Tautomeric equilibria of heterocyclic molecules. A test of the semiempirical AM1 and MNDO-PM3 methods

Tautomeric equilibria (mainly of the lactam-lactim type) for a rather large number of six-membered heterocyclic molecules are calculated by the semiempirical AM1, MNDO-PM3, and MNDO methods. Except for compounds with adjacent pyridine-like lone pairs both AM1 as well as MNDO-PM3 give rather reliable predictions for relative stabilities of the various tautomeric species–comparable to quite high level ab initio calculations. The known errors associated with MNDO in the treatment of heterocyclic tautomerism are thus largely corrected in AM1 as well as MNDO-PM3. For 2-hydroxypyridine-pyrid-2(1H)-one the effect of self-association is less satisfactorily described by MNDO-PM3 than by AM1. MNDO-PM3 calculated relative stabilities of methylated derivatives are, however, in considerably closer agreement with experimental values than those obtained by AM1. Ionization potentials, especially those for lone-pair orbitals, are overestimated by all three semiempirical methods. MNDO-PM3 results for nitrogen lone-pair orbital energies are slightly better than those obtained by the AM1 or MNDO method.     

Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

Role of the anomeric effect in methanediamines in the gas phase and aqueous solutions

An ab initio study of methylenediamine and several methylated derivatives in the gas phase and aqueous solution was performed. The conformational preferences can be considered adequately described at the HF/6‐31G**//HF/6‐31G** level, because these results agree with those obtained using larger basis sets and including ZPE and electron correlation. The energy ordering is clearly dependent on the number and position of the methyl groups present in a molecule. For a first set of the compounds, the energies obtained were interpreted in terms of the anomeric effect because the favored conformers show two or one anti orientation between the nitrogen lone pair and the C N polar bond. Reverse anomeric effects were found for a second set of compounds. The NBO analysis was used to interpret these energetic tendencies and the rotational barrier around the N C bonds. Thus, the preference for the anti‐Lp N C N orientations is mainly due to charge delocalization, always stronger than the electrostatic and steric contributions included in the Lewis term. However, the origin for the reverse anomeric effect may be related to the steric hindrance associated with the methylation. The influence of water on the conformational preferences was evaluated by means of the PCM method. Contrary to expectation, the anomeric effect is not reduced in water, and the most stable conformers in the gas phase are maintained in solution. The electrostatic term of the free solvation energy is the main responsible of the energetic changes, and depends strongly on local solute–solvent interactions. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 135–150, 2001     

Comparative Study of the Structure of Rhodanine, Isorhodanine, Thiazolidine-2,4-dione, and Thiorhodanine

Ab initio (HF and MP2 level) and semiempirical (AM1, PM3, MNDO) calculations on the relative stabilities and structures of the potential tautomeric forms of rhodanine, isorhodanine, thiazolidine-2,4-dione, and thiorhodanine are reported. Ab initio calculations predict that the thiooxo, oxothio, dioxo, and dithio tautomers are the most stable. These results correspond to the known experimental data. Infrared spectra of the investigated compounds were recorded for the region 4000-150 cm^-1, and the characteristic bands were compared with ab initio calculated frequencies at the HF/3-21G^(*)* level.     

Tautomerism of rhodanine

Semiempirical (MINDO/3, AM1, PM3, MNDO) and ab initio (4-31G and 4-3IG + dAO/S basis sets) calculations on the relative stabilities and structures of the five potential tautomeric forms of rhodanine are reported. It is shown that all methods (excepting PM3) predict as most stable 2-thioxo-4-thiazolidinone. These results correspond to the known experimental data. The infrared spectrum of rhodanine was recorded for the region 4000-150 cm^–1, and the characteristic bands were compared with AM1 and 4-31G + dAO/S calculated frequencies. The transition states between five pairs of all possible tautomeric forms of the rhodanine were found by the AM1 method.     

