Studies on the 1,4-oxazepine ring formation reaction using the molecular orbital method

1,4-Oxazepine formation reactions of 1,8-naphthyridine derivatives (1-4) with peroxy acid have been studied using a semiempirical MO method (AM1) and an ab initio molecular orbital method (Gaussian 94). The energies of molecules involved in the reaction paths were calculated and the transition states related to experimental products were obtained. For the reactions of 1-3, the calculated energies of the transition states predicted the previously obtained products. However, the calculated values for the reaction of 4 suggested a different type of oxazepine compound, which was verified in further experiments.     

Semiempirical and ab initio transition state calculations for the transformation of N-acetyltetrazoles into corresponding 1,3,4-oxadiazoles

The transformation of 2-acetyl-5-substituted-tetrazoles into the corresponding 1,3,4-oxadiazoles was studied with the semiempirical and ab initio methods. Two mechanisms, one with two transition states and the other with three, were elucidated by . The first mechanism supported by PM3 and MNDO has a two-step, almost concerted, mechanism for the elimination of a nitrogen molecule from the tetrazole ring and formation of the oxadiazole product from an open-chain intermediate through carbon C₅ and acetyl oxygen bond formation. The second mechanism supported by AM1 and MINDO/3 breaks the elimination of the nitrogen molecule into two steps: first breaking the N₄-C₅ and then the N₂-N₃ bonds. Even when the AM1 and MINDO/3 transition state structures were optimized by PM3 and MNDO, the obtained transition states present only one bond breaking. The HF/STO-3G and HF/3-21G ab initio methods agree with the first mechanism where two bonds are breaking almost simultaneously. Despite the disagreement in the mechanism of the nitrogen elimination, the transition state that presents the product formation from open-chain intermediates is quite similar for all methods studied. The semiempirical calculation of this transition state is possible only if it is assumed that it has biradical character. The activation energies calculated by PM3 seem to be insensitive to the nature of the substituents.     

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.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

Münchnone-Alkene Cycloadditions: Deviations from the FMO Theory. Theoretical Studies in the Search of the Transition State

The dipolar cycloaddition reactions of 3-methyl-2-(4-nitrophenyl)-4-phenyl-1,3-oxazolium-5-olate (1) and chiral nitroalkenes derived from D-galacto- and D-manno-hept-1-enitols 2 and 3 were found to proceed in a regiospecific manner to afford acyclic pyrrole C-nucleosides (5 and 6) in satisfactory yields. This protocol constitutes a novel and efficient route to such substances. Remarkably, the regiochemistry of this mesoionic-based cycloadditive process is exactly opposite that anticipated from the FMO view of 1,3-dipolar cycloadditions. A preliminary semiempirical PM3 study also reveals the inconsistencies of semiempirical studies with experimental data by applying the FMO approach to münchnone cycloadditions. The structural characteristics of the reagents, products, and transition states have been determined, and this calculation also evaluates the influence of steric and electronic factors involved. Ab initio MO calculations using a model system consisting of 1,3-oxazolium-5-olate with 2-(hydroxymethyl)nitroethylene were also performed. The ab initio study justifies, for the first time, the experimental results of 1,3-dipolar cycloadditions with münchnones. The process occurs through a concerted, slightly asynchronous transition state.     

Performance of semiempirical methods in fullerene chemistry: relative energies and nucleus-independent chemical shifts

Semiempirical MNDO, AM1, and PM3 calculations are reported for 153 fullerene isomers in an attempt to assess the reliability of these methods through comparisons with ab initio and density functional results. B3LYP/6-31G^* relative energies are generally reproduced quite well by these calculations. Qualitative trends in ab initio nucleus-independent chemical shifts at the cage centers are captured by the semiempirical GIAO-MNDO approach while underestimating their absolute values. The agreement between the semiempirical results and the ab initio or density functional reference data is generally better for the larger fullerenes (C₆₀–C₁₀₂) than for the smaller ones (C₂₀–C₅₀). These systematic comparisons clarify the accuracy that may be expected from semiempirical computations in fullerene chemistry.     

