Combined electron diffraction,conformational energy and vibrational investigations of cis-1,4-ditertiary butyl-cyclohexane

The structure of cis-1,4-ditertiarybutylcyclohexane(DTBC) was investigated by combined electron diffraction, conformational and vibrational analyses in order to obtain results which are more conclusive than those previously obtained by electron diffraction alone. In this study, first the minimum energy conformations for DTBC were calculated by the Westheimer-Hendrickson procedure using various force fields described in the literature; the same fields and the minimum energy conformations were used in subsequent vibrational analyses to calculate the mean amplitudes of vibration for each minimum energy conformation of DTBC; these mean amplitudes and the corresponding internuclear distances were then used to calculate the theoretical electron diffraction radial distribution curves which were compared to the experimental curves. The results indicate that the conformational energies of all the minimum energy chair and non-chair forms of DTBC are very similar. In excellent agreement with this, the theoretical radial distribution curves of all minimum energy forms have to be mixed for a best fit to the experimental radial distribution curve. A least squares analysis of the mixture under the described conditions yields for 110 °C a composition of approximately one third chair and two thirds non-chair forms. The quality of the empirical conformational force fields has a definite influence on the reliability of these results.     

A robust force field based method for calculating conformational energies of charged drug-like molecules

The binding affinity of a drug-like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, then the molecule is unlikely to bind to its target. Determination of the global minimum energy conformation and calculation of conformational penalties of binding is a prerequisite for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic compounds generated by conformational analysis with modified electrostatics are good approximations of the conformational distributions predicted by experimental data and with molecular dynamics performed in explicit solvent. Finally the method is used to calculate conformational penalties for zwitterionic GluA2 agonists and to filter false positives from a docking study.     

Chair/Twist-Boat Energy Gap in Monocyclic, Conformationally Unconstrained Polyalkylcyclohexanes

A conformational search procedure (HUNTER), in combination with the MM3(92) program, was used for the exploration of the conformational hypersurface of alkyl-substituted cyclohexanes and for the calculation of their chair/twist-boat (TB) energy gap. The systems studied were conformationally unconstrained polyalkylcyclohexanes (alkyl = methyl, ethyl, isopropyl, and tert-butyl) possessing either geminal and/or vicinal arrangements of the alkyl groups, but differing in the number of alkyl substituents and in their relative disposition (i.e., cis or trans). The calculations indicate that in 1,1,3,3,5,5-hexaisopropylcyclohexane the TB is the lowest energy form. Modification of the cis,trans relationship of vicinal alkyl groups changes the chair/TB energy gap, and in the minimum energy conformation of cis,trans,trans-1,2,3,4-tetraisopropylcyclohexane (23c) and cis,syn,cis-1,2,4,5-tetraisopropylcyclohexane (31c) the cyclohexyl ring adopts a TB conformation. The tetrasubstituted systems cis,syn,cis-1,2-diisopropyl-3,4-dimethylcyclohexane (46), cis,syn,cis-1,4-diisopropyl-2,5-dimethyl-cyclohexane (47), and cis,trans,trans-1,2-diisopropyl-3,4-dimethylcyclohexane (41) are the least crowded monocyclic unconstrained cyclohexanes found in which the TB conformation is of lower energy than the chair form. The present study indicates that two methyls and two isopropyl substituents are sufficient for stabilizing the TB form of a cyclohexyl ring relative to the chair form.     

Combined vibrational,conformational and electron diffraction studies of 2,2,6-trimethylcyclohexanone

The molecular structure of 2,2,6-trimethylcyclohexanone was studied by electron diffraction in the vapor phase combined with auxiliary vibrational and conformational calculations, r_a = 1.535 ± 0.004 and r_a = 1.108 ± 0.015 were found for the average C-H and C-C bonds, respectively, from data taken at both the Oslo and Arkansas electron diffraction units. Five local conformational energy minima (2 rigid (chair) and 3 flexible (boat) ones) were found for the molecule. Data analysis revealed that, at 70° C, the vapors of the compound contained essentially one conformer in a chair form with two of the three methyl-substituents in equatorial positions. Molecular mechanics results based on different force fields taken from the literature were compared, and found to be in fair agreement.     

