Conformational energy penalties of protein-bound ligands

The conformational energies required for ligands to adopt their bioactive conformations were calculated for 33 ligand–protein complexes including 28 different ligands. In order to monitor the force field dependence of the results, two force fields, MM3 and AMBER, were employed for the calculations. Conformational analyses were performed in vacuo and in aqueous solution by using the generalized Born/solvent accessible surface (GB/SA) solvation model. The protein-bound conformations were relaxed by using flat-bottomed Cartesian constraints. For about 70% of the ligand–protein complexes studied, the conformational energies of the bioactive conformations were calculated to be 3 kcal/mol. It is demonstrated that the aqueous conformational ensemble for the unbound ligand must be used as a reference state in this type of calculations. The calculations for the ligand–protein complexes with conformational energy penalties of the ligand calculated to be larger than 3 kcal/mol suffer from uncertainties in the interpretation of the experimental data or limitations of the computational methods. For example, in the case of long-chain flexible ligands (e.g. fatty acids), it is demonstrated that several conformations may be found which are very similar to the conformation determined by X-ray crystallography and which display significantly lower conformational energy penalties for binding than obtained by using the experimental conformation. For strongly polar molecules, e.g. amino acids, the results indicate that further developments of the force fields and of the dielectric continuum solvation model are required for reliable calculations on the conformational properties of this type of compounds.     

Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.     

Density functional theory calculations of the internal rotations and vibrational spectra of 2-, 3- and 4-formyl pyridine

The torsional potentials, molecular conformations and vibrational spectra, of 2-, 3- and 4-formyl pyridine have been investigated using density functional theory (DFT) method with 6-31+G* basis set. From the calculations, 2-formyl pyridine and 3-formyl pyridine were predicted to exist predominantly in cis conformation with the cis-trans rotational barrier of 9.38 kcal/mol and 8.55 kcal/mol, respectively. The two equivalent planar structures of 4-formyl pyridine are separated by an energy barrier of 7.18 kcal/mol. The vibrational wavenumbers and the corresponding vibrational assignments of molecules in C(s) symmetry were examined theoretically and the calculated Infrared of the molecules in the cis conformation was plotted. Observed wavenumbers for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of DFT force fields using the standard 6-31+G* basis set of the theoretical optimized geometry.     

Efficient search for all low energy conformations of polypeptides by Monte Carlo methods

The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below ?10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below ?10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.     

Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields

Ab initio self-consistent field (SCF) Hartree-Fock calculations of sulfates R? O? SO₃(?1) (R = Me, Et, i-Pr) and sulfamates R? NHSO₃(?1) (R = H, Me, Et, i-Pr) were performed at the 4-31G(*S*N) //3-21G(*S*N) basis set levels, where asterisks indicate d functions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6-31G*//6-31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the C? O bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single O? S bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn-periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the C? N bond and 3.3 kcal/mol around the N? S bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the N? S bond of only 1.7 kcal/mol. These and other data were used to parameterize the well-known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6-31G*//6-31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β-D -glucose-6-sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley & Sons, Inc.     

Quantum-Chemical and semiclassical calculations of intermolecular interactions of phospholipids

By use of empirical 0–1–6–12 atom–atom potential functions and the PCILOCC method intra- and intermolecular interactions of glycero–phosphoryl–ethanolamine model head groups in a planar layer crystal were calculated. Starting from investigations of the two-dimensional energy-contour diagrams the minima of energy as a function of all head group torsion angles were calculated using a gradient procedure. Within an interval of 15 kcal/mol above the energy of the global minimum we obtained about 30 local minima. These results demonstrate a high flexibility of the investigated phosphorylethanolamine head group in agreement with experiment. The ethanolamine moiety exists in enantiomeric conformations. With the torsion angles of the 0–1–6–12 energy minimization procedure PCILOCC calculations were carried out. These calculations yield the x-ray conformation as the most stable one (unit-cell stabilization energy = ?36.3 kcal/mol). The PCILOCC as well as the potential function calculations show that the conformation of phospholipid head groups in layer crystals is determined by intramolecular as well as by intermolecular interactions with neighboring phospholipid molecules.     

Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations.

A knowledge-based approach for generating conformations of molecules has been developed. The method described here provides a good sampling of the molecule's conformational space by restricting the generated conformations to those consistent with the reference database. The present approach, internally named et for enumerate torsions, differs from previous database-mining approaches by employing a library of much larger substructures while treating open chains, rings, and combinations of chains and rings in the same manner. In addition to knowledge in the form of observed torsion angles, some knowledge from the medicinal chemist is captured in the form of which substructures are identified. The knowledge-based approach is compared to Blaney et al.'s distance geometry (DG) algorithm for sampling the conformational space of molecules. The structures of 113 protein-bound molecules, determined by X-ray crystallography, were used to compare the methods. The present knowledge-based approach (i) generates conformations closer to the experimentally determined conformation, (ii) generates them sooner, and (iii) is significantly faster than the DG method.     

Rotational barriers in monomeric CH2=CX-COOH and CH2=CX-CONH2 (X is H or CH3) and vibrational analysis of methacrylic acid and methacrylamide

The internal rotations in acrylic and methacrylic acids CH2=CX-COOH and their amides CH2=CX-CONH2 (X is H or CH3) were investigated by DFT-B3LYP calculations with 6-311+G** basis set. The potential energy curves were consistent with two minima that correspond to planar cis and trans conformation in the case of the acids (or cis and near-trans forms in the case of the amides). Acrylic acid and acrylamide were predicted to have the cis form as the low and predominant conformation of the molecules. In the case of the methacrylic acid and methacrylamide, the conformational relative stability was predicted to reverse as going from the acrylic to the metha compounds. The trans conformer in methacrylic acid or the near-trans in methacrylamide were predicted to be thermodynamically low energy structures of the molecules. The CCCO rotational barrier was calculated to vary from 4 to 6kcal/mol in the four molecules. The OCOH and OCNH torsional barriers were calculated to be about 13 and 22kcal/mol in the acids and the amides, respectively. The vibrational frequencies of methacrylic acid and methacrylamide were computed at the DFT-B3LYP/6-311+G** level and reliable vibrational assignments were made on the basis of normal coordinate analyses and comparison with experimental data of both molecules in their low energy conformations.     

A Dynamic Study of the Stereoisomerization of Pentaphenylethane by Molecular Mechanics Methods

Two conformations, 1 and 2 , of pentaphenylethane are compared. The ground state conformation 2 results from an earlier computational work by force fields procedures [1], whereas 1 has been more recently observed in the crystalline state by X-ray diffraction methods. The strain energy of 1 minimizes very close to the value computed for 2 . These conformations belong to two distinct minima of the potential energy surface and are at the most separated by a barrier of about 7 kcal/mol. The pathway converting 1 into its enantiomer is shown to run over a barrier of only 1.5 kcal/mol.     

Conformational study of the structure of free 18-crown-6

A conformational search was performed for 18-crown-6 using the CONLEX method at the MM3 level. To have a more accurate energy order of the predicted conformations, the predicted conformations were geometry optimized at the HF/STO-3G level and the 198 lowest energy conformations, according to the HF/STO-3G energy order, were geometry optimized at the HF/6-31+G level. In addition, the 47 nonredundant lowest energy conformations, according to the MP2/6-31+G energy order at the HF/6-31+G optimized geometry, hereafter the MP2/6-31+G//HF/6-31+G energy order, were geometry optimized at the B3LYP/6-31+G level. According to the MP2/6-31+G//B3LYP/6-31+G energy order, three conformations had energies lower than the experimentally known Ci conformation of 18c6. At the MP2/6-31+G//B3LYP/6-31+G level, the S6 lowest energy conformation is more stable by 1.96 kcal/mol than this Ci conformation. This was confirmed by results at the MP2/6-31+G level with an energy difference of 1.84 kcal/mol. Comparison between the structure of the S6 conformation of 18c6 and the S4 lowest energy conformation of 12-crown-4, as well as other important conformations of both molecules, is made. It is concluded that the correlation energy is necessary to have an accurate energy order of the predicted conformations. A rationalization of the conformational energy order in terms of the hydrogen bonding and conformational dihedral angles is given. It is also suggested that to have a better energy order of the predicted conformations at the MM3 level, better empirical force fields corresponding to the hydrogen bond interactions are needed.     

