Basis set and correlation effects on computed proton affinities of some oxygen and nitrogen bases

Basis set expansion and correlation effects on the computed proton affinities of the oxygen and nitrogen bases CH₃OH, H₂CO, CO, CH₃NH₂, CH₂NH, and HCN have been evaluated. Basis set enhancements lead to systematic changes in computed proton affinities. These effects appear to be additive, and are greater for correlated proton affinities than for Hartree-Fock energies. Inclusion of correlation decreases proton affinities, with fourth-order Møller-Plesset energies bracketed by second and third order energies.     

MNDO calculations of proton and methyl-and ethyl-cation affinities of neutral carbon,nitrogen, and oxygen bases

Proton affinities (PA) of 80 neutral bases were calculated using the semiempirical molecular orbital procedure MNDO. These were compared with the corresponding experimental and, where available, ab initio STO-3G and 4-31G data. For the 12 bases studied which led to ions which were not hyperconjugatively stabilized, the mean absolute error between the calculated and experimental values was 7.2 kcal mol^?1. However, a plot of these data revealed a clear tendency of MNDO to underestimate the PAs of the more basic molecules. Where hyperconjugative stabilization of the ion was possible, the calculated PAS were underestimated by a further 7–10 kcal mol^?1 for each attached alkyl group. Calculated and observed methyl-and ethyl-cation affinities were compared for 18 bases with qualitatively similar results.     

Basis set and correlation effects on computed lithium ion affinities of some oxygen and nitrogen bases

Basis set expansion and correlation effects on computed lithium cation affinities have been evaluated for the oxygen and nitrogen bases CH₃OH, H₂CO, CO, CH₃NH₂, CH₂NH, and HCN. The presence of diffuse functions on nonhydrogen atoms is found to be the most important single enhancement of double- and triple-split valence plus polarization basis sets. With the triple-split basis, enhancement effects are nearly additive. Correlation usually decreases computed lithium ion affinities, with the second order Møller-Plesset correlation term being the dominant term.     

Anomalous effect of nitrogen on side-chain alkylation of toluene with methanol over solid bases

The alkylation of toluene with methanol was carried out at 500°C over various base catalysts. The activity of MgO was found to be highest when treated specially with nitrogen. The effect of nitrogen was anomalously large, 8, 8% ethylbenzene and 2.3% styrene being formed.

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500°C . MgO, . : 8,8% 2,3% .

     

Electron affinities of the DNA and RNA bases.

Adiabatic electron affinities (AEAs) for the DNA and RNA bases are predicted by using a range of density functionals with a double-zeta plus polarization plus diffuse (DZP++) basis set in an effort to bracket the true EAs. Although the AEAs exhibit moderate fluctuations with respect to the choice of functional, systematic trends show that the covalent uracil (U) and thymine (T) anions are bound by 0.05-0.25 eV while the adenine (A) anion is clearly unbound. The computed AEAs for cytosine (C) and guanine (G) oscillate between small positive and negative values for the three most reliable functional combinations (BP86, B3LYP, and BLYP), and it remains unclear if either covalent anion is bound. AEAs with B3LYP/TZ2P++ single points are 0.19 (U), 0.16 (T), 0.07 (G), -0.02 (C), and -0.17 eV (A). Favorable comparisons are made to experimental estimates extrapolated from photoelectron spectra data for the complexes of the nucleobases with water. However, experimental values scaled from liquid-phase reduction potentials are shown to overestimate the AEAs by as much as 1.5 eV. Because the uracil and thymine covalent EAs are in energy ranges near those of their dipole-bound counterparts, preparation and precise experimental measurement of the thermodynamically stable covalent anions may prove challenging.     

Compounds of oxozirconium(IV) alkoxides with oxygen and nitrogen bases

Pyridine, quinoline, 2,2-bipyridyl, dimethylformamide, dimethylacetamide and phthalimide combine with ZrOCl(OCHMe ₂)·2Me ₂CHOH to form complexes, ZrOCl(OCHMe ₂)·Base [with the exception of dimethylsulfoxide: Zr₂O₂Cl₂(OCHMe ₂)₂·3DMSO], whereas dialkoxides, ZrO(OR)₂·ROH (R=Me, Et, Pr ⁱ ), fail to react. The complexes have been characterized through infrared, molar conductance and thermal decomposition studies.

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Komplexe von Oxozirkonium(IV)-Alkoxiden mit Sauerstoff- und Stickstoff-Basen

Zusammenfassung Pyridin, Chinolin, 2,2-Bipyridyl, Dimethylformamid, Dimethylacetamid und Phthalimid geben mit ZrOCl(OCHMe ₂)·2Me ₂CHOH Komplexe vom Typ ZrOCl(OCHMe ₂)·Base [ausgenommenDMSO: Zr₂O₂Cl₂(OCHMe ₂)₂·3DMSO], während Dialkoxide, ZrO(OR)₂·ROH (R=Me, Et, Isopr), keine Reaktion ergeben. Die Komplexe wurden durch ihre IR-Spektren, molare Leitfähigkeit und mittels Untersuchung der thermischen Zersetzung charakterisiert.