Knoevenagel condensation of cyclic ketones with benzoylacetonitrile and N,N′-dimethylbarbituric acid. Application of sterically hindered condensation products in the synthesis of spiro and dispiropyrans by hetero-Diels-Alder reactions

Inverse-electron demand Diels-Alder cycloadditions of sterically hindered cycloalkylidene derivatives of benzoylacetonitrile and N,N′-dimethylbarbituric acid with enol ethers, cyclic enol ethers and also sterically hindered cycloalkylidenecycloalkanes were investigated. New spiro, dispirodihydropyrans, spirouracils, and dispirouracils were obtained. To confirm the experimental results, frontier orbital HOMO and LUMO energies of heterodienes and dienophiles were calculated by semi-empirical AM1, PM3 methods and ab initio Hartree-Fock calculations.     

Semiempirical NDDO/MC calculations of the excited states of the chromate ion

A new semiempirical method of calculating the excited states of transition metal complexes is developed. This technique uses the configuration interaction and semiempirical NDDO/MC methods to obtain the ground state of a set of Slater type valence spd-orbitals chosen from the optical spectra of transition metals together with the corresponding core integrals. The method is tested in calculations of the electronically excited states of the chromate ion. Good agreement with the experimental energies of vertical transitions and the results of ab initio calculations is achieved.     

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.     

Semiempirical study of the conformation of tetroxane and its halogenated derivatives

We have made a conformational study of tetroxane and its bi- and tetra-halogenated derivatives by means of the semiempirical AM1 and PM3 molecular orbital methods. The results are compared with previous semiempirical and ab initio studies as well as with available experimental data. We have found that in every case the AM1 method underestimates the peroxidic O-O bond length by approximately 12%, while the PM3 procedure describes such a bond in a better way. The degree of accuracy of these two semiempirical methods is discussed in relation with the tetroxane structure.     

Transition states and mechanisms of the hetero-Diels-Alder reactions of hyponitrous acid, nitrosoalkanes, nitrosoarenes, and nitrosocarbonyl compounds.

The transition states and energetics of Diels-Alder reactions for a variety of nitroso compounds with dienes were explored with density functional theory using the B3LYP functional and 6-31G basis set. The reactions involve HNO, various nitrosoalkanes and arenes (RNO and ArNO), and nitrosoformaldehyde (CHONO) as dienophiles with butadiene and a series of 1- and 2-substituted dienes. The mechanisms, activation energies, energies of reaction, stereoselectivities, and regioselectivities are predicted for these reactions. These predictions are compared to available experimental data. The mechanism is found to be concerted but involves highly asynchronous transition states. Although it is not evident in the products, we find that the endo path is very strongly favored over the exo alternative due to repulsion between the diene and nitrogen's lone pair. A range of experimental regioselectivities are reproduced by calculations and are found to hinge on a very sensitive balance between FMO interactions, electrostatics, and steric effects. A series of generalizations for predicting regioselectivity for untried diene-dienophile pairs are made.     

Experimental and theoretical studies of Diels-Alder dimerization of 1,2,3,4,5-pentachlorocyclopentadiene and of Diels-Alder cycloaddition of polychlorinated cyclopentadienes to norbornadiene

Diels-Alder cyclodimerization of 1,2,3,4,5-pentachlorocyclopentadiene (1) affords 2a as the exclusive reaction product. Diels-Alder cycloaddition of 1 to norbornadiene also proceeds stereoselectively to produce a single [4+2] cycloadduct, 4c. The structures of 2a and 4c were established unequivocally via application of single crystal X-ray crystallographic techniques. The origins of the observed diastereofacial selectivity in each of these cycloaddition processes have been investigated by application of semiempirical (AM1 Hamiltonian) and ab initio (Hartree-Fock 3-21G*) calculations. The computational results thereby obtained, which are based upon consideration of the kinetically favored transition state for each of the two cycloaddition reactions studied, are consistent with experiment. These semiempirical and ab initio methods also have been used to investigate the mechanisms of the Diels-Alder reactions that have been used to prepare aldrin and isodrin (7 and 8, respectively). The results thereby obtained suggest that isodrin formation via Diels-Alder cycloaddition of cyclopentadiene to 1,2,3,4,7,7-hexachloronorbornadiene proceeds with kinetic control of product stereochemistry.     

