Comparison of the use of the MNDO and MINDO/3 methods with ab initio methods to study tautomerism in histamine, 2- and 4-methylhistamine

The semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2-methylhistamine, and 4-methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree-Fock calculations using the 3-21G and STO-3G basis sets. Based on these results and previous comparisons of STO-3G results with x-ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3-21G and STO-3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3-21G and STO-3G results than the MINDO/3 method.     

Optimized Structures and Relative Stabilities of the Carboranes from Ab Initio Calculations

Ab initio calculations at the STO-3G level were performed on almost all of the possible isomers for the entire series of closo-carboranes, C₂B_n-2H_n, 5 ? n ? 12. Geometry optimizations using the gradient method were also included in all calculations. We report here the relative energies obtained for the various isomers as well as the optimized structures. These calculations confirm our previous predictions of relative stabilities obtained from topological charge stabilization. Comparisons of our structures with those from experimental data provide us with a measure of reliability for bond distances obtained using ab initio SCF MO calculations at the STO-3G level. Results from the geometry optimization substantiated the experimentally known fluxional behavior of the 8 and 11 atom polyhedra.     

A semiempirical and ab initio MO study of the tautomers ofN-unsubstituted pyrazolones [hydroxy pyrazoles]

Semiempirical (MNDOC, MINDO/3, AM1, and MNDO) and ab initio (STO-3G and 4-31G basis sets) calculations on the relative stabilities, structures, and dipole moments of the 8 theoretically possible tautomeric forms of pyrazolone are reported. It is shown that MNDO + CI and MINDO/3 predict that 5-hydroxy pyrazole, 3-hydroxy pyrazole, and 2-pyrazolin-5-on are the most stable. These results correspond to the known experimental data. Of all used quantum chemical methods, the MINDO/3 results for the dipole moments of the investigated tautomers are in best agreement with the known experimental data. The electronic excitation energies were calculated using the CNDO/S-CI method. The results are in good agreement with the experimental UV spectra.     

AM1 and PM3 Study of Tautomerism of Hypoxanthine in the Gas and Aqueous Phases

Heats of formation, entropies, Gibbs free energies, relative tautomerisation energies, tautomeric equilibrium constants, dipole moments, and ionization potentials for the eight possible tautomers of hypoxanthine have been studied using semiempirical AM1 and PM3 quantum-chemical calculations at the SCF level in the gas and aqueous phases, with full geometry optimization. The COSMO solvation model was employed for aqueous solution calculations. The calculations show that the two keto tautomers H17 and H19 are the predominant species at room temperature in the gas and aqueous phase. However, the tautomer H17 is the more dominant species in gas phase, while the H19 tautomer is the more dominant species in the aqueous phase. Comparison with available experimental data provides support for the results derived from theoretical computations. The entropy effect on the Gibbs free energy of hypoxanthine is very small and there is little significance for the tautomeric equilibria of the base. The enthalpic term is dominant in the determination of the equilibrium constant.     

Geometry optimization and electronic structures of molecules H_3AXAH_3

The geometries of molecules H_3AXAH_3(X=O,S,Se and A=C,Si)have been optimizedusing STO-3G ab initio calculations and gradient method and the results are in good agreement withreported experimental values.From the STO-3G optimized geometries,we have also calculated theelectronic structures of these molecules using 4-31G and 6-31G basis sets to obtain the MO energies.atomic net charges and dipole moments.The ionization potentials calculated by 6-31G basis set are ingood agreement with experimental values.     

Tautomerism of pyrimidine bases—uracil,cytosine, isocytosine: Theoretical study with complete optimization of geometry

The semiempirical MINDO /3 method with complete optimization of geometry is employed to calculate the electronic ground-state properties (dipole moments and ionization potentials) and the energies of various tautomeric forms of uracil, uracil monoanion, cytosine, and isocytosine. The results are shown to be consistent with most of the experimental data. Accuracy of various quantum–mechanical methods is discussed. Particular attention is paid to the influence of the geometry optimization on energy differences between various tautomers. Some qualitative conclusions of biological importance are drawn from these calculations.     