Conformational behavior of some hydroxamic acids

The conformational preferences of a few hydroxamic acids are investigated by the density functional B3LYP/6-311++G**//B3LYP16-31G* and semiempirical AM1 and PM3 methods in this work. It is found that both semiempirical methods give satisfactory results in comparison with sophisticated DFT and ab initio calculations, except for the activation barriers, which are overestimated. Of the two semiempirical methods, while the PM3 method gives better results for relative stabilities, AM1 geometries are in slightly better agreement with the experiments. The keto forms are found to be most stable and the reaction pathways for the interconversion between the keto and enol forms have been deduced. The effect of solvation on the reaction has also been investigated, as has the effect of methyl substitution at the carbon and nitrogen atoms. All the investigated acids exhibit N-acid behavior.     

A comparison of semiempirical and ab initio transition states for HF elimination in unimolecular decompositions

The transition states for unimolecular HF elimination from a series of methylene halides and vinyl halides have been located and properly characterized at the AM 1, MNDO , PM 3, RHF /6-311G (d, p), and MP 2/6-311G (d, p) levels. Whereas the semiempirical MO methods deal well with the structures of the stable molecules, the structural differences between the ab initio and semiempirical transition states are considerably larger. The AM 1 and PM 3 activation energies appear to be relatively more accurate. © 1994 John Wiley & Sons, Inc.     

An ab initio interpretation in gas phase and aqueous solution of the generalized anomeric effect in R?O?CR2?NR2 (R = H,CH3)

The conformational stability of aminomethanol and its methylated derivatives has been investigated by means of ab initio methods in the gas phase and aqueous solution. Among the computational levels employed, HF/6‐31G**//HF/6‐31G** calculations correctly describe the conformational features of this series of compounds, and agree well with the results obtained using larger basis sets and including ZPE or electron correlation corrections. Calculated energies and geometries follow the known trends associated to the generalized anomeric effect. Thus, the most stable conformers exhibit preferences for the trans orientations of the Lp N C O and Lp O C N moieties. However, reverse anomeric effects are observed when a methyl group is bonded to the oxygen, because the Lp O C N unit prefers a gauche orientation (that is, trans Me O C N). The natural bond orbital (NBO) method was employed to explain the cited conformational preferences. According to the NBO results, trans arrangements are preferred because the stabilization due to charge delocalization is more important than electrostatic and steric contributions. This explanation agrees with the conclusions obtained by other independent procedures based on energy decomposition schemes. The NBO method was also used to explain the origin of the rotational barriers around the C O and C N bonds in terms of the balance between unfavorable hyperconjugation and electrostatic and steric effects. Changes in conformational stability caused by methylations in different molecular positions were also explained by the influence of the methyl groups on lone‐pair delocalization and on steric effects. Finally, the effect of solvation was studied by means of the ab initio PCM method, and the significant changes on relative energies found were analyzed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 462–477, 2000     

AM1 calculations of rotation around essential single bonds and preferred conformations in conjugated molecules

Equilibrium twist angles, rotational barriers around essential single bonds, and preferred conformations for over 60 conjugated organic molecules were calculated using the semiempirical AM1 (Austin model 1) method. Comparison with ab initio and experimental data shows that AM1 can be applied quite successfully to conformational problems of this type. Relatively large errors are, however, found for compounds in which lone pair–hydrogen and especially lone pair–lone pair interactions are decisive for their conformational behavior. AM1-calculated rotational barriers in conjugated molecules, however, are found to be much too low. Moreover, AM1 does not seem to even correctly reproduce the trend of rotational barriers within a series of structurally related compounds. E/Z energy differences obtained by AM1 are also frequently considerably too low. In contrast to rotational barriers, their trends and thus conformational preferences, however, are quite satisfactorily calculated by this method. Ionization potentials obtained by AM1 are too high by about 0.5 eV. However, trends are quite well predicted.     