Near ab initio quality molecular electrostatic potential maps using hybridization displacement charges at PM3 level and effects of geometrical changes in amino groups

Charge distributions, dipole moments, and molecular electrostatic potentials (MEP) around several molecules consisting of carbon, nitrogen, oxygen, fluorine, sulfur, and chlorine atoms were studied using the PM3 semiempirical method and the results compared with those obtained using ab initio calculations at the RHF/6‐31G** level. Thus it is shown that relative MEP values near different atoms can be obtained using hybridization displacement charges (HDC) obtained by employing PM3 density matrices that usually agree quite satisfactorily with the ab initio ones. Further, positions of ab initio MEP minima are correctly located and the corresponding relative MEP values usually correctly predicted using the PM3(HDC) charges distributed continuously in three dimensions according to the forms of squares of valence s atomic orbitals. The necessary parameters for HDC calculations using the PM3 method were optimized. It is shown how within the frameworks of both PM3 and AM1 methods the π electrons or lone pairs associated with amino group nitrogen atoms and ring atoms can be satisfactorily treated in different situations. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 299–312, 2001     

Theoretical study of C24N4 molecule

Both ab initio 6-31G, 3-21G and STO-3G basis sets and semiempirical PM3 and AM1 molecular orbital calculations are carried out on the C₂₄N₄ molecule of the T_d symmetry group. Results on the fully optimized structure which constrained T_d symmetry, molecular orbitals and vibrational frequency were obtained by both ab initio and semiempirical methods. The binding energy and various thermodynamic properties were also calculated via the PM3 and AM1 semiempirical methods. All the evidence of this work proves that the C₂₄N₄ molecule is stable and that its four six-membered rings with a remarkable delocalized C…C bond are similar to the related rings in the C₆₀ buckminsterfullerene structure.     

Theoretical investigation of isotopic scrambling mechanisms in 2-chloroethyl methyl sulfide

Ab initio and semiempirical molecular orbital calculations have been applied to study the concerted and stepwise isotopic scrambling mechanisms of 2-chloroethyl methyl sulfide in the gas phase and in aqueous solution. The calculations reveal the structural details of the reactants, transition structures, and intermediates involved in this reaction and provide relative energy estimates. The concerted mechanism is found to be competitive with the stepwise mechanism in the gas phase, but the stepwise mechanism is favored in aqueous solution as no true transition structure for the concerted mechanism could be found using the solvation models. A combined approach of evaluating solvation energies with the generalized-Bom-plus-surface-tensions SM _x solvation models of Cramer and Truhlar at ab initio optimized geometries is found to deliver the best agreement with experimentally determined reaction barriers. Together with the recent experimental results of McManus and co-workers, the present study provides insights into the controlling factors involved in the elementary reaction steps of sulfur mustards and a solid foundation for investigations into more complex reactions of related compounds.     

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: comparison of semiempirical, ab initio, and density functional results

The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.     

AM1 semiempirical searching for suitable thiophene derivatives that will enable thiophenes to act as a diene in the diels-alder reactions

The AM1 semiempirical method was used for theoretical searching of activation of thiophene as a diene for the Diels-Alder reaction. The reactivity of thiophene, electron-withdrawing and electron-donating substituted thiophenes, as well as the S-methylthiophenium ion were studied as the diene for Diels-Alder reactions by evaluating their frontier orbital energies and by calculating reaction barriers with activated and deactivated dienophiles. It was demonstrated that slight activation of the thiophene ring can be obtained with both electron-donating and electron-withdrawing groups attached to the thiophene ring. It was predicted that the actual transformation of thiophenes into the corresponding S-methylthiophenium anions is the best means of activating the thiophenes. The calculated activation energies for normal (non-activated) dienophiles are moderate so mild reaction conditions are predicted. If dienophiles are activated with electron-donating substituents, AM1 calculations predict a two step cycloaddition reaction with a very small activation barrier.     

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

Two new semiempirical methods employing a Pairwise Distance Directed Gaussian modification have been developed: PDDG/PM3 and PDDG/MNDO; they are easily implemented in existing software, and yield heats of formation for compounds containing C, H, N, and O atoms with significantly improved accuracy over the standard NDDO schemes, PM5, PM3, AM1, and MNDO. The PDDG/PM3 results for heats of formation also show substantial improvement over density functional theory with large basis sets. The PDDG modifications consist of a single function, which is added to the existing pairwise core repulsion functions within PM3 and MNDO, a reparameterized semiempirical parameter set, and modified computation of the energy of formation of a gaseous atom. The PDDG addition introduces functional group information via pairwise atomic interactions using only atom-based parameters. For 622 diverse molecules containing C, H, N, and O atoms, mean absolute errors in calculated heats of formation are reduced from 4.4 to 3.2 kcal/mol and from 8.4 to 5.2 kcal/mol using the PDDG modified versions of PM3 and MNDO over the standard versions, respectively. Several specific problems are overcome, including the relative stability of hydrocarbon isomers, and energetics of small rings and molecules containing multiple heteroatoms. The internal consistency of PDDG energies is also significantly improved, enabling more reliable analysis of isomerization energies and trends across series of molecules; PDDG isomerization energies show significant improvement over B3LYP/6-31G* results. Comparison of heats of formation, ionization potentials, dipole moments, isomer, and conformer energetics, intermolecular interaction energies, activation energies, and molecular geometries from the PDDG techniques is made to experimental data and values from other semiempirical and ab initio methods.     

