Conformational study of cis-1,4-di-tert-butylcyclohexane by dynamic NMR spectroscopy and computational methods. Observation of chair and twist-boat conformations

[reaction: see text] Low-temperature 13C NMR spectra of cis-1,4-di-tert-butylcyclohexane (1) showed signals for the twist-boat (1a) and chair (1b) conformations. 13C NMR signals were assigned to specific carbons based on the different populations, different symmetries (time-averaged C(2v) for 1a and time-averaged C(s) for 1b), and calculated chemical shifts (GIAO, HF/6-311+G*). In addition to slow ring inversion and interconversion of the chair and twist-boat conformations, slow rotation of the tert-butyl groups was found. Most of the expected 13C peaks were observed. Free-energy barriers of 6.83 and 6.35 kcal/mol were found for interconversion of 1a (major) and 1b (minor) at -148.1 degrees C. Conformational space was searched with Allinger's MM3 and MM4 programs, and free energies were obtained for several low-energy conformations 1a-c. Calculations were repeated with ab initio methods up to the HF/6-311+G* level. Molecular symmetries, relative free energies, relative enthalpies and entropies, frequencies, and NMR chemical shifts were obtained. A boat conformation (1d; C(2v) symmetry) was generated and optimized as a transition state by ab initio, MM3, and MM4 calculations.     

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.     

Comparative conformational analysis of 1,3-dioxane and 1,3-dithiane

It was shown by ab initio quantum-chemical approximations HF/6-31G(d) and MP2/6-31G(d)//HF/6-31G(d) that the conformational isomerization of 1,3-dioxane and 1,3-dithiane proceeded along common routes. The potential energy surface of both compounds contains six minima including the chair invertomers and enantiomeric flexible forms. They are separated by several potential barriers. It was established by molecular dynamics method that the flexible conformers at heating and keeping at 295–300 K transformed into each other and in the chair conformer.     

Conformational deformation of ring C in 14β-estra- 1,3,5(10) 15-tetraen-17-ones

High-field n.m.r. analysis of four 3-methoxy-14β-estra-1,3,5(10), 15-tetraen-17-ones provides evidence for conformational deformation of ring C to a twist-boat form in solution. These observations are supported by molecular mechanics (MM2) calculations, which predict that the ring C chair and ring C twist-boat conformers have similar steric energies, slightly favouring the latter. An X-ray crystal structure determination on 3-methoxy-14-methyl-14β-estra-1,3,5(10), 15-tetraen-17-one revealed that ring C does indeed adopt a twist-boat conformation in the solid state.     

Structure and conformational properties of 1,3,3-trimethyl-1,3-azasilinane: gas electron diffraction, dynamic NMR, and theoretical study

Structure and the conformational properties of 1,3,3-trimethyl-1,3-azasilinane have been studied. According to gas electron diffraction (GED), the molecule exists in a slightly distorted chair conformation with the N-Me group in equatorial position. High-level quantum chemical calculations excellently reproduce the experimental geometry. Employing variable temperature (1)H and (13)C NMR spectroscopy down to 103 K, the conformational equilibrium could be frozen and the barrier to ring inversion determined.     

Development of a molecular mechanics (MM2) force field for α-chlorosilanes

Molecular mechanics (MM2) parameters for silanes which have a Si-C-Cl fragment have been developed based on available experimental data and ab initio molecular orbital (MO) calculations. Molecular properties, mainly rotational barriers and geometries, of α-chlorosilanes have been studied using our new MM2 parameter set. Changes in the Si-C bond lengths and several bond angles of α-chlorosilanes due to the additional attachment of polar atom(s) have been investigated utilizing ab initio calculations. An electronegativity correction to both bond lengths and angles helps MM2 to reproduce results from ab initio calculations. The new force field has been applied to the conformational analysis of l-(chloromethyl)-1,2-dimethylsilacyclopentane, a model used in our studies of rearrangements of α-halosilanes.     

Conformational dynamics in nitrogen-fused azabicycles

Using molecular mechanics (MM3 force field)-based methodology, conformational dynamics have been studied for 1-azabicyclo[2.2.0]hexane, 1-azabicylo[3.3.0]octane, and 1-azabicylo[4.4.0]decane. Obtained conformational schemes describe the flexibity of these parent azabicyles as well as permit us to estimate conformational mobility in related N-fused systems. Quantum mechanics ab initio calculations have been used in order to check the reliability of molecular mechanics-provided estimates of relative energy of conformers. The previous dynamic NMR (DNMR) data have been reinterpreted for some polycyclic alkaloids.     

