Theoretical conformational analysis of rutin

Abstract  

The structural properties of rutin were determined by using a computational multistep progression. In the first step a stochastic strategy based on a molecular mechanics calculation was adopted to obtain a preliminary screening of the low-energy rutin conformations. The most stable structures obtained by the random conformational search were used as a starting point for an Austin Model 1 (AM1) semiempirical optimization. After this treatment, 16 structures characterized by a more stable frontal in respect to back disposition of the glycosidic chain of rutin were identified. To validate the results found from the stochastic search a molecular dynamics simulation was carried out. The results evidenced the presence of a global minimum highly stabilized by a hydrogen bond between the hydroxyl in the 3′ position of the B ring and the endocyclic oxygen of the rhamnose unit followed by approximately 8 kJ mol⁻¹ less stable local minima with similar energy values. Finally, the reliability of the molecular model was confirmed by comparing the calculated electronic absorption spectrum with that measured on a methanolic rutin solution.     

Theoretical conformational analysis of divinyl selenide

Theoretical conformational analysis of divinyl selenide was performed in terms of the Møller-Plesset second-order perturbation theory (MP2/6-311G**). Angular distribution of the probability density of populations of its rotational conformers was determined by analysis of the rotational potential energy surface. Divinyl sulfide was found to exist as an equilibrium mixture of three conformers having essentially nonplanar structure; the major conformer is syn-s-cis-s-trans, and the two others are syn- and anti-s-trans-s-trans with higher energy.     

Theoretical conformational analysis of tripeptides with a glycine residue

Summary 1. The conformational states of glycine residues — R, B, L, P — in the low-energy forms of the tripeptides (I–III) are found with equal frequency.2. The conformations of the main chain in sections of protein with glycine residues correspond to the preferred forms of the tripeptide fragments (I–III).3. The close-, medium-, and long-range interactions in proteins do not contradict one another and exist at the favorable forms of the main chain.M. M. Shemyakin Institute of Bioorganic Chemistry, Academy of Sciences of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 631–637, September–October, 1975.     

Theoretical conformational analysis considering solvent effects

The conformational structure of some biologically important compounds (formamide, 1-methyl-1,4-dihydronicotinamide, and chlorocholine) was examined using quantum-chemical methods. For each of the systems studied a theoretical model (supermolecule approximation, classical continuum model, or hydration shell model) was selected to estimate the influence of solvents on the conformational structure.     

Theoretical conformational analysis of some hydroxyazoic dyes

The optimum structures of p-hydroxy azobenzene, 4-phenyl azo 1-naphthalene and 4-phenyl azo 1-napthol are determined theoretically using the quantum mechanical MO method PCILO. The conformational minima are obtained by simultaneous optimization of the geometric parameters. The conformers equilibria and their temperature dependence, suggested by experimental dipole moments results, are discussed on the basis of our PCILO calculations.     

Theoretical conformational analysis of unsaturated phospines and phosphinechalcogenides

A theoretical conformational analysis was performed for vinylphosphine CH₂=CHPH₂ and three vinylphosphinechalcogenides CH₂=CHPXH₂ (X = O, S, Se). According to the quantum-chemical calculations on the level of the second order perturbation theory MP2/6-311G** the prevailing conformations, their molar ratios, and relative energies were established for each compound. The analysis of the angular distribution of the probability density for the population of the rotational conformations calculated proceeding from the potential curves of the internal rotation made it possible to establish that each compound from this series existed as a mixture of two conformers, planar s-cis and twice degenerate orthogonal. The conformers transform into each other through the corresponding transition states whose nature was established as a result of the harmonic vibration analysis carried out in every case.     

Theoretical conformational analysis of substituted nitroethenes in solution

Theoretical conformational analysis of 1-nitro- and 1-bromo-1-nitro-2-(trichloromethyl)ethenes dissolved in methylene chloride and benzene was carried out by the B3LYP/6-31G* method. The calculated structures of these compounds were found to nicely fit experiment: Both in the gas phase and in solution, 1-nitro-(2-trichloromethyl)ethene is an E isomer, while its bromine-containing analog is a Z isomer.     

Theoretical conformational analysis of cyclic hexadepsipeptides. Enniatins

Chemistry of Natural Compounds - The spatial conformation of the “polar” form of enniatin B has been established. A conformation of the N1 type has been proposed for the...     

Theoretical conformational analysis of cyclic hexadepsipeptides. Enniatins

Conclusions The spatial conformation of the polar form of enniatin B has been established. A conformation of the N₁ type has been proposed for the nonpolar form.Institute of the Chemistry of Natural Compounds, Academy of Sciences of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 616–622, September–October, 1970.     

Theoretical studies of conformational analysis and intramolecular dynamic phenomena

Structural Chemistry - This review reports our computational studies of a variety of topics related to conformational analyses and intramolecular dynamic phenomena. Single and double bonds, open...     

Theoretical conformational analysis of the methylamide of N-acetyl-L-alanyl-L-prolyl-L-alanine. II

Summary 1. Spatial forms of Ac-L-Ala-L-Pro-L-Ala-NHMe with trans peptide bonds are the most preferred. Elongation of the peptide chain promotes the stabilization of the trans configuration of the tertiary amide group.2. In the structure of the compound investigated, the dominating role is played by the interaction of the neighboring residues.3. Of the six types of conformations of X-Pro-Y observed in proteins, the first four belong to the preferred forms of the Ac-L-Ala-L-Pro-L-Ala-NHMe molecule.M. M. Shemyakin Institute of Bioorganic Chemistry, Academy of Science of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 626–630, September–October, 1975.     

A simple lennard-jones model for computer simulation of conformational disordering in polymers

A simple generalized model is proposed to describe the phenomenon of conformational disordering in polymers. The model represents a two-dimensional system of flexible particles interacting through a modified Lennard-Jones potential. Monte Carlo simulation of the phase behavior of the model system shows that the model is quite adequate to describe all essential features inherent in the transition to the conformationally disordered state.