Hydrogen bonds: a comparison of semiempirical and ab initio treatments

H-bonding interactions calculated using the AM1, PM3 and SAM1 semiempirical molecular orbital methods are compared with the best available ab initio calculations for several intermolecular interactions of interest: acetic acid dimers, water/ acetylene, water/HCN, formaldehyde/acetylene, formaldehyde/HCN, ozone/acetylene, ozone/HCN, acetylacetone, melamine/ cyanuric acid, and nitromethane/ammonia. Experimental values are also presented where available. The energetic comparisons are based upon enthalpies of interaction from the ab initio calculations after counterpoise and vibrational corrections have been applied. Overall, AM1 seems to do best, except for O---H…O interactions, where none of the three methods excel.     

Theoretical study of the energetics of the reactions of triplet dioxygen with hydroquinone, semiquinone, and their protonated forms: relation to the mechanism of superoxide generation in the respiratory chain

One-electron reduction of the dioxygen molecule by the reduced form of mitochondrial ubiquinones (Q) of the NADH dehydrogenase (complex I) and mitochondrial cytochrome bc1 (complex III) is believed to be the main source of the superoxide anion radical O2*- and the hydroperoxide radical OOH*. In this work, we modeled the energetics of four possible reactions of the triplet ((3)Sigma(g)) dioxygen-molecule reduction by fully reduced and protonated ubiquinone (QH2; reaction 1), its deprotonated form (QH-; reaction 2), the semiquinone radical (QH*; reaction 3), and the semiquinone anion radical (Q*-; reaction 4), by means of ab initio calculations with the 6-31G(d) and 6-31+G(d) basis set in the restricted open-shell Hartree-Fock (ROHF), unrestricted Hartree-Fock (UHF), and complete active space self-consistent field (CASSCF) with dynamic correlation [at the second-order M?ller-Plesset (MP2) or multiple reference M?ller-Plesset (MRMP), respectively] schemes and the basis set superposition error (BSSE) correction included, as well as semiempirical AM1 and PM3 calculations in the UHF and ROHF schemes. 2-Butene-1,4-dione and p-benzoquinone were selected as model compounds. For the reduced forms of both compounds, reaction 1 turned out to be energetically unfavorable at all levels of theory, this agreeing with the experimentally observed diminished reductive properties of hydroquinone derivatives at low pH. For 2-butene-1,4-dione treated at the most advanced MRMP/CASSCF/6-31+G(d) level, the energies of reactions 1-4 are 4.7, -34.3, -15.0, and -4.1 kcal/mol, respectively. This finding suggests that reactions 2 and 3 are the most likely mechanisms of electron transfer to molecular oxygen in aprotic environments and that proton transfer is involved in this process. Nearly the same energies of reactions 2 and 3 were calculated at the MRMP/CASSCF/6-31+G(d) level for reduced forms of p-benzoquinone. Inclusion of diffuse functions in the basis set and dynamic correlation at the CASSCF level appears essential. Because deprotonated ubiquinol is unlikely to exist in physiological environments, reaction 3 appears to be the most likely mechanism of one-electron reduction of oxygen; however, if oxygen can penetrate cytochrome bc1 as far as the Q(o) center where ubiquinol can be deprotonated, reaction 2 can also come into play. The energies of reactions 2 and 3 calculated at the MRMP/CASSCF/6-31+G(d) level are most closely reproduced in the ab initio and semiempirical UHF PM3 calculations. Additional semiempirical calculations on more realistic models of ubiquinone, 2,3-dimethoxy-6-methyl-p-benzoquinone and 2,3-dimethoxy-5-isoprenyl-6-methyl-p-benzoquinone, gave qualitatively the same relations between the energies of reactions 2 and 3 as those carried out for p-benzoquinone species, thereby suggesting that this method could be used in studying electron-transfer reactions from reduced quinone derivatives to molecular oxygen in more complex systems, such as a model of the Q(o) site of cytochrome bc1, where applying ab initio methods is unfeasible.