Toward accurate relative energy predictions of the bioactive conformation of drugs

Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol(-1) of a local minimum, with penalties above 2.0 kcal mol(-1) being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery.     

Substituent effects on structural stability of formyl ketene and analysis of vibrational spectra of formyl haloketenes and formyl methylketene.

The conformational behavior and the structural stability of formyl fluoroketene, formyl chloroketene and formyl methylketene were investigated by utilizing quantum mechanical DFT calculations at B3LYP/6-31I + + G** and ab initio calculations at MP2/6-311 + + G** levels. The three molecules were predicted to have a planar s-cis<-->s-trans conformational equilibrium. From the calculations, the direction of the conformational equilibrium was found to be dependent on the nature of the substituting group. In formyl haloketenes, the cis conformation, where the C=O group eclipses the ketenic group, was expected to be of lower energy than the trans conformer. In the case of formyl methylketene the conformational stability was reversed and the trans form (the aldehydic hydrogen eclipsing the ketenic group) was calculated to be about 2 kcal mol(-1) lower in energy than the cis form. The calculated cis-trans energy barrier was found to be in the order: fluoride (15.3 kcal mol(-1)) > chloride (13.1 kcal mol(-1)) > methyl (11.7 kcal mol(-1). Full optimization was performed at the ground and the transition states of the molecules. The vibrational frequencies for the stable conformers of the three ketenic systems were computed at the DFT-B3LYP level, and the zero-point corrections were included into the calculated rotational barriers. Complete vibrational assignments were made on the basis of both normal coordinate calculations and comparison with experimental results of similar molecules.     

A fast and efficient method to generate biologically relevant conformations

Summary Mutual binding between a ligand of low molecular weight and its macromolecular receptor demands structural complementarity of both species at the recognition site. To predict binding properties of new molecules before synthesis, information about possible conformations of drug molecules at the active site is required, especially if the 3D structure of the receptor is not known. The statistical analysis of small-molecule crystal data allows one to elucidate conformational preferences of molecular fragments and accordingly to compile libraries of putative ligand conformations. A comparison of geometries adopted by corresponding fragments in ligands bound to proteins shows similar distributions in conformation space. We have developed an automatic procedure that generates different conformers of a given ligand. The entire molecule is decomposed into its individual ring and open-chain torsional fragments, each used in a variety of favorable conformations. The latter ones are produced according to the library information about conformational preferences. During this building process, an extensive energy ranking is applied. Conformers ranked as energetically favorable are subjected to an optimization in torsion angle space. During minimization, unfavorable van der Waals interactions are removed while keeping the open-chain torsion angles as close as possible to the experimentally most frequently observed values. In order to assess how well the generated conformers map conformation space, a comparison with experimental data has been performed. This comparison gives some confidence in the efficiency and completeness of this approach. For some ligands that had been structurally characterized by protein crystallography, the program was used to generate sets of some 10 to 100 conformers. Among these, geometries are found that fall convincingly close to the conformations actually adopted by these ligands at the binding site.     

