Conformational flexibility of longifolene

The flexibility of the bicyclo[2.2.1]heptane-based tricyclic bridged system in longifolene is analysed based on x-ray structural data. In this context, the molecular structure of three differently substituted longifolenes has been analysed. The highly substituentdependent conformation provides scope for the synthesis of a variety of commercially oriented products. NCL Communication Number 3459     

Conformational flexibility of six-membered dihydrocycles

The conformational flexibility of six-membered 1,4- and 1,2-dihydrocycles caused by a flattened shape of the minimum on the potential energy surface is discussed. The effect of the conformational flexibility of the rings on the physicochemical characteristics of compounds is considered. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2095–2105, December, 1997.     

Conformational flexibility and aromaticity of azanaphthalenes

Conformational flexibility of naphthalene and its different mono-and diaza analogues has been studied by MP2/6-31G(d, p) quantum chemical computations. It is shown that all molecules possess a considerable conformational flexibility. The out-of-plane deformation energy of both a bicyclic π-system on the whole and separate rings directly depends on the degree of aromaticity of the conjugated system. Effects of the amount and arrangement of nitrogen atoms on conformational features and aromaticity of the molecules considered were analyzed.     

Conformational flexibility of the twelve-membered siloxane ring

Conclusions The conformational analysis of the molecules of twelve-membered cis- and trans-2,8-dihydroxycyclohexasiloxanes showed that intramolecular dehydration with the formation of a bicyclic system is possible for the cis isomer with the approach of the OH groups on account of the large conformational flexibility of the ring. For the trans isomer this approach is only possible with cleavage of the bonds in the ring at the intermediate stages.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1871–1874, August, 1984.     

Conformational flexibility of 1,4-dihydroazine carbonyl derivatives

Summary The molecular geometry of 4-oxo derivatives of 1,4-dihydropyridine, 1,4-dihydropyrimidine, 1,4-dihydropyridazine, and 1,4-dihydro-1,3,5-triazine has been calculated by the semi-empirical quantum-chemical AM1 method. It could be shown that the dihydrocycle in these compounds is not conformationally rigid. Changing the angle between the endocyclic double bond planes ±15° causes less than 1 kcal/mol increase of energy.

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Konformative Flexibilität von 1,4-Dihydroazin-carbonyl-Derivaten (Kurze Mitt.)

Zusammenfassung Die molekulare Geometrie von 4-Oxo-Derivaten von 1,4-Dihydropyridin, 1,4-Dihydropyrimidin, 1,4-Dihydropyridazin und 1,4-Dihydro-1,3,5-triazin wurde mittels der semiempirischen quantenchemischen AM1-Methode berechnet. Es konnte gezeigt werden, daß der zweifach hydrierte Ring in diesen Verbindungen nicht starr ist. Eine Änderung des Winkels zwischen den Ebenen der endocyclischen Doppelbindungen um ±15° bewirkt eine Energieerhöhung von weniger als 1 kcal/mol.

     

Conformational flexibility of nickel(II) benziporphyrins

(1)H NMR spectra of three paramagnetic Ni(II) complexes of benziporphyrins have been investigated in a broad temperature range. For the m- and p-benziporphyrin complexes, the line widths of certain signals exhibit an unusual temperature dependence characteristic of a dynamic process. This behavior is interpreted in terms of an equilibrium in which one of the forms is present at a very small concentration and cannot be observed directly. For the benziporphodimethene complex, the two exchanging forms are present at comparable concentrations and can yield separate signals in the slow exchange limit. To account for the observed exchange process, a mechanism is proposed involving the motion of the phenylene moiety. This hypothesis is further explored with DFT modeling, which indicates that the postulated conformers are thermally accessible.     