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site

A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).     

Formation of eight-membered ring β-keto lactones via the intramolecular trapping of hydroxy acylketenes

Eight-membered ring β-keto lactones were prepared from 2,2,6-trimethyl-4H-1,3-dioxin-4-one in three steps involving conjugate addition to α,β-unsaturated aldehydes or ketones, followed by conversion to an alcohol and thermolysis. The formation of these eight-membered rings involves the intramolecular trapping of a hydroxy acyl ketene intermediate and is facilitated by a suppressed ring strain and an unfavorable intramolecular hydrogen bond, which is suggested to favor the formation of oligomers. These aspects of the reaction were supported by molecular mechanics calculations.     

Alcohols,ethers, carbohydrates,and related compounds. III. The 1,2-dimethoxyethane system

Ethylene glycol, its dimethyl ether, and some related compounds have been studied using the MM4 molecular mechanics force field. The MM4 calculated structural and energetic results have been brought into satisfactory agreement with a considerable number of experimental data and MP2/6-311++G(2d,2p) ab initio calculations. The heats of formation of these compounds are also well calculated. The MM4 ethylene glycol conformations in particular are in good agreement, both geometrically and in terms of energy, with those from the ab initio calculations. The corresponding dimethyl ether is of special interest, because it has been suggested that the trans-gauche conformation is unusually stable due to the hydrogen bonding of a hydrogen on a methyl group with the more distant oxygen. It is shown in the present work that while this conformation is more stable than might have been expected, the energy is adequately calculated by MM4 without using any hydrogen bonding between the Cbond;H bond and the oxygen. If such hydrogen bonding occurs, it amounts to no more than about 0.5 kcal/mol in energy, and is too small to detect with certainty. Additionally, energetic relationships in trans-1,2-dimethoxycyclohexane, 1,3,5,7-tetraoxadecalin, and 3-methoxytetrahydropyran have been studied, and the calculated results are compared with experimental information, which is adequately reproduced.     

Calculations of molecular properties in hybrid coupled-cluster and molecular mechanics approach

We report benchmark calculations obtained with our new coupled-cluster singles and doubles (CCSD) code for calculating the first- and second-order molecular properties. This code can be easily incorporated into combined [Valiev, M.; Kowalski, K. J. Chem. Phys. 2006, 125, 211101] classical molecular mechanics (MM) and ab initio coupled-cluster (CC) calculations using NWChem, enabling us to study molecular properties in a realistic environment. To test this methodology, we discuss the results of calculations of dipole moments and static polarizabilities for the Cl2O system in the CCl4 solution using the CCSD (CC with singles and doubles) linear response approach. We also discuss the application of the asymptotic extrapolation scheme (AES) [Kowalski, K.; Valiev, M. J. Phys. Chem. A 2006, 110, 13106] in reducing the numerical cost of CCSD calculations.     

Conformational design for 13alpha-steroids

The diastereomeric 16-bromo- and 16-azido-17-alcohols 5-8, 11, 12, 16, and 17 and 17-ketones 3, 4, 9, and 10 of the 13alpha-estra-1,3, 5(10)-triene series were synthesized as precursors for biologically active compounds and chiral ligands for metal complexation. Conformational investigations of these and some other compounds via X-ray analysis and (1)H NMR spectroscopy show the existence of compounds with the classical steroid conformation (ring C chair, restricted conformation of ring D) and such with an atypical ring C twist-boat and a flexible ring D conformation. It could be shown that 17beta-substituents or flattening of the D-ring are responsible for the twist-boat conformation, whereas compounds containing a 17alpha-substituent or 17-keto group possess the classical conformation. By varying the substituents, compounds with either of these conformations can be intentionally synthesized. MO calculations confirmed the relative stability of the twist-boat conformation.     

Structure,conformation and NMR studies on 1,2-dioxane and halogen substituted 1,2-dioxane molecules

Molecular structure and conformational stability of chair and twist conformers of 1,2-dioxane and halogen substituted compounds of the 1,2-dioxane have been studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 1,2-dioxane, 3,6-difluoro, 3,6-dichloro, 3,3,6,6-tetrafluoro and 3,3,6,6-tetrachloro 1,2-dioxane compounds were optimized at HF, MP2, B3LYP and B3PW91 levels of theory by implementing 6-31G* basis set. To study the effect of polar medium, self-consistent reaction field theory is used to optimize the conformers at B3LYP/6-31G* level of theory. The geometrical parameters of chair and twist conformers have been discussed in the light of interaction between lone pair electrons present in the oxygen and substituted halogen atoms. The relative stability of the conformers have been studied using relative energy, maximum hardness principle and thermodynamical quantities. The 13C-NMR chemical shift study for carbon atoms in the title compounds are calculated and the results have been discussed.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package

