Conformational analysis by energy embedding

The distance geometry approach to conformational calculation has been shown to be very effective at producing large molecular structures satisfying many given, long-range constraints on the interatomic distances. I now present a significant extension of the method that handles strictly geometric constraints as well as before while also locating conformers of very low energy. The main feature of the algorithm is a projection of the molecule from a low energy conformation in a high dimensional space to three dimensions in such a way as to perturb the energy as little as possible. Tests of the method on very small systems with simple energy functions completely explored by independent means show that the global minimum of energy is sometimes attained. In every case the final energy is very low, and geometric constraints are completely satisfied.     

Conformational analysis by scaled energy embedding

Distance geometry has been used for some years to find conformations of molecules consistent with given bounds on the interatomic distances. A recent extension of the method, called energy embedding, enforces the geometric constraints as before, but also biases the results toward low-energy structures. Now a significant improvement on energy embedding is presented, which is less dependent on local optimization for satisfying the geometric constraints. Tests on very small systems with well understood energy functions show that the global minimum energy value is often attained, and geometric constraints are always satisfied.     

Conformational analysis: a new approach by means of chemometrics

In conformational analysis, the systematic search method completely maps the space but suffers from the combinatorial explosion problem because the number of conformations increases exponentially with the number of free rotation angles. This study introduces a new methodology of conformational analysis that controls the combinatorial explosion. It is based on a dimensional reduction of the system through the use of principal component analysis. The results are exactly the same as those obtained for the complete search but, in this case, the number of conformations increases only quadratically with the number of free rotation angles. The method is applied to a series of three drugs: omeprazole, pantoprazole, lansoprazole-benzimidazoles that suppress gastric-acid secretion by means of H+, K+-ATPase enzyme inhibition.     

Search for strategies by computer: the CONAN approach. Application to steroid and taxane frameworks

We describe the CONAN (CONnectivity ANalysis) program the aim of which is to search for strategies by simplification of the target skeleton by different types of disconnection. The options available for the disconnections of the target are: add one bond, delete one or two bonds, search for linear precursors, for convergent strategies, for precursors containing a given number of rings and linear chains, and then disconnection of rings by formal [x+y] reaction types like [2+2], [4+2], etc. Taxane and steroid skeletons have been studied. CONAN runs on PC's microcomputers.     

Conformational analysis of lipid molecules by self-organizing maps

The authors have studied the use of the self-organizing map (SOM) in the analysis of lipid conformations produced by atomic-scale molecular dynamics simulations. First, focusing on the methodological aspects, they have systematically studied how the SOM can be employed in the analysis of lipid conformations in a controlled and reliable fashion. For this purpose, they have used a previously reported 50 ns atomistic molecular dynamics simulation of a 1-palmitoyl-2-linoeayl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer and analyzed separately the conformations of the headgroup and the glycerol regions, as well as the diunsaturated fatty acid chain. They have elucidated the effect of training parameters on the quality of the results, as well as the effect of the size of the SOM. It turns out that the main conformational states of each region in the molecule are easily distinguished together with a variety of other typical structural features. As a second topic, the authors applied the SOM to the PLPC data to demonstrate how it can be used in the analysis that goes beyond the standard methods commonly used to study the structure and dynamics of lipid membranes. Overall, the results suggest that the SOM method provides a relatively simple and robust tool for quickly gaining a qualitative understanding of the most important features of the conformations of the system, without a priori knowledge. It seems plausible that the insight given by the SOM could be applied to a variety of biomolecular systems and the design of coarse-grained models for these systems.     

Conformational analysis of tetraarylethanes

NMR evidence establishes that both diastereomers of 1,2-diphenyl-1,2-bis(4-pyridyl)ethane (2), identified by optical resolution of the racemic form, exist predominantly in the anti conformation. Furthermore, empirical force field calculations show that the gauche conformer of 1,1,2,2-tetrakis(2,6-dimethylphenyl)ethane (3) is less stable by ca. 10 $\text{kcal}\text{mol}$ than the anti structure. It thus appears that neither polar effects nor steric congestion are effective in reversing the marked preference of 1,1,2,2-tetraphenylethane (1) and other unclamped tetraarylethanes for an anti ground state. In contrast, as predicted by empirical force field calculations and confirmed by X-ray and NMR evidence, the ground state structure of 9,9'-bifluorenyl (4) is gauche. The conformational behavior of 1–4 is discussed in terms of the intramolecular aryl ring stacking in clamped and unclamped tetraarylethanes.     

Conformational analysis of cinnamanilides

The conformational analysis of cinnamanilides has been carried out using IR spectroscopy. All the anilides studied were found to exist as equilibrium mixtures ofs-cis ands-trans forms in benzene. Thes-cis form was predominant over thes-trans in all the anilides except in thep-nitro anilide in which thes-trans form was predominant. The relative stabilities of the conformers were found to depend upon the electrostatic repulsions between the anilide nitrogen and the β-carbon atom in thes-trans form and those between the π-electrons of the C=O and C=C bonds in thes-cis form.     

Conformational analysis of chiral helical perfluoroalkyl chains by VCD

Vibrational circular dichroism (VCD) technique successfully revealed the absolute configuration of the biased helix of perfluoroalkyl chains in solution with the aid of theoretical calculations, which was supported by an X-ray crystallographic study.     