     

Evaluation of MNDO calculated proton affinities

A large set of charged species arising mainly from protonation or deprotonation of hydrocarbons, alcohols, ethers, carboxylic acids, amines, imines, and nitriles has been studied by means of the semiempirical self-consistent-field (SCF ) molecular orbital (MO ) MNDO method. From the calculated heats of formation of such charged species and those of neutral molecules, MNDO -estimated proton affinities have been obtained and the results compared with experimental gas-phase proton affinities. If the small size anions and acetylides, for which the method predicts heats of formation too large, are ruled out, the mean absolute error in calculated proton affinities is ca. 7 kcal/mol for hydrocarbons (22 acid-base pairs) and ca. 8 kcal/mol for oxygen-containing compounds (25 acid-base pairs). For nitrogen-containing molecules it is necessary to discard, in addition, the values corresponding to the protonation of alkylamines and imines in order to achieve a reasonable mean absolute error of 7–8 kcal/mol.     

Proton affinities of N-heterocyclic carbene super bases

The gas-phase proton affinity of the N-heterocyclic carbene, 1-ethyl-3-methylimidazol-2-ylidene, was determined to be 251.3 +/- 4 kcal/mol using the kinetic method, a value which makes the carbene one of the strongest bases reported thus far. Density functional theory calculations have been carried out at the B3LYP/6-31+G(d) level to compare the high experimental value with that estimated theoretically. Experimental results also show that two other N-heterocyclic carbenes with larger substituents have even higher proton affinities. [structure: see text]     

1H NMR studies of proton transfer and σ-complex formation in the reactions of N-substituted picramides with oxygen and nitrogen bases

¹H NMR measurements of N-substituted picramides in dimethyl sulphoxide-methanol containing sodium methoxide show that the two major modes of 1:1 interaction involve transfer of an amino proton to give the conjugate base or methoxide attack at the 3-position to give a σ-adduct. The proportion of parent reacting by the latter pathway increases as the proportion of methanol in the solvent increases. Some comparative measurements in isopropanol-dimethyl sulphoxide show that relative to methoxide the isopropoxide ion has a greater propensity for proton abstraction than for base addition. Reaction of the substrates with amide ions derived from piperidine or from benzylamine gives σ-complexes by attack at unsubstituted ring positions. In the benzylamide adducts spin coupling is observed between the amino proton and the adjacent ring and methylene protons.     

Proton affinities of molecules containing nitrogen and oxygen: Comparing density functional results to experiment

Summary Proton affinities were calculated using density functional theory for 11 small molecules whose primary protonation site is on nitrogen, and eight small molecules that protonate on oxygen. Calculations were performed using both the local spin density approximation and nonlocal gradient corrections to the exchange correlation functional. The results were not sensitive to whether the nonlocal gradient correction was implemented on the final local spin density optimized geometry or whether the correction was included in the self-consistent calculation of the energy at each optimization step. Although negligible basis set dependence was found using the analytic Gaussian basis sets, numerical basis sets required augmentation by a double set of polarization functions to achieve reasonable agreement with experiment. All calculations systematically underestimated oxygen proton affinities.     

Assessment of density functionals for pi systems: Energy differences between cumulenes and poly-ynes; proton affinities, bond length alternation, and torsional potentials of conjugated polyenes; and proton affinities of conjugated Shiff bases

Woodcock et al. [J. Phys. Chem. A 2002, 106, 11923] pointed out that no density functional was able to obtain the correct sign of the relative energies of the allene and propyne isomers of C3H4 and that density functional theory (DFT) predicts that poly-ynes are insufficiently stabilized over cumulenes for higher homologues. In the present work, we show that the recent M05 density functional predicts the correct ordering of allene and propyne and gives a mean unsigned error (MUE) of only 1.8 kcal/mol for the relative energies of the two isomers of C3H4, C5H4, and C7H4. Two other recent functionals, M05-2X and PWB6K, also give reasonably low MUEs, 2.7 and 3.0 kcal/mol, respectively, as compared to 6.2 kcal/mol for the popular B3LYP functional. Another challenging problem for density functionals has been a tendency to overpolarize conjugated pi systems. We test this here by considering proton affinities of conjugated polyenes and conjugated Schiff bases. Again M05-2X performs quite well, with MUEs of 2.1 and 3.9 kcal/ mol, respectively, as compared to 5.8 and 5.9 kcal/mol for B3LYP. Averaged over the three problems, M05-2X has a MUE of 3.0 kcal/mol, the BMK functional of Boese et al. has an MUE of 3.2 kcal/mol, and M05 has an MUE of 5.1 kcal/mol. Twenty-two other tested functionals have MUEs of 5.2-8.1 kcal/mol averaged over the three test problems. Both M05 and M05-2X do quite well, compared to other density functionals, for torsion potentials in butadiene and styrene, and M05 does very well for bond length alternation in conjugated polyenes. Since the M05 functional has broad accuracy for main group and transition metal chemistry and M05-2X has broad accuracy for main group chemistry, we conclude that significant progress is being made in improving the performance of DFT across a wide range of problem types.     