Structural and spectroscopic properties of trans-dichlorobis(2,2-dimethyl-1,3-diaminopropane)chromium(III) chloride

The structure of trans-[CrCl(2)(Me(2)tn)(2)]Cl (Me(2)tn=2,2-dimethylpropane-1,3-diamine) has been determined by a single-crystal X-ray diffraction study at 150K. The analysis reveals that there are two independent Cr(III) complex cations in the structure, one with crystallographic inversion symmetry and the other with two-fold rotation symmetry, which are conformational isomers of each other. In both conformations, the chromium atom adopts a distorted octahedral structure with the four nitrogen atoms of two Me(2)tn ligands occupying the equatorial plane and two chlorine atoms occupying trans-axial positions. The six-membered chelate rings are in stable chair conformations with N-Cr-N angles of 87.03(8) degrees and 88.99(8) degrees . The two chelate rings in the centrosymmetric complex cation 1 are anti, while those in the rotation-symmetric complex cation 2 are in syn conformations. The mean Cr-N and Cr-Cl bond lengths are 2.0922 and 2.3253 A, respectively. The infrared and UV-visible absorption spectra of trans-[CrCl(2)(Me(2)tn)(2)]Cl have also been measured. The resolved band maxima of the electronic d-d spectrum are fitted with a secular determinant for a quartet energy state of the d(3) configuration in a tetragonal field including configurational but neglecting spin-orbit coupling. It is confirmed that the nitrogen atoms of the Me(2)tn ligand have a strong sigma-donor character, but the chloro ligand has weak sigma- and pi-donor properties toward the chromium(III) ion.     

The Conformation of Cycloartenol Investigated by NMR and Molecular Mechanics

Cycloartenol ( 4 ), a natural plant sterol, was shown to be an effective membrane reinforcer; this was attributed to its conformation. We now present a conformational analysis of 4 by molecular modeling and NMR. Molecular modeling suggests that two conformations I and II coexist, differing mainly at the level of ring C, and of nearly equal energy, I and II each having ring A and B in a chair and half-chair conformation, respectively, with ring C 1,3-diplanar in I (solid-state structure as determined by X-ray crystallography) and in chair conformation in II . A complete assignment of the ¹H- and ¹³C-NMR spectra of 4 and the entire coupling network in rings A and B is determined by various modern NMR techniques. The conformation of rings A and B thus determined is in agreement with conformations I and II . Low-temperature NMR experiments show a fast equilibrium between two conformations, presumably I and II . It is concluded, therefore, that the cyclopropane ring of 4 produces a flexibility at the level of ring C which may be important for the membrane properties.     

Konformative Beweglichkeit Flexibler Ringsysteme—XIII: Untersuchungen mit Hilfe der Protonenresonanzspektroskopie die Konformation des Ungesättigten Siebenringes im Benzocyclohepten und in symmetrisch substituierten derivaten

The confromations of the unsaturated seven membered ring in 4,4,6,6-tetradeuterium-1,2-benzocycloheptene-(1) ( 1 ) and five benzocycloheptene derivatives were determined by NMR spectroscopy. For all investigated compounds at ?80°C only one conformer was present in detectable quantity. By analysis of the NMR data – molecular symmetry, coupling constants and chemical shift – it can be shown that the conformation is always the chair form. The free conformational enthalpy of both the other conformations with boat or twist form of the ring is for all six compounds more than 1.8 kcal/mole. The experimental results agree with those from model calculations: thus for benzocycloheptene, the 5,5-dimethyl derivative ( 2 ) and the 4,4,6,6-tetramethyl derivative ( 4 ) the lowest energy was found for the chair conformation; the second most stable conformations were found to be the boat for 1 and 4 , and the twist form for 2 .     

Analysis of vibrational spectra of 3-halo-1-propanols CH(2)XCH(2)CH(2)OH (X is Cl and Br)

The conformational stability and the three rotor internal rotations in 3-chloro- and 3-bromo-1-propanols were investigated by DFT-B3LYP/6-311+G and ab initio MP2/6-311+G, MP3/6-311+G and MP4(SDTQ)//MP3/6-311+G levels of theory. On the calculated potential energy surface twelve distinct minima were located all of which were not predicted to have imaginary frequencies at the B3LYP level of theory. The calculated lowest energy minimum in the potential curves of both molecules was predicted to correspond to the Gauche-gauche-trans (Ggt) conformer in excellent agreement with earlier microwave and electron diffraction results. The equilibrium constants for the conformational interconversion of the two 3-halo-1-propanols were calculated at the B3LYP/6-311+G level of calculation and found to correspond to an equilibrium mixture of about 32% Ggt, 18% Ggg1, 13% Tgt, 8% Tgg and 8% Gtt conformations for 3-chloro-1-propanol and 34% Ggt, 15% Tgt, 13% Ggg1, 9% Tgg and 7% Gtt conformations for 3-bromo-1-propanol at 298.15K. The nature of the high energy conformations was verified by carrying out solvent experiments using formamide ( epsilon=109.5) and MP3 and MP4//MP3 calculations. The vibrational frequencies of each molecule in its three most stable forms were computed at the B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecules.     