Hyperconjugation and the increasing bulk of OCOCX3 substituents in trans-1,4-disubstituted cyclohexanes destabilize the diequatorial conformer

The trans diesters of 1,4-cyclohexanediol with a number of acetic acid analogues, CX3COOH, of varying steric hindrance and polarity (CX3 = Me, Et, iso-Pr, tert-Bu, CF3, CH2Cl, CHCl2, CCl3, CH2Br, CHBr2, CBr3) were synthesized, and the axial,axial/equatorial,equatorial conformational equilibria were studied by low-temperature 1H NMR spectroscopy in CD2Cl2. The structures and relative energies of the axial,axial and equatorial,equatorial conformers were calculated at both the MP2/6-311G* and the MP2/6-311+G* levels of theory, and it was only by including diffuse functions that a good correlation of deltaG(o)calcd vs deltaG(o)exptl could be obtained. Both the structures and the energy differences of the axial,axial and equatorial,equatorial conformers are discussed with respect to the established models of conformational analysis, viz., steric 1,3-diaxial and hyperconjugative interactions. Interestingly, the hyperconjugative interactions sigma(C-C)/sigma(C-H) --> sigma*(C-O), together with a steric effect which also destabilizes the equatorial,equatorial conformers on increasing bulk of the substituents, proved to dominate the position of the conformational equilibria. In addition, the preference of the axial,axial conformers with respect to their equatorial,equatorial analogues was greater than expected from the conformational energies of the corresponding substituents in the monosubstituted cyclohexyl esters. The reason for this very interesting and unexpected result is also discussed.     

Quantum chemical studies on tautomerism of 2-, 3- or 4-hydroxyquinoline derivatives along with their thio and azo analogs

The geometries, relative stabilities and proton affinities for the different tautomers of 2-, 3- and 4-hydroxyquinoline derivatives and their thio and azo analogs along with their fixed forms (i.e. model molecules in which the proton migration is eliminated) were calculated with full geometry optimization using AM1, PM3 and MNDO methods. The predominance of oxo forms over hydroxy forms were confirmed with all three methods both in gas and liquid phases, as cited in the literature, with the exception of 3-hydroxyquinoline for which the AM1 and MNDO methods both in gas and liquid phases suggest the predominance of the hydroxy form. For the thio analogs the predominance of thione forms over mercapto forms and for the amino analogs the predominance of the amino forms over imino forms were confirmed both in gas and liquid phases with all three methods as indicated in the literature.     

Conformation energy around the N(sp3)?O single bond

A detailed conformational analysis was performed on simple substituted hydroxylamines using either ab initio (from HF/6-31G* to RQCISD/6-311G**) or popular semiempirical (MNDO, AM1, PM3) methods to ascertain the allowed conformations and to establish the influence of the level of theory on the results. All the ab initio results (provision being made for their expected divergences) are similar and show a simple twofold character for the > N? O? rotational energy, without any appreciable populations of the cis conformer. On the other hand, the predictive value of the semiempirical methods for structural and energetical parameters of molecules bearing > N? O? moieties is limited, a situation like that prevailing for peptide bonds. The inversional barriers for the methyl-substituted hydroxylamines were also calculated and compared to the corresponding rotational energy barriers. Rotation is generally favored over inversion for hydroxylamine and its methylated derivatives. © 1994 by John Wiley & Sons, Inc.     

Stable conformations of CH3CH2OCH2CH2OH: A comparison of theoretical methods

This article presents the results of an extensive examination of the stable conformations of CH₃CH₂OCH₂CH₂OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.     

Pathways of conformational isomerization of 4-phenyl-1,3-dioxane

A study of the potential energy surface of 4-phenyl-1,3-dioxane by non-empirical quantum chemical RHF/STO-3G and 6-31G(d) approximations reveals six energetically inequivalent pathways of conformational isomerization of equatorial and axial chair forms.     

Electronic and steric substituent influences on the conformational equilibria of cyclohexyl esters: the anomeric effect is not anomalous!