Viability of möbius topologies in [26]- and [28]hexaphyrins

Recently, hexaphyrins have emerged as a promising class of π-conjugated molecules that display a range of interesting electronic, optical, and conformational properties, including the formation of stable M?bius aromatic systems. Besides the M?bius topology, hexaphyrins can adopt a variety of conformations with Hückel and twisted Hückel topologies, which can be interconverted under certain conditions. To determine the optimum conditions for viable M?bius topologies, the conformational preferences of [26]- and [28]hexaphyrins and the dynamic interconversion between the M?bius and Hückel topologies were investigated by density functional calculations. In the absence of meso?substituents, [26]hexaphyrin prefers a planar dumbbell conformation, strongly aromatic and relatively strain free. The M?bius topology is highly improbable: the most stable tautomer is 33?kcal?mol(-1) higher in energy than the global minimum. On the other hand, the M?bius conformer of [28]hexaphyrin is only 6.5?kcal?mol(-1) higher in energy than the most stable dumbbell conformation. This marked difference is due to aromatic stabilization in the M?bius 4n electron macrocycle as opposed to antiaromatic destabilization in the 4n+2 electron system, as revealed by several energetic, magnetic, structural, and reactivity indices of aromaticity. For [28]hexaphyrins, the computed activation barrier for interconversion between the M?bius aromatic and Hückel antiaromatic conformers ranges from 7.2 to 10.2?kcal?mol(-1) , in very good agreement with the available experimental data. The conformation of the hexaphyrin macrocycle is strongly dependent on oxidation state and solvent, and this feature creates a promising platform for the development of molecular switches.     

Sigma- and pi-bond strengths in main group 3-5 compounds

The sigma- and pi-bond strengths for the molecules BH2NH2, BH2PH2, AlH2NH2, and AlH2PH2 have been calculated by using ab initio molecular electronic structure theory at the CCSD(T)/CBS level. The adiabatic pi-bond energy is defined as the rotation barrier between the equilibrium ground-state configuration and the C(s)symmetry transition state for torsion about the A-X bond. We also report intrinsic pi-bond energies corresponding to the adiabatic rotation barrier corrected for the inversion barrier at N or P. The adiabatic sigma-bond energy is defined as the dissociation energy of AH2XH2 to AH2 + XH2 in their ground states minus the adiabatic pi-bond energy. The adiabatic sigma-bond strengths for the molecules BH2NH2, BH2PH2, AlH2NH2, and AlH2PH2 are 109.8, 98.8, 77.6, and 68.3 kcal/mol, respectively, and the corresponding adiabatic pi-bond strengths are 29.9, 10.5, 9.2, and 2.7 kcal/mol, respectively.     

Conformational properties of permethylcyclohexane as compared to cyclohexane: A force field study

The conformational properties of the recently synthesized highly strained permethylcyclohexane molecule 2 have been studied by empirical force field calculations using three different potentials (CFF, MM2, MM2′) and second-derivative optimization methods. A comparison of the results with the conformational behavior of parent cyclohexane 1 leads to the following conclusions: The best conformation of 2 is a chair minimum whose six-membered ring is flatter than that of 1 , due to the strong H…H repulsions introduced by the methyl groups. The twist minimum of 2 is energetically less favorable than the chair by an amount similar to 1 . A potential energy barrier Δ V^# for the chair inversion of 2 of 15.32 kcal/mol results with the CFF, only about three kcal/mol higher than for 1 . The free energy of activation ΔG^# for this process obtained with the CFF is 16.96 kcal/mol (at 333 K) and agrees well with the experimental value of 16.7(2) kcal/mol.¹ MM2 and MM2′ give substantially lower and higher potential energy inversion barriers Δ V^# of 9.03 and 20.29 kcal/mol, respectively, which is attributed to inappropriate torsional energy terms in these force fields. The characteristic difference in the conformational behavior of 2 and 1 concerns the boat forms which are substantially less favorable in the per-methyl compound than in 1 . Expectedly, strong H…H repulsions between the 1,4 diaxial flagpole–bowsprit methyl groups in 2 are responsible for this difference. The particularly high strain of the boat forms of 2 leads to flexibility differences as compared to 1 which in turn affect the relative entropies of the various statiomers (stationary point conformations); e.g., the chair ring inversion activation entropies of 2 and 1 are predicted by the CFF calculations to have opposite signs (?4.82 and 3.41 cal/mol K, respectively, at 298 K). The twist and half-twist statiomers of 2 are much more rigid than those of 1 , which is a consequence of the substantially larger boat barriers along their pseudorotational interconversion paths. The boat transition state separating two enantiomeric twist minima represents a barrier calculated to be more than tenfold higher for 2 than for 1 (CFF Δ V^# values 11.14 and 0.92 kcal/mol, respectively); likewise the half-boat chair inversion barrier of 2 is calculated 5.07 kcal/mol less favorable than the respective half-twist barrier. These statiomers are practically equienergetic in the case of 1 . Except for the axial flagpole–bowsprit CH₃ substituents of the boat forms, the methyl groups of all the relevant calculated statiomers of 2 are more or less staggered. The rotational barrier of the equatorial methyl groups of the chair minimum of 2 is computationally predicted to be 5.78 kcal/mol (ΔG^#), i.e., unusually high. Interesting vibrational effects are brought about by the strong H…H repulsions in 2 ; thus the chair minimum has a largest C? H stretching frequency estimated to be 3050 cm^?1 and involves several particularly low frequencies which have a substantial influence on its entropy. CFF calculations for the lower homologue permethylcyclopentane 5 indicate that its pseudorotational properties are similar to those of cyclopentane 4 , in contradistinction to the pair 2/1 .     

