Method Of Conformational Analysis Research Articles

NMR spectra of carotenoporphyrins. Computer‐assisted conformational analysis

AbstractA computer‐assisted method of conformational analysis for porphyrin molecules bearing flexible side‐chains has been developed. The method utilizes the ring current‐induced chemical shift changes of the side‐chain protons which arise from the porphyrin macrocycle and any attached aryl rings. The treatment has been applied to a series of carotenoporphyrin molecules, which are important as models for a variety of photophysical processes in biological systems. Chemical shift data of sufficient accuracy for the conformational analysis were obtained from 500 MHz NMR experiments. The conformations of the carotenoporphyrins varied from extended ones with the carotenoid well away from the porphyrin ring to tightly folded species, depending on molecular constitution. The analytical method can be extended to other porphyrin‐based systems.

The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem

A new approach to the long-standing local minimum problem of molecular energy minimization is proposed. The approach relies upon a field of computer mathematics known as combinatorial optimization, together with methods of conformational analysis derived from distance geometry. The advantages over the usual numerical techniques of optimization are, first, that the algorithms derived are globally convergent, and second, that the mathematical problems involved are well-posed and suitable for study within the modern theory of computational complexity. In this paper we introduce the approach, and describe a computer program based on it.

Dynamics of Native Globular Proteins in Terms of Dihedral Angles

Problems are discussed that are associated with extension of the time-independent method of conformational energy analysis of biopolymers, in which only dihedral angles are treated as independent variables, to time dependent one. For molecules with small amplitudes of fluctuations internal motions of atoms due to variations of dihedral angles are shown to be defined with respect to a coordinate system which is defined by the Eckart's condition and is moving with the molecule. Computationally efficient and explicit expressions are given (i) for a coefficient matrix to convert small changes in dihedral angles to small atomic displacements from the mean positions, and (ii) for a coefficient matrix in the expression of the kinetic energy of internal motions in terms of first order time derivatives of variable dihedral angles.

Crystalline conformation and structure of lichenan and barley β-glucan

An investigation based on X-ray fiber diffraetion and conformational analysis methods has provided a proposed chain conformation and crystalline structure for lichenan, a poly β(1 → 3) cellotriose. The analysis of the fiber diagram of the hydrated form of lichenan led to a trigonal unit cell of dimension a = b = 9.92 Å and c (fiber axis) = 42.03 Å, with cellotriose as the asymmetric unit and six cellotriose residues per unit cell. A unit cell of the dry form is also trigonal with a = b = 9.36 Å and c = 42.03 Å. A right-handed threefold helix made up of three cellotriose residues was derived from a comparison of experimental helical parameters with isoenenergy conformational maps made by plotting dihedral angles ([Formula: see text], ψ) at the β(1 → 3) linkage. A virtual bond approach was also used to arrive at the proposed conformation which is stabilized by intramolecular hydrogen bonds between all carbohydrate units. The refinement of geometrical and packing parameters produced results consistent with an antiparallel arrangement of the two chains corresponding to a space group symmetry of P31. The naturally occurring copolysaccharides known as mixed (1 → 3) and (1 → 4) β-glucans from the cell walls of barley endosperm have been shown to crystallize in the same fashion as lichenan.

Conformational analysis and hydration models of copper threoninates and isoleucinates

The Consistent Force Field (CFF) method of conformational analysis was applied to ionic copper complexes with naturally occurring and allo-isomers of isoleucine and threonine, namely, [Cu(Thr) 2H −2] −2, (Cu(Ile)] +, and (Cu(Thr)] + Hydration stabilization by means of a hydration shell model, as well as the effect of ligated water, were also computed. The difference in stability between the complexes of naturally occurring and allo-isoleucine is in accordance with experimental data. The theoretical results on [Cu(Thr)] + complexes suggest a possible role of specific intramolecular interactions in determining the observed stability difference.

Stereochemical studies. XI. Equilibria between δ-hydroxy-acids and δ-lactones in aqueous tetrahydrofuran. Relative stabilities of isomeric δ-lactones

The equilibrium constants K′ for the hydrolysis of 13 δ-lactones to hydroxy-acids in 54% (mol/mol) aqueous tetrahydrofuran at 25 °C have been determined. The equilibrium constants for the isomerization of the five δ-lactones into their epimers, and for the isomerization of their hydroxy-acids into their epimers, have been calculated by the methods of conformational analysis. These calculated values are consistent with the experimental values of K′. Addition of methyl groups to a hydroxy-acid decreases K′ (the Thorpe–Ingold effect).