The cyclohexyl esters of a series of carboxylic acids, RCO₂H, spanning a range of electronegativities and quotients of steric hindrance for the R substituent (R=Me, Et, iPr, tBu, CF₃, CH₂Cl, CHCl₂, CCl₃, CH₂Br, CHBr₂, and CBr₃) were prepared. Their conformational equilibria in CD₂Cl₂ were examined by low‐temperature ¹H NMR spectroscopy to study the axial or equatorial orientation of the ester functionality with respect to the adopted chair conformation of the cyclohexane ring. The ab initio and DFT geometry‐optimized structures and relative free energies of the axial and equatorial conformers were also calculated at the HF/6‐311G**, MP2/6‐311G**, and B3LYP/6‐31G** levels of theory, both in the gas phase and in solution. In the latter case, a self‐consistent isodensity polarized continuum model was employed. Only by including electron correlation in the modeling calculations for the solvated molecules was it possible to obtain a reasonable correlation between ΔG°_calcd and ΔG°_exp. Both the structures and the free energy differences of the axial and equatorial conformers were evaluated with respect to the factors normally influencing conformational preference, namely, 1,3‐diaxial steric interactions in the axial conformer and hyperconjugation. It was assessed that hyperconjugative interactions, σ_{C? C}/σ_{C? H} and σ*_{C? O}, together with a steric effect—the destabilization of the equatorial conformer with increasing bulk of the R group—were the determinant factors for the position of the conformational equilibria. Thus, because hyperconjugation is held responsible as the mitigating factor for the anomeric effect in 2‐substituted, six‐membered saturated heterocyclic rings, and since it is also similarly responsible, at least partly, in these monosubstituted cyclohexanes for a preferential shift towards the axial conformer, the question is therefore raised: can the anomeric effect really be construed as anomalous?     

Estimation of the relative stability of chair forms of hexahydropyrimidine

Nonempirical approximations HF/6-31G(d), MP2/6-31G(d)//HF/6-31G(d), PBE/3z, and RI-MP2/λ2 were applied to the calculation of the relative stability and parameters of the conformational equilibrium of three chair forms of the unsubstituted hexahydropyrimidine with different orientation of the N-H bonds. It was established that in the framework of the used methods the most stable are the conformers of diaxial and axial-equatorial chairs. The occupancy of the diequatorial chair form at the room temperature does not exceed 1.7%.     

Rotamer stability in cis-[Pt(diA)G2] complexes (diA = diamine derivative and G = guanine derivative) mediated by carrier-ligand amine stereochemistry as revealed by circular dichroism spectroscopy

Extensive investigations of cis-[Pt(diA)G2] complexes (in which G = a guanine ligand; diA = a single diamine ligand) revealed the types of interactions between the two G ligands and between the G and the cis-amine substituents when diA is a diamine ligand with substituents on each nitrogen atom being a small hydrogen atom and a bulky group able to slow the rotation about the Pt-G bond. All these interactions are shown to apply also when diA = dach (1,2-diaminocyclohexane), even though this chiral primary diamine has only small N-H atoms on each side of the coordination plane. However, a slight difference in the stereochemistry of the two protons (one N-H has "quasi axial" and the other "quasi equatorial" character) is sufficient to induce a significant change in the relative stabilities of the [Pt(dach)G2] deltaHT and lambdaHT rotamers (HT = head-to-tail). The new results show that at acidic and neutral pH the induction of asymmetry from the dach ligand to the HT rotamers is governed by the G-to-G dipole-dipole interaction, which is greater for the six-membered ring of each guanine leaning towards the cis-G. Such a "six-in" canting of the two guanine ligands can be hampered by the steric interaction between the H8 of each guanine and the substituent on the cis-amine that is on the same side of the coordination plane. Such a repulsion is greater for a "quasi equatorial" N-H than for a "quasi axial" N-H. Under basic pH conditions, deprotonation of the guanine N1-H renders the O6 atom a much better hydrogen-bond acceptor; therefore, the stability of the HT rotamers is governed by the hydrogen-bond interaction of guanine O6 and the cis-amine N-H group. Such a guanine O6/N-H cis-amine interaction is stronger for a "quasi axial" than for a "quasi equatorial" N-H group. In the head-to-head (HH) rotamer, in which the electrostatic repulsion between electron-rich O6 atoms, both on the same side of the platinum coordination plane, tends to place the six-membered rings of each guanine further from the cis-guanine and closer to the cis-amine, we can expect better N-H...O6 hydrogen bonding for the "quasi equatorial" N-H groups.     