Development of polyphosphate parameters for use with the AMBER force field

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems.     

An ab initio study of the geometries and rotational barriers of 1-, 2-, and 5-phenylimidazole

The torsional barrier was calculated in the 3-21G basis set for 1-, 2-, and 5-phenylimidazole. Full geometry optimization was carried out at inter-ring torsional angles of 0°, 30°, 60°, 90°, 120°, 150°, 180°, and additional intermediate angles. All torsional potential energies were found to be symmetric with respect to the 90° conformation. The 2-phenylimidazole torsional energy exhibits a minimum at 0° (and 180°) and a maximum at 90° with a barrier height of 5.83 kcal/mol relative to the 0° conformation. The minima in the 1- and 5-phenylimidazole torsional potential energies correspond to non-planar conformations, resulting in a double-well potential with maxima at 0° (180°) and 90°. The 1-phenylimidazole minima are located at 46.5 and 133.5°; the 5-phenylimidazole minima, at 35.3 and 144.7°. In the 0° (180°) and 90° conformations, 1-phenylimidazole exhibits torsional barriers of 1.84 and 0.75 kcal/mol, respectively, relative to the energy of the 46.5° conformation. For 5-phenylimidazole, these barriers are 0.94 and 1.89 kcal/mol, relative to the energy of the 35.3° conformation. The energy of 5-phenylimidazole in the 35.3° conformation corresponds to a relative tautomeric energy difference of 1.80 kcal/mol compared to the 0° conformer of the 4-phenylimidazole tautomer.     

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base.

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C(11)-C(12) double bond is characterized by variation of both the twist angle delta(C(10)-C(11)-C(12)-C(13)) and the bond length d(C(11)-C(12)). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all-trans conformation is more stable by 3.7 kcal/mol than the 11-cis geometry. For the first excited state, S(1,) the 90 degrees twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90 degrees minimum conformation is more stable than the all-trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S(1) surface of the retinal Schiff base with an almost barrier-less geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.     

Conformational analysis of azepane, oxepane, silepane, phosphepane, thiepane and the azepanium cation by high level quantum mechanics

A complete conformational analysis of the title compounds was performed by quantum mechanics at the B3LYP and the CCSD(T) levels of theory with the triple-zeta quality basis set 6-311+G(d,p). The results are compared with the well-established results of cycloheptane. Without exception, twist-chair conformations are found to be stable conformations with the chair forms as transition states. Second row hetero atoms lower the relative energy of the boat conformations relative to the chair forms. The barrier of interconversion between the chair and boat families of conformations is found to be around 8 kcal/mol, except for phosphepane where it is 2 kcal/mol lower and for silepane, where the barrier is only 2.7 kcal/mol.