Conformational analysis of colchicine and isocolchicine by molecular mechanics

The structures of isocolchicine ( ) and colchicine ( ) have been calculated using the MMX routine. The low energy conformations for isocolchicine and colchicine fit well with x-ray crystallographic data. The B ring atropisomer of isocolchicine, which can be spectroscopically observed, is calculated to be <1 kcal/mole higher in energy than . The boat-boat inversion conformer of colchicine, which has been predicted to be important in the binding of to tubulin, is also calculated. The B ring geometry of this isomer does not differ to the extent previously predicted.     

Conformational analysis of dimethylmethylphosphonate

The results of a CNDO/2 conformation analysis on dimethylmethylphosphonate are reported. Six stable conformers were found; their relative stabilities can be understood in terms of steric hindrance and gauche effect. Calculated barriers to internal rotation around P—O and O—C bonds are tabulated.     

Conformational analysis—CXIII : The isomeric cyclooctadienes

1,3-Cyclooctadiene, and 1,4- and 1,5-isomers were studied by the force field method. The former is calculated to be a mixture of two conformations, one of which has a C₂ axis, and one is irregular (C₁). There are for the 1,4-isomer two conformations, a boat-boat and a boat-chair, both of which have C_s symmetry. The 1,4-isomer is substantially all in the boat-chair conformation, while the 1,5-isomer is known to be preferentially a twist-boat (C₂) conformation. The calculations indicate the 1,3-isomer is much more stable, followed in turn by the 1,4- and the 1,5. An experimental measurement of the equilibrium between the isomers was also made, and is in semi-quantitative agreement with the calculations.     

Conformational analysis—XXI : H NMR Conformational Study of Alkyl-Substituted 2-Oxo-1,3,2-Dioxathianes

2-Oxo-1,3,2-dioxathiane and all methyl- and several alkyl-substituted 2-oxo-1,3,2-dioxathianes were prepared for a ¹H NMR conformational study. The conformational energy of the axial SO group in CCl₄, - ΔG^θ_SO = 14.8±0.3kJ mol^?1, was determined by chemical equilibration of the epimeric cis-4,6-dimethyl derivatives and it was found to decrease with the increasing solvent polarity. The conformational equilibria of alkyl-substituted derivatives were solved and the proportions of the conformers estimated using ¹H NMR chemical shifts, vicinal coupling constants and in three cases also dipole moments. The configurational interactions in the C₄C₅C₆ moiety are close to the corresponding values of 1,3-dioxanes.     

Conformational analysis of double-helical polynucleotides

The intramolecular interaction energy of the regular double-helical polynucleotide as a function of variables that determine the mutual position of base pairs and sugar pucker was calculated using atom–atom potentials. The calculations showed the existence of two valley-like regions with minimal values on the energetic surface. One of them corresponds to the A family of nucleic acids, the other to the B family. The points that correspond to the models constructed by means of x-ray data are placed in a conformational space near the lines that describe the position of the bottom of the valleys.     

Conformational analysis of polysilanes by the empirical force field method

Empirical force field (EFF) parameters have been developed for molecules containing Si-Si bonds. These parameters have been adjoined to those of a standard EFF and the extended force field has been used to calculate structures and relative conformational energies for a variety of acyclic and cyclic catenated polysilanes.     

Conformational analysis of some ortho-hydroxyazoic dyes by the PCILO method

The quantum mechanical MO method PCILO is used to perform a detailed conformational analysis of ortho-hydroxyazobenzene and 1-phenyl azo 2-napthol. Several energy minima are obtained for each compound, after a simultaneous optimization of the main geometric parameters. Comparison is made with the corresponding para compounds. The calculated results are discussed in relation to the available experimental data.     

Conformational analysis by UV spectroscopy: the decisive contribution of environment-induced electronic Stark effects

UV chromophores are frequently used as probes of the molecular structure. In particular, they are sensitive to the electric field generated by the molecular environment, resulting in the observation of Stark effects on UV spectra. While these environment-induced electronic Stark effects (EI-ESE) are already used for conformational analysis in the condensed phase, this work explores the potential of such an approach when performed at much higher conformational resolution in the gas phase. By investigating model alkali benzylacetate and 4-phenylbutyrate ion pairs, where the electric field applied to the phenyl ring is chemically tuned by changing the nature of the alkali cation, this work demonstrates that precise conformational assignments can be proposed based on the correlation between the conformation-dependent calculated electric fields and the frequency of the electronic transitions observed in the experimental UV spectra. Remarkably, the sole analysis of Stark effects and fragmentation patterns in mass-selected UV spectra provided an accurate and complete conformational analysis, where spectral differences as small as a few cm⁻¹ between electronic transitions were rationalized. This case study illustrates that the identification of EI-ESE together with their interpretation at the modest cost of a ground state electric field calculation qualify UV spectroscopy as a powerful tool for conformational analysis.

The correlation between experimental electronic transitions and calculated electric fields leads to precise conformational assignments and opens up the possibility of interpreting electronic spectra in a quantitative manner at the wavenumber scale.     

Conformational analysis of rigid enol-ethers by proton nuclear magnetic resonance

Z,E isomers of rigid enol-ethers were studied by proton nuclear magnetic resonance. As with oximes, it was found that the chemical shift difference (Δδ=δ_z?δ_E) for the protons α to the function in question depends on the dihedral angle between the C_α? H and C?C bonds. This phenomenon can be explained by an electric field effect and not by a magnetic anisotropy effect. The present study has allowed the derivation of values of the volume magnetic susceptibility and the product of b×the dipole moment for the C? O bond.