Theoretical calculations of proton affinities of azines. Prediction of the relative basicities and preferred protonation sites

Theoretical calculations at the 3-21G and 3-21 + G ab initio levels and at the MNDO and AM1 semiempirical levels of several six-membered nitrogenated heterocycles and their protonated species have been carried out. The 3–21G calculated proton affinities are systematically too high, in relation to the available experimental data, and it is estimated that inclusion of electron correlation and zero-point corrections is not sufficient to reach the desired agreement; however, additional inclusion of diffuse functions (3-21 + G/3-21G calculations) lowers the calculated proton affinities by 5.4–6.8 kcal/mol, a good agreement being thus obtained, at least for 1–7 . On the other hand, semiempirical methods underestimate the repulsion between each pair of vicinal nitrogens; however, if a correction of ?9 kcal/mol is added to the AM1 results for each pair of neighboring nitrogens containing lone pairs of electrons, the corresponding proton affinities match fairly well the available exoerimental data and corrected 3-21 + G results. As expected, all methods predict that the introduction of additional nitrogens decreases the overall absolute basicity. Futhermore, comparison of the relative basicity of the isomers and of the preferred protonation site for each isomer indicates that nitrogen atoms with (only) one α-nitrogen and without a γ-nitrogen are more basic than any others. In benzazines, MNDO and AM1 suggest that the 2,3-diaza arrangement has a higher intrinsic basicity than the 1,2-diaza arrangement.     

含苯并五元环方酸衍生物的二阶非线性光学性质的理论研究

利用从头算HF/6-31G*方法对用苯并五元环取代的方酸衍生物体系SQ1～SQ15进行几何构型优化和电子结构计算. 以优化后的构型为基础, 应用ZINDO方法计算电子光谱. 同时应用从头算CPHF/6-31G*方法和半经验FF/AM1, FF/PM3, FF/MNDO等有限场方法计算了分子的二阶非线性光学系数β_μ. 研究几何结构、电子结构和前线分子轨道能与β_μ之间的关系, 为设计性能优良的有机非线性光学材料提供理论指导, 并对这四种计算方法的结果进行了比较.     

Conformational study and electron density analysis of 9-[tetrahydropyran-3-yl]purine derivatives

A conformational analysis was carried out on cis-6-chloro-9-[2-(2-hydroxyethyl)-2,3,5,6-tetrahydro-4H-pyran-3-yl]purine and several related model compounds at the HF/6-31++G(d,p) and B3LYP/6-311++G(2d,2p) levels, and also using the semiempirical methods AM1 and PM3. The result of this analysis shows that the molecule prefers an axial disposition of the purine ring, with an approximate cis orientation of C4-N9-C1′-H1′ dihedral angle. The stability of this conformation comes mainly from the formation of a C-H?O?H-O intramolecular three-center hydrogen bond. In this structure, the tetrahydropyran oxygen acts as an acceptor, while both H8 of the purine ring and the hydroxylic hydrogen of the hydroxyethyl group act as donors. Also, the equatorial disposition of the hydroxyethyl group in this conformer reduces its repulsions with the purine ring and the tetrahydropyran hydrogens. The quantum theory of atoms in molecules was applied to study the electronic effects produced by the conformational changes, bonding between tetrahydropyran and purine rings, chlorine substitution, and intramolecular hydrogen bonding.