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PubMed1997

Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu): synthesis and biophysical studies of Gly-Nleu-Pro sequences by circular dichroism and optical rotation.

Single-chain peptide-peptoid structures, Ac-(Gly-Nleu-Pro)n-NH2 (n = 3, 6, and 10) and (Gly-Nleu-Pro)n-NH2 (n = 1 and 9), and template-assembled collagen analogs, KTA-[Gly-(Gly-Nleu-Pro)n-NH2]3 (n = 3 and 6; KTA represents cis,cis-1,3,5-trimethylcyclohexane-1,3, 5-tricarboxylic acid, also known as the Kemp triacid; Nleu denotes N-isobutylglycine), were prepared by solid-phase peptide synthesis methods. Biophysical studies using circular dichroism (CD) and optical rotation measurements show that these collagen analogs form triple-helical conformations when the chain is longer than a critical length. Unlike collagen-based structures composed of Gly-Pro-Hyp and Gly-Pro-Nleu sequences, results reveal that the presence of a positive CD peak between 220 and 225 nm is indicative of triple-helical conformations for these collagen-based structures composed of Gly-Nleu-Pro sequences. Results also indicate that the Gly-Nleu-Pro sequence possesses a higher triple-helical propensity than the Gly-Pro-Nleu sequence as demonstrated by the higher melting temperatures, the faster triple-helix folding, and the lower minimum concentration necessary to detect triple-helicity for the single-chain structures. Therefore, we conclude that the Nleu residue in the second position of the trimeric repeat is more effective in inducing triple-helix formation than Pro in the same position.

Amino Acid Sequence↗
PubMed1996

Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu): synthesis and biophysical studies of Gly-Pro-Nleu sequences by circular dichroism, ultraviolet absorbance, and optical rotation.

A peptoid residue N-isobutylglycine (Nleu) was introduced as a proline surrogate in collagen-like triple helical structures. A series of single chain and template-assembled collagen-based peptide-peptoid structures composed of Gly-Pro-Nleu sequences were prepared by solid-phase segment condensation methods. Both a synthetic route in solution and a solid phase method were employed to couple the KTA (cis,cis-1,3,5-trimethylcyclohexane-1,3,5-tricarboxylic acid, also known as the Kemp triacid) based template, KTA-(Gly-OH)3, to peptide-peptoid chains. Biophysical studies using CD, uv absorbance, and optical rotation measurements demonstrated that these compounds form triple-helical structures when the chains are longer than critical lengths. Results from melting curve measurements indicated that the Gly-Pro-Nleu sequence is comparable to the Gly-Pro-Pro sequence in stabilizing a triple-helical conformation. The KTA-based template stabilized triple-helical structures as can be seen by the increased melting temperatures as compared to equivalent single chain molecules. In addition, the template reduced the minimum chain length necessary to form a triple helix from six to only three trimer repeats.

Biophysical Phenomena↗
PubMed2001

High-performance liquid chromatography applications of optical rotation detection with compensation for scattering and absorbance at the laser wavelength.

Use of instrumentation developed to enable simultaneous monitoring of optical rotation (OR) and transmittance allows OR measurements to be made in the presence of high levels of absorbance, scattering or other effects that change the intensity of the plane-polarised light at the photodiode detector. This extends the application of OR detection to areas where it was previously difficult. Examples of the application of high-performance liquid chromatography (HPLC) with the improved OR detector include (i) the analytical scale separation of fructose and sucrose and (ii) the semi-preparative separation of enantiomers of warfarin and Trögers base. A signal-to-noise improvement of up to 150% is found when comparing signals with and without correction for transmittance changes. The improved OR detector has been used in series with a UV detector and the system shown to be suitable for on-line measurement of peak purity in separations using a chiral column under overload conditions.

Chromatography, High Pressure Liquid↗
PubMed2006

Determination of absolute configuration using density functional theory calculations of optical rotation and electronic circular dichroism: chiral alkenes.

In principle, the absolute configuration (AC) of a chiral molecule can be deduced from its optical rotation (OR) and/or its electronic circular dichroism (ECD). In practice, this requires reliable methodologies for predicting OR and ECD. The recent application of ab initio time-dependent density functional theory (TDDFT) to the calculation of transparent spectral region OR and ECD has greatly enhanced the reliability with which these phenomena can be predicted. TDDFT calculations of OR and ECD are being increasingly utilized in determining ACs. Nevertheless, such calculations are not perfect, and as a result, ACs determined are not 100% reliable. In this paper, we examine the reliability of the TDDFT methods in the case of chiral alkenes. Sodium d line specific rotations, [alpha]D, are predicted for 26 conformationally rigid alkenes of known AC, ranging in size from 5 to 20 C atoms, and with [alpha]D values in the range of 0-500. The mean absolute deviation of predicted [alpha]D values from experimental values is 28.7. With one exception, beta-pinene, the signs of [alpha]D are correctly predicted. Errors in calculated [alpha]D values are approximately random. Our results define a "zone of indeterminacy" within which calculated [alpha]D values cannot be used to determine ACs with >95% confidence. TDDFT ECD spectra are predicted for eight of the alkenes and compared to experimental spectra. Agreement ranges from modestly good to poor, leading to the conclusion that TDDFT calculations of ECD spectra are not yet of sufficient accuracy to routinely provide highly reliable ACs. TDDFT OR calculations for two conformationally flexible alkenes, 3-tert-butylcyclohexene and trans-4-carene, are also reported. For the former, predicted rotations are incorrect in sign over the range 589-365 nm. It is possible that the AC of this molecule has been incorrectly assigned.