Conformational flexibility of metalloporphyrins studied by density-functional calculations

Reliable energetic data on the conformational flexibility of organic molecules are important ingredients to better understand the adsorption of such molecules on solid surfaces. Herein, the conformational flexibility of the phenyl substituents in metallo tetraphenyl porphyrins (M-TPP, M = Zn, Co) and metallo tert-butyl tetraphenyl porphyrins (M-TTBPP, M = Zn, Co) has been studied in detail for the first time using density-functional methods. For each molecule, a relaxed two-dimensional potential energy surface scan has been calculated for the two angles describing the rotation and the out-of-plane bending of the phenyl substituents. The results quantify that the molecules are rather flexible close to the energetic minimum while more extreme twisting or tilting of the phenyl substituents results in high-energy deformations of the porphyrin core from planarity due to steric repulsions of adjacent hydrogen atoms.     

Conformational flexibility and structure of creatine kinase.

The structural flexibility of creatine kinase has been investigated with the covalent hydrophobic probe 2-[4'-(2"-iodoacetamido) phenyl] aminonaphthalene-6-sulfonic acid (IAANS) which reacts at vastly different rates with the two subunits to give a protein conjugate with fluorescence characteristic of reaction with a site in a hydrophobic cleft. Binding of purine nucleotides greatly enhances the probe fluorescence while pyrimidine nucleotides quench the fluorescence. Small anions bind to nucleotide-free creatine kinase near the location of the transferable phosphoryl group and quench both the IAANS fluorescence of modified creatine kinase and the tryptophan fluorescence of native creatine kinase. Chloride and nitrate non-competitively inhibit MgADP binding both with and without creatine. Fluorescence energy transfer demonstrates that the active sites of creatine kinase are well separated and become further apart after the nucleotide-induced conformational change.     

Conformational flexibility of 1,3-cyclohexadiene and its aza analogs

The conformational flexibility of 1,3-cyclohexadiene and its analogs — pyridine and pyrimidine derivatives— was studied by HF/6-31G** ab initio quantum chemical calculations. The potential surface calculations and normal vibration shape analysis show that the molecules exhibit two weakly coupled ring deformation modes. One of the modes may be described as rotation around the C(sp₃)-C(sp₂) bond leading to a transition state of the ring inversion process. The other mode involves flattening of the butadiene fragment and a loss of planarity for endocyclic double bonds without any pronounced changes in the conformation of the saturated part of the molecule. An accurate calculation of the ring inversion barrier demands inclusion of electron correlation effects. Translated fromZhurnal Strukturnoi Khimii, Vol. 41, No. 3, pp. 474-479, May-June, 2000.     

Conformational flexibility in hydrated sugars: the glycolaldehyde-water complex

Conformational flexibility in the smallest hydrated sugar, the glycolaldehyde-water complex, has been investigated in the gas phase by means of a combination of a microwave Fourier transform spectroscopy experiment in a supersonic molecular beam and ab initio quantum chemistry calculations. The water molecule inserts into glycolaldehyde using H-bonding selectivity: the two lowest energy conformations are stabilized by two intermolecular hydrogen bonds, and the next two by one intra- plus one intermolecular hydrogen bond. A dynamical flexibility associated with the two lowest energy conformations has been experimentally observed and accurately modeled with a two-dimensional potential energy surface involving the hydroxyl group and the free OH water group coordinates. The conclusions drawn from the role played in the conformational flexibility by the hydroxyl and carbonyl groups are extended to other carbohydrates and biomolecules.     

Conformational flexibility of the group B meningococcal polysaccharide in solution

To elucidate the role of secondary structure in the immune response against alpha(2-->8)-linked polysialic acid, the capsular polysaccharide of Group B meningococci, we have investigated its solution dynamics by using specific models of molecular motion and hydrodynamic modeling to interpret experimental NMR data. (13)C-[(1)H] NMR relaxation times and steady-state NOE enhancements were measured for two aqueous solutions of alpha(2-->8)-linked sialic acid polysaccharides. Each contained a unique distribution of polysaccharide chain lengths, with average lengths estimated at 40 or 400 residues. Models for rigid molecule tumbling, including two based on helical conformations proposed for the polysaccharide,(31) could not explain the NMR measurements. In general for these helices, the correlation times for their overall tumbling that best account for the NMR data correspond to polysaccharide chains between 9 and 18 residues in length, far short of the average lengths estimated for either solution. The effects of internal motions incorporated into these helices was modeled with an effective correlation time representing helix tumbling as well as internal motion. This modeling demonstrated that even with extreme amounts of internal motion, "flexible helices" of 25 residues or more still could not produce the NMR measurements. All data are consistent with internal and segmental motions dominating the nuclear magnetic relaxation of the polysaccharide and not molecular tumbling. Statistical distributions of correlation times have been found specifically for the pyranose rings, linkage groups, and methoxy groups that can account for the measured relaxation times and NOE enhancements. The distributions suggest that considerable flexibility attends the polysaccharide in solution, and the ranges of motional frequencies for the linkage groups and pyranose rings are comparable. We conclude that the Group B meningococcal polysaccharide is a random coil chain in solution, and therefore, does not have antigenic epitopes dependent upon a rigid, ordered conformation.     