Applications of a new method of conformational analysis

A simple method of theoretical conformational analysis based on electrostatic repulsion and attraction is much faster than existing methods and seems capable of being widely applied even with real-time graphics systems.

Conformational analysis of the calcium--A23187 complex at a lipid--water interface.

A possible conformation of the complex formed by one calcium ion and two molecules of the ionophore A23187 at a simulated lipid--water interface was predicted by a variant method for conformational analysis. This method takes into account, in addition to the Van der Waals energy, electrostatic interaction, and torsional potential, the alteration of electrostatic forces attributable to changes in dielectric constant at the interface and the transfer energy for each part of the complex as it moves through the lipid-water interface. The most probable conformer was characterized by a two-fold axial symmetry that was maintained during transition to the hydrophobic bulk conformation. Minor changes in the interfacial structure were sufficient to achieve the configuration characteristic of the hydrophobic bulk phase.

Conformational analysis of cyclohexenes by a simple graphical method using a Karplus-type equation

A graphical method of conformational analysis is presented. Vicinal coupling constants in a given conformation are plotted as a function of the sum of the chemical shifts of the interacting protons. The method works for both flexible and rigid types of cyclic molecules.

A New Method for Conformational Analysis by Photoelectron Spectroscopy with Application to Alkyl-substituted Styrenes

Abstract A new method for molecular conformational analysis using photoelectron spectral data was developed and applied to alkyl-substituted styrenes as an example. The dihedral angle between the phenyl ring and the olefinic group planes, θ, in each molecule is evaluated by comparing the observed difference between the first and the third vertical ionization energies, ΔEiv1.3, with the empirically estimated ΔEiv1.3 vs. θ curve, the alkyl substituent effect being taken into account by the first order perturbation theory. The new method gives reasonable results consistent qualitatively with those given by other former methods.

Analyse conformationnelle a l'aide de la notation des angles de torsion X: Interprétation de la régiosélectivité d'ouverture des époxydes de composés bicycliques incorporant des cycles petits et moyens

Using the dynamic method of conformational analysis through the implementation of the torsion angle notation and applying the rules of distortion compatibility at the junction of fused rings, permits the interpretation or prediction of the regioselective opening of epoxides and analogous three-membered heterocycles of the halonium type fused to small and medium rings.

ChemInform Abstract: CONFORMATIONAL ANALYSIS BY PHOTOELECTRON SPECTROSCOPY

The conformation of organic molecules may be determined by means of photoelectron (PE) spectroscopy if there are orbital interactions present which depend on a dihedral angle. Straightforward application of the method requires that all ionization bands of interest can be assigned unambiguously and that inductive effects and secondary orbital interactions do not occur or can be accounted for appropriately. In many cases, this method complements conventional methods of conformational analysis. PE conformational analysis is particularly suited to compounds containing vicinal lone pairs of ..pi.. systems. 105 references, 10 figures, 2 tables.

Conformational Analysis by Photoelectron Spectroscopy

AbstractThe conformation of organic molecules may be determined by means of photoelectron (PE) spectroscopy if there are orbital interactions present which depend on a dihedral angle. Straightforward application of the method requires that all ionization bands of interest can be assigned unambiguously and that inductive effects and secondary orbital interactions do not occur or can be accounted for appropriately. In many cases, this method complements conventional methods of conformational analysis. PE conformational analysis is particularly suited to compounds containing vicinal lone pairs or π systems.

Conformational analysis of a snake neurotoxin by prediction from sequence, circular dichroism, and Raman spectroscopy

The secondary structure of the major neurotoxin from the sea snake Lapemis hardwickii was investigated by several methods of conformational analysis: structure prediction, circular dichroism, and laser Raman spectroscopy. From the primary structure, secondary structure prediction yielded two regions of β-sheet structure at residues 1–7 and 41–45. β-Turns were predicted at residues 14–17, 20–23, 30–33, 37–40, and 46–49. From the predictions, the toxin appears to be composed of approximately 20% β-sheet and 33% β-turn. The CD spectrum of the native toxin appears to be a hybrid of model spectra for β-sheet and β-turn proteins. The pH perturbation studies on the toxin observed by CD demonstrated that the toxin is a very stable molecule except at extremely high or low pH values. The Raman data indicated that the toxin contains both antiparallel β-sheet and β-turn structure. Using two methods of secondary structure quantitation from Raman spectra the molecule was calculated to contain 35% β-sheet from one method and 27% from the other. Overall, the various methods demonstrate that the toxin is composed of β-sheet and β-turn structure with little or no α-helix present. From the comparison of these different techniques appreciation can be gained for the necessity of several methods when identifying and quantitating secondary structure.