Electronic structure and spectroscopy of nucleic acid bases: ionization energies, ionization-induced structural changes, and photoelectron spectra

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C), and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized the five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using the equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the ωB97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series, G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25, and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67, and 7.75-7.87 eV for A, T, C, and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 ± 0.05, 8.95 ± 0.05, 8.60 ± 0.05, and 7.75 ± 0.05 eV). Vibrational progressions for the S(0)-D(0) vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra and differentiated PIE curves.     

Semiempirical NDDO calculations with STO-3G and 4-31G basis sets

Possible refinements of semiempirical methods include the use of larger basis sets and of correlated wave functions. These possibilities are investigated in semiempirical NDDO SCF calculations with the STO-3G and 4-31G basis sets, and in correlated calculations at the STO-3G level. The present approach is characterized by the analytical evaluation of all one-center terms and two-electron integrals, and the semiempirical adjustment of the remaining one-electron integrals and the nuclear repulsions. The NDDO SCF results tend to reproduce the correspondingab initio results more closely than experimental data, even if they are parametrized with respect to experiment. The explicit inclusion of electron correlation at the STO-3G level improves the calculated results only slightly.     

A note on a non-empirical molecular orbital study of some cytosine and thymine tautomers

The relative stabilities of a series of cytosine and thymine tautomers have been investigated by means of non-empirical (ab initio) LCAO-MO-SCF Hartree-Fock-Roothaan calculations employing a small contracted Gaussian basis set (STO-3G) in all cases. The relative stabilities of the various tautomeric forms agree in general with the results of earlier empirical and semi-empirical calculations on these molecules. In particular, the “enol forms” of cytosine and thymine, within the isolated molecule approximation inherent in these MO calculations, are predicted to possess greater stability than the forms commonly assigned to these molecules in aqueous solution and found in the solid state by X-ray crystallographic studies.     

Investigation of the structure of and the properties of the potentially tautomeric 1,2,3,4-tetrahydro-5,7-dimethyl-6H-pyrrolo[3,4-d]pyridazine-1,4-diones in the gaseous and aqueous phases using the AM1 semi-empirical method

Potentially tautomeric 1,2,3,4-tetrahydro-5,7-dimethyl-6H-pyrrolo[3,4-d]pyridazine-1,4-diones and their fixed tautomeric forms have been studied in order to predict their tautomeric equilibrium constants and pK_a values using semi-empirical AM1 quantum-chemical calculations at the SCF level in the gas phase and in aqueous solution. Hydroxy-oxo forms were found to be more stable than dioxo and dihydroxy forms. The results obtained from the tautomeric equilibria and basicity calculations are in good agreement with experimental data.     

An analysis of the through-bond interaction using the localized molecular orbitals with ab initio calculations—II : Lone-pair orbital energies in bicyclo compounds: 7-azabicyclo[2.2.1]heptane and 2-azabicyclo[2.2.2]octane,and their n-methyl derivatives

Ab intio SCF MO calculations using STO-3G basis set were performed on 7-azabicyclo[2.2.1]heptane, N-methyl-7-azabicyclo[2.2.1]heptane, 2-azabicyclo[2.2.2)octane, N-methyl-2-azabicyclo[2.2.2)octane, and their model molecules. The orbital energies obtained by these calculations were compared with the experimental ionization potentials The canonical MOs obtained for the model molecules were then transformed into the localized Mos. With the use of the localized MOs thus obtained, the lone-pair orbital energies were pursued in the light of the through-space and/or the through-bond interactions between thw specified localized MOs. As a result of this analysis, it was found that the effects of the inner shell orbitals, 1s electrons of the N atom, and of the neighbouring N-C bonds of the skeleton (through-bond interaction) play a dominant role in the interaction with the lone-pair orbitals. It was also found that the effect of the N-Me group on the lone-pair orbital energy is considerably important.     