X-Ray Crystallographic and MO Studies on the Conformation of Corynoline and the Related Compounds

The crystal structure of (±)-corynoline ( 1 ) has been determined by X-ray diffraction methods. The rings B and C form the half-chair and the twist-half-chair conformations, respectively. The B/C ring conjunction exists in an anti-cis conformation, with a N …? H? O intramolecular H-bond. Conformational energy calculation by the CNDO/2 method show that the conformations of 1 , (+)-chelidonine ( 2 ), and their acetates, observed in crystal structures, are all in the one of total energy minimum.     

Why are silyl ethers conformationally different from alkyl ethers? Chair-chair conformational equilibria in silyloxycyclohexanes and their dependence on the substituents on silicon. The wider roles of eclipsing, of 1,3-repulsive steric interactions, and of attractive steric interactions

An NMR study of the diaxial/diequatorial chair equilibrium in a range of silylated derivatives of trans-1,4- and trans-1,2-dihydroxycyclohexane is reported and discussed with a view to explaining unusually large populations of chair conformations with axial substituents, noted previously for some monosilyloxycyclohexanes and in some silylated sugars. X-ray diffraction studies of three bis-triphenylsilyloxycyclohexanes are reported and show both axial and equatorial silyloxy groups with the exocyclic bonds eclipsed. Eclipsing is also suggested by molecular mechanics (MM3) calculations on such derivatives. Both axial and equatorial tertiary silyl groups have 1,3-repulsive interactions with whatever substituents or hydrogen atoms are at the two adjacent equatorial positions, and these are relieved by rotation toward the eclipsed conformation of the exocyclic C-O bond. The three substituents on silicon interact attractively with the nine atoms at the 3, 4, and 5-positions of the cyclohexane ring and calculations suggest that these stabilizing interactions are significantly greater in the axial than in the equatorial conformation. An equatorial C-OSiR(3) bond with one or two equatorial neighbors has a restricted potential energy well that becomes much broader when the bond is axial without any equatorial neighbors in the alternative chair. Adjacent silyl groups in the 1,2-disubstituted series interact in a stabilizing way overall in all conformations, this being particularly marked in the diaxial conformation of the more complex ethers. These factors lead to unusually large axial populations.     

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 computational investigation of the effect of the double bond on the conformations of seven membered rings

The effect of the presence of an exo- and/or an endo double bond on the geometry of seven membered rings has been investigated by a conformational analysis of methylenecycloheptane, cycloheptamine, borepane, and 4-, 3- and 2-cyclohepten-1-one by the B3LYP/6-311+G(d,p) and CCSD(T)/6-311+G(d,p) levels of theory. The results indicate that both methylenecycloheptane and cycloheptamine have low energy barriers with respect to pseudorotation and a broad potential well centred on the most symmetrical twist-chair conformation. Borepane shows similar characteristics, but with drastically different relative energy values. The introduction of an extra endo double bond in the conformationally flexible cycloheptanone, fixes the family of chair conformations to a single rigid form, but lowers the relative energy of the boat conformations to compete in stability with the former.     

The histamine H1-receptor antagonist binding site. Part I: Active conformation of cyproheptadine

Summary The active conformation of several histamine H₁-antagonists is investigated. As a template molecule we used the antagonist cyproheptadine, which consists of a piperidylene ring connected to a tricyclic system. The piperidylene moiety is shown to be flexible. The global minimum is a chair conformation but, additionally, a second chair and various boat conformations have to be considered, as their energies are less than 5 kcal/mol above the energy of the global minimum. Two semi-rigid histamine H₁-antagonists, phenindamine and triprolidine, were fitted onto the various conformations of cyproheptadine in order to derive the pharmacologically active conformation of cyproheptadine. At the same time, the active conformation of both phenindamine and triprolidine was derived. It is demonstrated that, within the receptor-bound conformation of cyproheptadine, the piperidylene ring most probably exists in a boat form.     

A Conformational Study on Silacyclohexane. Comparison of ab initio (HF,MP2), DFT,and Molecular Mechanics Calculations. Conformational Energy Surface of Silacyclohexane