The quantitation of nuclear Overhauser effect methods for total conformational analysis of peptides in solution. Application to gramicidin S

The [1H:1H] nuclear Overhauser effects (NOE's) and spin-lattice relaxation times (T1's) are reported for the backbone protons of the decapeptide gramicidin S. Several methods for calculating interproton distances from these measurements are presented. Ratios of interproton distances were obtained from [1H:1H] NOE's and from the combination of [1H:1H]NOE'S and T1 values. Actual proton-proton distances were calculated from these ratios either by using the known distance between two geminal protons or distances derived from scalar coupling constants. The interproton distances calculated for gramicidin S are consistent with a II' beta-turn/antiparallel beta-sheet conformation.

Molecular orbitals from group orbitals. 5. Role of steric effects in the perturbational molecular orbital method of conformational analysis

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular orbitals from group orbitals. 5. Role of steric effects in the perturbational molecular orbital method of conformational analysisSaul Wolfe, David J. Mitchell, and Myung-Hwan WhangboCite this: J. Am. Chem. Soc. 1978, 100, 6, 1936–1938Publication Date (Print):March 1, 1978Publication History Published online1 May 2002Published inissue 1 March 1978https://doi.org/10.1021/ja00474a055RIGHTS & PERMISSIONSArticle Views98Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (367 KB) Get e-Alerts Get e-Alerts

CONFORMATIONS ANALYSIS OF SOME CYCLIC PEPTIDES USING DIFFERENTIAL N-METHYLATION

Abstract Partial N-methylation of peptides with CH3I–Ag2O in DMF constitutes a new potential method of conformational analysis. Reactivity of peptide NH′s with the methylating reagent reflects their degree of exposure to the solvent. The method was applied to the samples of micromolar quantities of a Gramicidin S derivative and two destruxins.

Theoretical conformational analysis by the positive core potential energy method

A simple combination of quantum mechanical and classical methods appears to lead to a new method for theoretical conformational analysis.

Conformational analysis of N,N‐diisopropylamides by combined use of n.m.r. lanthanide‐induced shifts and conformational energy calculations

AbstractA new method of conformational analysis has been developed, in which energy minimization calculations are combined with lanthanide‐induced shift data. First, exhaustive energy calculations are carried out on the free molecules in order to determine the conformations of lowest energy. Then, the coordinates of all low energy conformations or pairs of conformations are used in the pseudocontact shift equation for lanthanide‐induced shifts in order to find which of the theoretically obtained conformation(s) gives the best agreement with experiment. The molecules complexed to the lanthanide shift reagent were N,N‐diisopropylformamide (DIPF) and N,N‐diisopropylacetamide (DIPA). Two different lanthanide shift reagents were used, Eu(fod)3Fod is the anion of 1,1,1,2,2,3,3‐heptafluoro‐7,7‐dimethyl‐4,6‐octanedione‐d27. and Pr(fod)3, in order to check the validity of the method. Proton magnetic resonance spectra were taken at 6 °C in carbon tetrachloride solution. The principal conformation found was different for each amide. DIPF was found to exist as a mixture of I (39 mol%) and II (61 mol%) with Eu(fod)3, and a mixture of I (37%) and II magnified image (63%) with Pr(fod)3. DIPA was found to exist as a mixture of I (79%) and IV (21%) with Eu(fod)3 and a mixture of I (87%) and IV (13%) with Pr(fod)3. For both molecules, the two conformations of lowest computed energy were also the pair which gave the best fit to the lanthanide shift reagent data. The location of the principal magnetic axis of the complex was found to lie between 0° and 14° from the lanthanide atom–oxygen atom bond axis. The technique of combining lanthanide shift reagent data with energy calculations shows great promise in conformational analysis.

Nuclear magnetic resonance study of the conformations of atropine and scopolamine cations in aqueous solution

We have measured the 1H and 13C chemical shifts and 1H–1H coupling constants from the n.m.r. spectra of atropine and scopolamine cations. For both species, nuclei in symmetrical positions in the tropane ring shown non-equivalence because they experience different shielding effects from the aromatic substituent. We have estimated the different ring current shift contributions at the tropane ring nuclei for a wide range of conformations (varying the torsion angles ϕ2–ϕ5) and searched for the conformations which give the best fit to the measured chemical shift differences for the symmetrical pairs of nuclei. We find that the aromatic ring in atropine and scopolamine occupies approximately the same region of conformational space in both the crystal and solution states. In this special case where we are calculating several shielding differences (which can be measured accurately) attributed to ring current shifts this method of conformational analysis would be expected to give reliable results.