Conformational flexibility of pyrimidine ring in adenine and related compounds

The structural non-rigidity of aromatic pyrimidine rings in adenine and selected related compounds has been investigated by quantum chemical non-empirical methods of calculation at the MP2 and DFT levels of theory. The results of the calculations demonstrate that the pyrimidine ring possesses a notable degree of conformational flexibility despite its aromatic character. The transition of the heterocycle from a planar equilibrium geometry to a non-planar structure with an endocyclic torsion angle of ±20° results in an energy increase of less than 2.8 kcal/mol. An analysis of the population of ground and excited vibrational levels for the lowest out-of-plane vibration of the ring indicates that in adenine 45% of the molecules have a non-planar pyrimidine ring with relevant torsion angle up to ±17° at any moment of time.     

Conformational Transmission in DNA

Abstract

This poster presents our recent results on DNA dimers in which a stable trigonal bipyramidal pentacoordinated phosphorus (P^v) structure forms the internucleoside linkage. Conformational analysis of the systems 1-4 with 300 and 500 ¹H NMR has shown that the P^v structure results in a distorted conformation of the backbone structuE (1).     

Conformational flexibility and pseudosymmetric aggregation in a betainium salt hydrate

Structural Chemistry - The cation of 3-(trimethylammonium)-benzoic acid exhibits a considerable conformational flexibility connected to the orientation of carboxyl group, coupled to the proton...     

Conformational changes of non-B DNA

In contrast to B-DNA that has a right-handed double helical structure with Watson-Crick base pairing under the ordinary physiological conditions, repetitive DNA sequences under certain conditions have the potential to fold into non-B DNA structures such as hairpin, triplex, cruciform, left-handed Z-form, tetraplex, A-motif, etc. Since the non-B DNA-forming sequences induce the genetic instability and consequently can cause human diseases, the molecular mechanism for their genetic instability has been extensively investigated. On the contrary, non-B DNA can be widely used for application in biotechnology because many DNA breakage hotspots are mapped in or near the sequences that have the potential to adopt non-B DNA structures. In addition, they are regarded as a fascinating material for the nanotechnology using non-B DNAs because they do not produce any toxic byproducts and are robust enough for the repetitive working cycle. This being the case, an understanding on the mechanism and dynamics of their structural changes is important. In this critical review, we describe the latest studies on the conformational dynamics of non-B DNAs, with a focus on G-quadruplex, i-motif, Z-DNA, A-motif, hairpin and triplex (189 references).     

Conformational flexibility in open chain molecules: chiral and achiral alkanes

Conformational partition functions of chiral and achiral alkanes have been computed by using a continuum approach (instead of rotational isomeric state approximations). The accessible conformational space per bond depends upon the structure of the compound and is only in the range of 5–13% of the maximum accessible range. In order to partly overcome the intrinsic ambiguity of the term “conformational flexibility”, the distinction between number flexibility (a measure of the number of accessible energy minima) and space flexibility (a measure of the total allotted space) is proposed. Further, the conformational versatility of each bond of a molecule is evaluated in terms of the a priori probability density function of that bond, and it is shown that the use of this function permits a comparison of the relative conformational flexibilities of the individual bonds, which is particularly useful for molecules having more than two rotation angles (where the conventional energy maps cannot be used). Optical rotations are calculated for a series of chiral alkanes by combining the continuum approach for conformational analysis and a recent optical activity calculation scheme. Contributions of single bonds to the molar optical rotation are evaluated and discussed. The influence of temperature upon conformational and chiral properties is evaluated.     