Self-consistent charge density functional tight-binding (SCC-DFTB) is a semiempirical method based on density functional theory and has in many cases been shown to provide relative energies and geometries comparable in accuracy to full DFT or ab initio MP2 calculations using large basis sets. This article shows an implementation of the SCC-DFTB method as part of the new QM/MM support in the AMBER 9 molecular dynamics program suite. Details of the implementation and examples of applications are shown.     

A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene

MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Q(ij) and K(ij), whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of K(ij) extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s-cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted.     

Structures and stabilities of diacetylene-expanded polyhedranes by quantum mechanics and molecular mechanics

The structures, heats of formation, and strain energies of diacetylene (buta-1,3-diynediyl) expanded molecules have been computed with ab initio and molecular mechanics calculations. Expanded cubane, prismane, tetrahedrane, and expanded monocyclics and bicyclics were optimized at the HF/6-31G(d) and B3LYP/6-31G(d) levels. The heats of formation of these systems were obtained from isodesmic equations at the HF/6-31G(d) level. Heats of formation were also calculated from Benson group equivalents. The strain energies of these expanded molecules were estimated by several independent methods. An adapted MM3 molecular mechanics force field, specifically parametrized to treat conjugated acetylene units, was employed for one measure of strain energy and as an additional method for structural analysis. Expanded dodecahedrane and icosahedrane were calculated by this method. Expanded molecules were considered structurally in the context of their potential material applications.     

Synthesis,structural investigations,and DFT calculations on novel 3-(1,3-dioxan-2-yl)-10-methyl-10H-phenothiazine derivatives with fluorescence properties

Comparison studies on the acetalization of 10-methyl-10H-phenothiazine-carbaldehyde with 1,3-propanediol, or 2-substituted-1,3-propanediols, under conventional versus microwave assisted conditions and standard organic solvents versus water, were performed as an attempt toward more environmentally benign synthetic methods. New 3-(1,3-dioxan-2-yl)-10-methyl-10H-phenothiazine derivatives were obtained in high yields by azeotropic distillation of water and in moderate yields by microwave assisted synthesis in different solvents, including water under superheated conditions. The solvent influence upon stabilizing the key intermediates involved in the acetalization mechanism was assumed based on DFT calculations, which indicated a favorable enthalpy profile in water solvent. Structural investigations of the new compounds based on spectroscopic methods (NMR, FT-IR, UV–vis, and MS), were completed with molecular mechanics and semi-empirical DFT calculations, which supported an anancomeric chair conformation of the 1,3-dioxane ring with the phenothiazine substituent in the equatorial position and possible free rotation about the single bond linking the two heterocyclic units. The new compounds display daylight fluorescence characterized by remarkably large Stokes shifts determined by LE spectroscopy.     

CF3 Rotation in 3-(Trifluoromethyl)phenanthrene: Solid State 19F and 1H NMR relaxation and Bloch-Wangsness-Redfield theory

We have observed and modeled the 1H and 19F solid-state nuclear spin relaxation process in polycrystalline 3-(trifluoromethyl)phenanthrene. The relaxation rates for the two spin species were observed from 85 to 300 K at the low NMR frequencies of omega/2pi = 22.5 and 53.0 MHz where CF3 rotation, characterized by a mean time tau between hops, is the only motion on the NMR time scale. All motional time scales (omegatau < 1, omegatau approximately 1, and omegatau > 1) are observed. The 1H spins are immobile on the NMR time scale but are coupled to the 19F spins via the unlike-spin dipole-dipole interaction. The temperature dependence of the observed relaxation rates (the relaxation is biexponential) shows considerable structure and a thorough analysis of Bloch-Wangsness-Redfield theory for this coupled spin system is provided. The activation energy for CF3 rotation is 11.5 +/- 0.7 kJ/mol, in excellent agreement with the calculation in a 13-molecule cluster provided in the companion paper where the crystal structure is reported and detailed ab initio electronic structure calculations are performed [Wang, X.; Mallory F. B.; Mallory, C. W; Beckmann, P. A.; Rheingold, A. L.; Francl, M. M J. Phys. Chem. A 2006, 110, 3954].     

Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data

A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).