using phosphorus(III) thiochloride, SPCl, as a precursor passed over heated silver cyanide at about 350 degrees C. The products were characterized by the infrared spectra of their vapors. The low resolution gas phase Fourier transform infrared spectrum shows three of six characterized fundamental modes of SPCN within the range of the spectrometer used at 2151, 743 and 622 cm(-1) These three bands were assigned to nu(1)(C[triple bond]N stretch), nu(2)(S=P stretch), and nu(3)(C--P stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and M?ller-Plesset second-order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and the vibrational frequencies of SPCN.     

Fourier-transform infrared and Raman spectra,and ab initio calculations for cadmium-n-di-iso-propylphosphorylguanidine-di-chloride (CdDPGCl2) complex

Cadmium-n-di-isopropylphosphorylguanidine-di-chloride (CdDPGCl2) was synthesized in the solid phase and characterized previously. The Fourier transform infrared and Raman spectra of (CdDPGCl2) in the solid state were recorded and analyzed. Emphasis was placed on the vibrational assignment of the [(O2P=O-[CdCl2]-HN=C) fragment of the complete molecular structure. With the aim of assisting the vibrational assignment of the experimental spectra, a comparison with the spectra of N-di-isopropylphosphorylguanidine ligand was carried out and ab initio calculations have been performed with several effective core potentials and valence basis sets (Hay-Wadt (HW) and Stevens-Basch-Krauss (SBK)). Due to our limited computational resources, hydrogen atoms replaced the isopropyl groups. The calculated geometrical parameters showed excellent agreement with the experimental, as well as the RHF/MP2 calculated infrared wave numbers, when compared to the IR/Raman experimental wave numbers.     

Hydrogen bonding between phenols and fatty acid esters: (1)H NMR study and ab initio calculations

[structure: see text] (1)H NMR measurements and ab initio calculations were used to study the interactions between hindered/nonhindered phenols and carboxylic acid esters. The dihedral angle (phi) between the OH group and a plane of the aromatic ring is close to 0 degrees in the hydrogen-bonded nonhindered phenols, whereas for 2,6-di-tert-butyl-4-methylphenol the OH group is completely twisted out of the aromatic plane (phi approximately 90 degrees ).     

Microwave spectra, ab initio calculations, and r0 structural parameters for (methylamino)thiophosphoryl difluoride

The microwave spectra of (methylamino)thiophosphoryl difluoride, CH(3)NHP(=S)F(2), and two deuterated species, CH(3)NDP(=S)F(2) and CD(3)NHP(=S)F(2), have been investigated in the region from 26.5 to 39.0 GHz. The rotational constants of the ground vibrational state have been determined and have been shown to be only consistent with the trans conformer (CH(3) group antiperiplanar to the P=S bond) with C(s) symmetry. The a-type R branch transitions have been assigned for the trans conformer for the three isotopomers on the basis of the rigid rotor model. Near-trans and near-cis forms without molecular planes of symmetry are predicted by all ab initio calculations with the near-trans form being more stable. However, the double-well potentials governing the interchange between the two enantiomeric near-trans as well as the two near-cis forms are too shallow to accommodate the zero-point energies of the nu(24) asymmetric torsion. Thus, the trans conformation with C(s) symmetry may be more accurate in explaining the microwave experimental data. The "adjusted" r(0) structural parameters have been obtained by systematically adjusting the ab initio MP2(full)/6-311+G(d,p) structure of the trans conformer with C(s) symmetry to fit the microwave rotational constants. The determined heavy atom distances are r(C-N) = 1.459(5), r(P-N) = 1.621(5), r(P=S) = 1.879(5), and r(P-F) = 1.550(5) A, and the heavy atom angles are angleCNP = 124.7(5) degrees , angleNPS = 118.3(5) degrees , angleNPF = 103.2(5) degrees , angleFPS = 117.0(5) degrees , and angleFPF = 94.6(5) degrees . The adjusted r(0) parameters have also been obtained for aminodifluorophosphine, H(2)NPF(2), with a slightly pyramidal -PNH(2) moiety. The results indicate that the previously reported short distance of 0.981(5) A for the N-H(o)(outer) bond from the microwave study is too short, and the adjusted r(0) value of 1.007(3) A is obtained from the combined data. Adjusted r(0) parameters are also reported for (dimethylamino)difluorophosphine, (CH(3))(2)NPF(2), with C(s) symmetry with the PNC(2) portion of the molecule being planar. The previously reported C-H distances from the electron diffraction study are too long, and the anglePNC(i) and angleC(o)NC(i) angles are also found to be in error. These results provide a reasonable explanation why the microwave and electron diffraction results differ for the structures of these latter two molecules.