Anab initio molecular orbital study of substituted carbonyl compounds

Ab initio SCF calculations with a minimal STO-3G basis set have been performed to determine the equilibrium geometries of two series of carbonyl compounds, RCHO and R₂ CO. For the mono-substituted compounds, R may be CH₃, NH₂, OH, F, CHO, and C₂ H₃. In the disubstituted compounds, R has been restricted to the isoelectronic saturated groups. The computed equilibrium geometries of these compounds are in satisfactory agreement with the experimentally-determined geometries, with an average difference of 0.021 Å between computed and experimental bond lengths, and 1.9 ° in corresponding bond angles. An analysis of the effect of the substituent on the electronic structure of the carbonyl group has also been made. The saturated groups are found to be electron-withdrawing groups relative to H, with the electron withdrawing ability increasing in the order CH₃ 2 2H₂ are also electron withdrawing relative to H, and comparable to CH₃ in acetaldehyde. Vertical ionization potentials andn* transition energies have also been calculated for these molecules at their optimized geometries, experimental geometries, and geometries given by a standard model. The effect of changes in molecular geometry on these computed properties has been analyzed.     

Oxygen-induced next-nearest neighbour effects on the C1s-levels in polymer XPS-spectra

This letter reports the results of ab initio quantum chemical calculations on the C_1s core levels of model systems for a number of oxygen containing polymers. Conformational effects were studied. SCF calculations have been carried out with STO-3G and 4-31G basis sets, and Koopmans' theorem was applied to obtain the core-level binding energies. To evaluate the performance of the procedure SCF calculations were carried out on polyacrylic acid. The existence of oxygen-induced secondary substituent effects in the XPS-(ESCA-)spectra is discussed. A comparison with semi-empirical CNDO/2 results from Clark and Thomas has been made.     

Ab initio calculations of the equilibrium geometry of cis and trans methylglyoxal using the force method

Ab initio calculations of the equilibrium ground-state conformation of trans-methylglyoxal, CH₃COCHO, have been carried out using the gradient method and a 4-3 IG basis set. The results are compared with experiment and with a theoretical geometry computed using an STO-3G basis set, and the more usual stepwise optimization of the parameters. The molecular orbital energies, dipole moment and ionization energy are calulated. Calculations are also carried out on the cis-isomer and the barrier to cis-trans isomerization is obtained.     

A non-empirical LCAO MO SCF investigation of electronic relaxation accompanying core ionization in a series of saturated alkanes

Ab initio LCAO MO ΔSCF binding energies and relaxation energies have been computed at the STO-4.31G level for linear and branched alkanes (up to C₆) and are compared with experimental data. The structural dependence of binding energies and relaxation energies is discussed, and it is concluded that binding enegy shifts in these alkanes (compared with methane) arise mainly from relaxation energy changes.     

SINDO1 II. Application to ground states of molecules containing carbon,nitrogen and oxygen atoms

Molecular geometries, binding energies, ionization potentials and dipole moments are calculated by the SINDO1 method for a large number of molecules containing C, N and O atoms. Comparison is made with MINDO/3, MNDO and where possible with STO-3G results. The explicit data and an error statistics show the relative merits of SINDO1.     

Dicyanoketene and its isomers

Ab initio STO-3G calculations have been performed on dicyanoketene and its isomeric forms. Optimized nuclear configurations and relative stabilities are examined and compared with those of ketene and oxirene. Heats of formation and bond substitution energies are estimated.     

Guanidinium-Type resonance stabilization and its biological implications. I. the guanidine and extended-guanidine series

An unusual type of π-electron delocalization in Y-shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO -3G and 3-21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen-substituted guanidine series (urea, carbamic, and carbonic acids); “extended-guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended-guanidine group is incorporated (3-amino-1,2,4-triazole, 2,4-diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π-bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended-guanidinium group resemble those of the group when incorporated within 6-membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.     

Thin‐Film Properties of DNA and RNA Bases: A Combined Experimental and Theoretical Study

The structures of the DNA and RNA bases cytosine, uracil, and thymine in thin films with a nominal film thickness of about 20 nm are studied by using X‐ray photoemission spectroscopy (XPS) and Fourier‐transform infrared spectroscopy. The molecules are evaporated in situ from powder on a gold foil. The experimental results indicate that cytosine is composed of two energetically close tautomeric forms, whereas uracil and thymine exist in only one tautomeric form. Additionally, quantum chemical calculations are performed to complement the experimental results. The relative energies of the tautomeric forms of cytosine, uracil, and thymine are calculated using Hartree–Fock (HF), density functional theory (DFT), and post‐HF methods. Furthermore, the assignment of the XPS spectra is supported by using simple model considerations employing Koopmans ionization energies and Mulliken net atomic charges.     

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N₂) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol⁻¹ lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.