Conformational flexibility in 2,2'-Dioxybiphenyl-chloro-cyclotetraphosphazenes and its relevance to polyphosphazene analogues

The reaction of the cyclotetraphosphazene, [N4P4Cl8], with the difunctional reagent, 2,2'-biphenol, in the presence of potassium carbonate in acetone produced the spiro-substituted derivatives, 2,2'-dioxybiphenylhexachlorocyclotetraphosphazene, bis(2,2'-dioxybiphenyl)tetrachloro-cyclotetraphosphazene, and tris(2,2'-dioxybiphenyl)dichlorocyclotetraphosphazene. Both cis and trans geometrical isomers of the bis compound are observed. Although chromatographic separation of these was unsuccessful, a sample of the trans isomer was obtained by fractional crystallization. The compounds all show non-first-order 31P NMR spectra which were simulated to extract the spectral parameters. Single-crystal X-ray structures of both the trans bis and the tris compounds show that the cyclophosphazene rings exhibit conformational flexibility which gives rise to different crystalline forms being obtained from the same solvent systems. Crystals of trans-bis(2,2'-dioxybiphenyl)tetrachloro-cyclotetraphosphazene were obtained in two different space groups: Pnna (orthorhombic) and P21/n (monoclinic). In the orthorhombic structure, the dominant (72%) conformation of one phosphazene ring is a chair form, and the other (28%) resembles a boat. While for the monoclinic structure, the ring is virtually flat with an oval shape. In both cases the dioxybiphenyl groups are found in R and S configurations in the same molecule and are pi stacked in columns (Pnna) or involved in pi-pi or pi-H interactions (P21/n), thus anchoring the phosphorus atoms of the cyclotetraphosphazenes but still allowing flexibility in the ring conformations. Three crystalline modifications of tris(2,2'-dioxybiphenyl)dichloro-cyclotetraphosphazene were obtained: two in space group P (triclinic), which contained two molecules of dichloromethane in the unit cell, and one solvent-free form in space group P21/n (monoclinic). The cyclophosphazene rings exhibit puckered conformations with the trans-dioxybiphenyl moieties having opposing RS or SR conformations. DFT calculations were carried out on each of the phosphazene ring conformations in trans-bis(2,2'-dioxybiphenyl)tetrachlorocyclotetraphosphazene identified from the X-ray diffraction analysis. It is concluded that intermolecular interactions (i.e., pi-pi or pi-H) between the dioxybiphenyl groups is a factor that modifies the nature of the potential energy surface between the different conformers. The flexibility of the phosphazene ring is supported computationally through the calculated low-energy barriers and experimentally through the highly disordered phosphazene ring conformations observed in the solid state. The results on 2,2'-dioxybiphenyl-substituted cyclotetraphosphazenes provide evidence that microcrystalline domains in their 2,2'-dioxybiphenyl-substituted polyphosphazene analogues will be generated by similar pi-pi and pi-H interactions.     

Conformational flexibility and the mechanisms of allosteric transitions in topologically similar proteins

Conformational flexibility plays a central role in allosteric transition of proteins. In this paper, we extend the analysis of our previous study [S. Tripathi and J. J. Portman, Proc. Natl. Acad. Sci. U.S.A. 106, 2104 (2009)] to investigate how relatively minor structural changes of the meta-stable states can significantly influence the conformational flexibility and allosteric transition mechanism. We use the allosteric transitions of the domains of calmodulin as an example system to highlight the relationship between the transition mechanism and the inter-residue contacts present in the meta-stable states. In particular, we focus on the origin of transient local unfolding (cracking), a mechanism that can lower free energy barriers of allosteric transitions, in terms of the inter-residue contacts of the meta-stable states and the pattern of local strain that develops during the transition. We find that the magnitude of the local strain in the protein is not the sole factor determining whether a region will ultimately crack during the transition. These results emphasize that the residue interactions found exclusively in one of the two meta-stable states is the key in understanding the mechanism of allosteric conformational change.