The structures and relative energies for the basic conformations of silacyclohexane 1 have been calculated using HF, RI‐MP2, RI‐DFT and MM3 methods. All methods predict the chair form to be the dominant conformation and all of them predict structures which are in good agreement with experimental data. The conformational energy surface of 1 has been calculated using MM3. It is found that there are two symmetric lowest energy pathways for the chair‐to‐chair inversion. Each of them consists of two sofa‐like transition states, two twist forms with C₁ symmetry (twist‐C₁), two boat forms with Si in a gunnel position (C₁ symmetry), and one twist form with C₂ symmetry (twist‐C₂). All methods calculate the relative energy to increase in the order chair < twist‐C₂ < twist‐C₁ < boat. At the MP2 level of theory and using TZVP and TZVPP (Si atoms) basis sets the relative energies are calculated to be 3.76, 4.80, and 5.47 kcal mol^–1 for the twist‐C₂, twist‐C₁, and boat conformations, respectively. The energy barrier from the chair to the twisted conformations of 1 is found to be 6.6 and 5.7 kcal mol^–1 from MM3 and RI‐DFT calculations, respectively. The boat form with Si at the prow (C_s symmetry) does not correspond to a local minimum nor a saddle point on the MM3 energy surface, whereas a RI‐DFT optimization under C_s symmetry constraint resulted in a local minimum. In both cases its energy is above that of the chair‐to‐twist‐C₁ transition state, however, and it is clearly not a part of the chair‐to‐chair inversion.     

4,6‐Dimethyl‐2‐[(4‐phenylpiperidin‐1‐yl)methyl]isothiazolo[5,4‐b]pyridin‐3(2H)‐one and 4,6‐dimethyl‐2‐[(4‐phenyl‐1,2,3,6‐tetrahydropyridin‐1‐yl)methyl]isothiazolo[5,4‐b]pyridin‐3(2H)‐one

In the crystal structures of the title compounds, C₂₀H₂₃N₃OS, (II), and C₂₀H₂₁N₃OS, (III), significant differences occur in the conformation of, respectively, the phenylpiperidine and phenyltetrahydropyridine substituents at the 2‐position of the isothiazolopyridine system. The piperidine ring adopts a chair conformation, while the tetrahydropyridine ring assumes a half‐chair form. The phenylpiperidine and phenyltetrahydropyridine fragments exhibit different conformations resulting from the steric and conjugation effects in the phenyl ring, respectively. Theoretical calculations show that both conformations are energetically stable and correspond to a minimum of energy for the analyzed systems. The molecular packing in (II) is influenced by π–π interactions of the isothiazolopyridine systems, with a shortest centroid‐to‐centroid separation of 3.5843 (11) Å between pyridine rings. In the crystal structure of (III), the molecules are linked by C—H...O hydrogen bonds and C—H...π interactions.     

Dodecatwistarene Imides with Zigzag‐Twisted Conformation for Organic Electronics

1D nonplanar graphene nanoribbons generally have three possible conformers: helical, zigzag, and mixed conformations. Now, a kind of 1D nonplanar graphene nanoribbon, namely dodecatwistarene imides featuring twelve linearly fused benzene rings, was obtained by bottom‐up synthesis of palladium‐catalyzed Stille coupling and C?H activation. Single‐crystal X‐ray diffraction analyses revealed that it displays a zigzag‐twisted conformation caused by steric hindrance between imide groups and neighboring annulated benzene rings with the pendulum angle of 53°. This conformation is very stable and could not convert into other conformations even when heated up to 250 °C for 6 h. Despite of the highly twisted topology, organic field‐effect transistor based on it exhibits electron mobility up to 1.5 cm² V^?1 s^?1 after annealing.     

(3R,4S)-4-(4-Fluorophenyl)-3-hydroxymethyl-1-methylpiperidine: conformation and structure monitoring by vibrational circular dichroism.

Absorption and vibrational circular dichroism (VCD) spectra of the title compound, a common intermediate in synthesis of many pharmaceuticals, were measured and analyzed in order to determine its absolute configuration and prevailing conformations. The analysis was combined with a systematic conformer search based on relative energies as well as with comparison of experimental and computed NMR shifts. The spectra were interpreted on the basis of ab initio simulations. The results indicate that the compound adopts exclusively a chair conformation of the piperidine ring with all the fluorophenyl, hydroxymethyl, and methyl substituents attached in equatorial positions. A limited rotation of the hydroxymethyl group is most consistent with the observed VCD pattern. VCD parameters were found significantly more sensitive to conformational changes than absorption or NMR. Concentration dependence of the absorption spectra indicated aggregation in concentrated solutions, but involved hydrogen bonds probably do not influence molecular conformation.     

Gas-phase electron diffraction,vibrational spectroscopy,and quantum chemical studies of the molecular structure of 3,3-dimethyl-3-silathiane

The 3,3-dimethyl-3-silathiane molecule was studied by gas-phase electron diffraction and vibrational spectroscopy. The initial geometrical parameters and the force field were calculated by the B3LYP/6-311+G** method; the vibrational amplitudes of atomic pairs and vibrational corrections were calculated using the scaled B3LYP/6-311+G** force field. The molecular conformation was found to be a distorted chair with structural parameters close to the expected ones.