X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

The proton affinities and proton transfer in imine, amidine and guanidine series

The enthalpies of formation of neutral and protonated alkyl imines, amidine and guanidine are obtained by ab initio theoretical means using an isodesmic reaction technique. The corresponding proton affinities are obtained and discussed in terms of thermochemical stabilization energies. Their relation to the proton transfer process is examined and discussed. To this end, the structure and properties of various molecular complexes obtained between these molecules of interest and formic acid are explored. The sensitivity of this process to the presence of a neighbour water molecule is commented.     

Heats of formation and proton affinities by the G3 method

Proton affinities of 29 simple organic molecules calculated with the G3 method agree well with experimental results from the literature as well as with results obtained with the G2(MP2) and CBS-Q methods. The choice of empirical correction in the G3 method introduces a small systematic error on either G3 heats of formation or G3 proton affinities.     

Semiempirical evaluation for proton affinities of phosphorus compounds

We here report the AM 1 and PM 3 evaluation of proton affinities for phosphorus compounds. The substituent effects, the preferred site of protonation, and the geometry changes produced upon protonation are discussed in terms of the present semiempirical calculations that are compared with experimental data and previous ab initio results. © 1993 John Wiley & Sons, Inc.     

Apparent proton affinities of highly charged peptide ions

The apparent proton affinities (PA) of various charge states of three highly basic peptides [(KAP)₁₀, (KAP)₈, (KAA)₈] were measured by the “bracketing” method. For all three peptides the apparent PA decreases as the charge state increases and the magnitude of the decrease is consistent with an increase in coulombic repulsion in the highly protonated species. Based on a simple electrostatic model, theoretical PAs were predicted for each charge state and the values for (KAP)₁₀ and (KAP)₈ were within 10 kcal/mol of the experimental values. The maximum charge state of these peptides was observed in all cases even when the most volatile solvent was sufficiently basic to deprotonate that charge state in the gas phase. In solution (KAP)₈ exhibits a random coil secondary structure while (KAA)₈ exhibits an α-helix structure. Comparison of measured and calculated apparent PAs suggests that (KAP)₈ retains its solution random coil structure in the gas phase and (KAA)₈ retains the solution compact α-helix structure in the lower charge states but opens up to a β structure in the gas phase to minimize electrostatic repulsions in higher charge states.     

Protonation of glycine and alanine: proton affinities, intrinsic basicities and proton transfer path

Proton affinities and intrinsic basicities for nitrogen and oxygen protonation in the gas phase of the amino acids glycine and alanine were calculated using density functional theory (DFT) and ab initio methods at different levels of theory from Hartree-Fock (HF) to G2 approximations. All methods gave good agreement for proton affinities for nitrogen protonation for both amino acids. However, dramatic differences were found between DFT, MP4//MP2, and G2 results on one hand, and MP4//HF results on the other to the calculation of structural and energetic characteristics of oxygen protonation in glycine and alanine. An investigation into the source of these differences revealed that electron correlation effects are chiefly responsible for the differences in calculated oxygen proton affinities between the various methods. It has been found that proton transfer between nitrogen and oxygen protonation sites in both amino acids occurs without a transfer path barrier when correlated methods were used to calculate the path energetics.     

Mononucleotide gas-phase proton affinities as determined by the kinetic method

The goal of this work is to determine the proton affinities of (deoxy)nucleoside 5'- and 3'-monophosphates (mononucleotides) using the kinetic method with fast atom bombardment mass spectrometry. The proton affinities of the (deoxy)nucleoside 5'- and 3'-monophosphates yielded the following trend: (deoxy)adenosine monophosphates > (deoxy)guanosine monophosphates > (deoxy)cytidine monophosphates > deoxythymidine/uridine monophosphates. In all cases the proton affinity decreases or remains the same with the addition of the phosphate group from those values reported for nucleosides. The proton affinity is dependent on the location of the phosphate backbone (5'-vs. 3'-phosphates): the 3'-monophosphates have lower proton affinities than the 5'-monophosphates except for the thymidine/uridine monophosphates where the trend is reversed. Molecular modeling was utilized to determine if multiple protonation sites and intramolecular hydrogen bond formation would influence the proton affinity measurements. Semiempirical calculations of the proton affinities at various locations on each mononucleotide were performed and compared to the experimental results. The possible influence of intramolecular hydrogen bonding between the nucleobases and the phosphate group on the measured and calculated proton affinities is discussed.