Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.     

Ab initio SCF calculations on low-energy conformers of cyclohexaglycine

Results from ab initio self-consistent field (SCF) calculations with a 3-21G and a double-zeta-plus polarization (DZP) basis set on four low-energy conformations of cyclohexaglycine are reported. In agreement with results from semiempirical and molecular mechanics force field calculations, the lowest-energy conformation found at the DZP level is a conformation forming six C₇ turns. However, the energy difference to the β-turn conformers is significantly smaller at the ab initio DZP level than calculated by the other methods. In contrast to the results obtained with some of the other methods, the present ab initio calculations show that both the double-type-I β turn and the double-type-II β-turn conformer of cyclohexaglycine are stable low-energy structures. © 1995 by John Wiley & Sons, Inc.     

Theoretical investigations on 1,2-ethanediol: The problem of intramolecular hydrogen bonds

The conformational space of 1,2-ethanediol is studied on the basis of ab initio and semiempirical calculations. All possible conformers are treated. The relative energies of the conformers are systematically studied using various basis sets up to 6–311 + G(3df, 3pd) in order to perform calculations as accurate as possible within a reasonable amount of computer time. Electron correlation is included using Møller-Plesset perturbation theory. We propose two methods to evaluate the basis set superposition error associated with the intramolecular hydrogen bond appearing in some of the conformers. The results of semiempirical calculations are compared with these ab initio calculations. © 1996 by John Wiley & Sons, Inc.     

The application of molecular mechanics to the structures of carbohydrates

A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C? O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C? C? O? H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C? C and C? O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.     

Computational methods for conformational analysis of unsymmetrical 1,3-diamines: 3-aminotropanes

A comparative study has been performed to evaluate the ability of a range of computational theories to predict the relative basicity and the conformations of diamine systems. Specifically, molecular mechanics (MM3), semiempirical (AM1), and ab initio (Hartree–Fock) methods have been used in the conformational analyses of unprotonated, monoprotonated, and diprotonated 3-aminotropanes, a pair of isomeric 1,3-diamines. Use of the molecular mechanics force field, with the recently determined parameter set for protonated amines, affords results that are in agreement with experimental data, when corrected for water solvent (by setting the dielectric constant to 80). Ab initio and semiempirical calculations, in contrast, give inconsistent and incorrect results. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1371–1378, 1999     

Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations

The conformational features of a large number of hydroperoxides ROOH and peroxides ROOR′, where R and R′ are alkyl groups of different and increasing size and phenyl rings, including ortho substituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results of ab initio calculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF₃ group, the calculated values are subject to large errors and heats of formation were obtained from ab initio total energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation of R·, ·OR, and ·OOR radicals were employed and several of them had to be calculated. Different approaches were employed—molecular mechanics calculations, ab initio energies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of the R and R′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John Wiley & Sons, Inc.     

A CNDO/INDO molecular orbital formalism for the elements H to Br. applications

The CNDO/INDO molecular orbital formalism introduced in the preceding paper has been applied to a large number of atom combinations up to bromine under the inclusion of the first transition metal series. The results are compared with experimental data (geometries, ionization potentials, dipole moments) or with the results of sophisticatedab initio calculations (one electron energies, net charges, atomic populations). The semiempirical model reproduces for a wide range of molecules the experimental andab initio data with remarkable success.     

Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

Employing introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001     

Conformational energetics of 1,3-dichloropropane as predicted by several calculations methods

Two semiempirical methods (MNDO and AM1), a molecular mechanics technique (MM2) and two ab initio approaches (6–31G* full optimization and 3–21G/6–31G*) were used to calculate the ordering of and energy difference between conformers in 1,3-dichloropropane. The semiempirical methods did not order the conformers properly or predict correct energy differences. Both ab initio methods ordered the conformers and predicted energy differences correctly, with the 6–31G* full optimization performing slightly better. The MM2 results were presented for calculations involving a force field with no hydrogens and a full force field of all atoms. The full force field properly ordered the conformers but did not correctly predict the energy differences. The nonhydrogen field ordered the conformers based on the Cl…Cl nonbonded distance. The data show that conformer stability is not a simple matter of maximizing the Cl…Cl nonbonded distance, but is also related to some other stabilizing interaction(s).     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Conformational analysis,part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide‐Induced‐Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide ( 1 ), N‐methylbenzamide ( 2 ), N,N‐dimethylbenzamide ( 3 ) and the conformational equilibria of 2‐fluoro ( 4 ), 2‐chloro ( 5 ) and N‐methyl‐2‐methoxy benzamide ( 6 ). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20–25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2 , the N‐methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3 , good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X‐ray and B3LYP geometries were not as good. The two substituted compounds 4 , 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non‐planar. Both the cis and trans conformers of 5 are non‐planar. There is an additional degree of freedom in 6 due to the 2‐methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis‐Etrans in 4 > 2.3 kcal/mol (CDCl₃) and 1.7 kcal/mol (CD₃CN), in 5 0.0 kcal/mol (CD₃CN) and in 6 > 2.5 kcal/mol (CDCl₃) and 2.0 kcal/mol (CD₃CN). These values were used with the observed versus calculated ¹H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis‐Etrans 1.1, ?0.1 and 1.8 kcal/mol for ( 4 ), ( 5 ) and ( 6 ). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in ( 4 ) by ca. 2 kcal/mol. Copyright © 2015 John Wiley & Sons, Ltd.     

An ab initio Molecular Orbital Study of the Conformational Properties of all-( Z )-Cyclododeca-1,4,7,10-tetraene

 Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods.     

Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree–Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by “breaking” bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468–1494, 1999     

An ab initio and molecular mechanical investigation of ureas and amide derivatives

Ab initio molecular orbital theory with the 6-31G* basis set has been used to investigate the geometries and preferred conformations for urea, derivatives of urea, and a few complicated amide derivatives. The results from the ab initio calculations provide insight into the gas-phase rotational barrier about the C? N bond and have been used to generate parameters for the MM2(87) molecular mechanics program. When applicable, theoretical structures are compared with corresponding previously reported experimental geometries. Urea is predicted to be nonplanar with pyramidal amino groups.     

Conformational study of the cholinergic agonist pilocarpidine,isopilocarpidine, and related species

A conformational study on the energies and geometries of the stable conformers of the cholinergic agonist pilocarpidine and of its inactive isomer, isopilocarpidine, has been carried out by molecular mechanics MM2 and by semiempirical quantum chemical AM1. The former predicts an envelope conformation of the -lactone nucleus, whereas AM1 predicts a planar conformation. The relative energies of the different conformations of both isomers are strongly dependent on the relative orientation of the imidazole moiety. Other related species, intermediate steps in their synthesis, and the anion intermediate in the epimerization are also discussed.     

Molecular Structure, Vibrational Spectrum and Ionization Energy of m-Dimethoxybenzene

The optimized molecular geometries of the three rotamers of m-dimethoxybenzene in the ground So and electronically excited Sl states were predicted by ab initio and density functional theory （DFF） calculations. Their vibrational spectra in the St state were studied by one color resonant two photon ionization （1C-R2PI） method, and their ionization energies were measured by two color resonant two photon ionization （2C-R2PI） experiment. The optimized molecular geometries showed that the total energy of conformer a was the lowest in the So state. Most of the active vibrations assigned from the 1C-R2PI spectrum were found to be of the in-plane ring modes. The ionization energies （IE） of conformers a, b and c were determined to be 63521, 64487 and 63755 cm^-1, respectively.     

An ab initio Molecular Orbital Study of the Conformational Properties of all-(Z)-Cyclododeca-1,4,7,10-tetraene

Summary.  Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods. Received July 9, 2001. Accepted September 26, 2001     

Conformational origin of glassy-state relaxation and ductility in aromatic polycarbonates

A new two-state conformational transition is proposed to explain the large, low-temperature mechanical loss peak seen in glassy polycarbonates. Restricted Hartree Fock ab initio calculations at the 6–31G7 level for diphenyl carbonate (DPC), a key model compound of bisphenol-A polycarbonate, reveal two inequivalent trans-trans carbonate-ring conformations both of which will exist in solution, melt or glassy states. These calculations appear to be the first high level ones (with full geometry optimization) reported for DPC, and the findings are consistent with earlier ab initio results for phenyl formate and other smaller model compounds and also with single-crystal X-ray data for DPC and oligomers. In addition to a trans-trans conformer of DPC with both phenyl rings on the same side of the carbonate unit (called the ‘syn’ conformer) which is seen in the crystalline state of DPC, an ‘anti’ conformer of lower energy is found, which has its two phenyl rings located on opposite sides of the plane of the carbonate unit. Analysis of these calculated ground state geometries and energies as well as experimental single crystal X-ray results indicates that the ‘anti’ conformer has the lowest energy in the gas phase and solution, while the ‘syn’ conformation is stabilized relative to the ‘anti’ in the bulk, probably because of aromatic ring interactions between neighbour chain segments. In the glassy state of either DPC or polycarbonate, one expects a nearly random mixture of ‘syn/anti’ conformers, and the prominent low-temperature mechanical loss peak observed in many polycarbonates is consistent with a molecular level two-state process consisting of ‘syn/ anti’ carbonate conformer conversions. These conformational transitions must involve rotation and translation of both the carbonate units and, most importantly, the neighbouring phenyl groups. The possible influence of these conformational changes and the accompanying correlated molecular motions on polymer ductility and ageing is briefly discussed.