Journal Article↗
PubMed1997

Optical rotation of the second harmonic radiation from retinal in bacteriorhodopsin monomers in Langmuir-Blodgett film: evidence for nonplanar retinal structure.

We observed optical rotation of the plane of polarization of the second harmonic (SH) radiation at 532 nm (in resonance with the retinal absorption) generated in reflection geometry in Langmuir-Blodgett film of bacteriorhodopsin (bR). The analysis of the experimental data showed that this effect arises from the nonvanishing contribution of the antisymmetrical part of the hyperpolarizability tensor. This requires that the dipole moment of the resonant electronic transition, the change of the dipole moment upon electronic excitation, and the long axis of the retinal not be coplanar. Such conditions are satisfied only if the retinal has a nonplanar geometry, a conclusion that could lend support to the heterogeneity model of the origin of the biphasic band shape of the linear CD spectrum of the retinal in bR. On the basis of our theoretical analysis, we were able to estimate the angle between the induced dipole moment and the plan that contains the long axis of the chromophore and the transition dipole moment of the retinal absorption.

Bacteriorhodopsins↗
PubMed2004

Determination of the absolute configuration of [3(2)](1,4)barrelenophanedicarbonitrile using concerted time-dependent density functional theory calculations of optical rotation and electronic circular dichroism.

The technique of time-dependent density functional theory (TDDFT) has very recently been applied to the calculation of both transparent spectral region optical rotations and electronic circular dichroism (CD). Here, we report the concerted application of the new methodologies to the determination of the absolute configuration (AC) of [3(2)](1,4)barrelenophanedicarbonitrile, 1, the first optically active barrelenophane. 1 is conformationally flexible: the two three-carbon bridges of 1 can each exhibit two conformations, leading to three inequivalent conformations of 1: a, b, and c. Conformational structures and energies are predicted using DFT at the B3LYP/6-31G level. Comparison of the calculated structures to structures obtained via X-ray crystallography of (+)-1 shows that (remarkably) all three conformations a-c are simultaneously present in crystalline (+)-1. The sodium D line specific rotations, [alpha](D), and CD spectra of a-c are calculated using TDDFT at the B3LYP/aug-cc-pVDZ level. Comparison of the conformationally averaged specific rotation and CD spectrum to the experimental data of Matsuda-Sentou and Shinmyozu leads to the AC 9S,12S(+)/9R,12R(-). The same AC is obtained both from [alpha](D) and from the CD, strongly supporting its reliability.

Journal Article↗
PubMed1990

Carcinogenic optical rotation.

It is suggested that viral nucleic acid inserts in vulnerable regions of host cell DNA contribute to cell transformation by introducing 43 degrees of optical rotation at 425 nm, and that a carcinogenic event caused by DNA inserts and adducts is spurious electron ejection from important adenine molecules that may be far from insert/adduct sites.

Cell Transformation, Neoplastic↗
PubMed2006

Optical rotation of achiral pentaerythritol.

The optical rotatory power of achiral crystals of achiral pentaerythritol molecules was measured. The maximum rotations were found to be +/-6 degrees /mm. The quantum mechanically computed rotation of pentaerythritol molecules using linear response theory was 6 times larger although the experimental and theoretical tensors were similarly oriented to within 5 degrees .

Journal Article↗
PubMed2006

Fluorescent monodisperse silica ellipsoids for optical rotational diffusion studies.

We report on the preparation of monodisperse, fluorescent hematite-silica core-shell ellipsoids, with adjustable shapes ranging from spindles to nearly spheres, that are suitable for optical rotational diffusion studies. Hematite cores are grafted with poly(vinylpyrrolidone) which ensures colloidal stability during the silica coating provided by the base-catalyzed hydrolysis and polymerization of tetraethoxysilane. Using tetramethylammonium hydroxide as base instead of the volatile ammonia facilitates continuous seeded growth of silica to colloids with a desired aspect ratio. A convenient feature of the hematite-silica particles is the rapid dissolution of the iron oxide core by acid, producing hollow silica ellipsoids that can be optically matched to near transparency. The control of shape and size of the silica ellipsoids, their optical properties, and the fairly high yield in comparison to other preparation methods for nonspherical model colloids make the ellipsoids very suitable for quantitative studies. As a case in point, we have measured the rotational diffusion coefficient of fluorescent ellipsoids with rotational fluorescence recovery after photobleaching. Dye-labeled ellipsoids can be imaged with confocal microscopy.

Journal Article↗
PubMed2002

Determination of absolute configuration using optical rotation calculated using density functional theory.

[structure: see text] We report the first determinations of the absolute configurations (ACs) of chiral molecules using discrete frequency, transparent spectral region optical rotations calculated using density functional theory (DFT). The ACs of 2H-naphtho[1,8-bc]thiophene 1-oxide (3), naphtho[1,8-cd]-1,2-dithiole 1-oxide (4), and 9-phenanthryl methyl sulfoxide (5) are determined by comparison of their specific rotations to values calculated via the time-dependent DFT/gauge-invariant atomic orbital (TDDFT/GIAO) methodology using the B3LYP functional and the aug-cc-pVDZ basis set.

Journal Article↗
PubMed2004

Determination of absolute configuration using density functional theory calculation of optical rotation: chiral alkanes.

The recently developed Gauge-Invariant (Including) Atomic Orbital (GIAO) based Time-Dependent Density Functional Theory (TDDFT) methodology for the calculation of transparent spectral region optical rotations of chiral molecules provides a new approach to the determination of absolute configurations. Here, we discuss the application of the TDDFT/GIAO methodology to chiral alkanes. We report B3LYP/aug-cc-pVDZ calculations of the specific rotations of the 22 chiral alkanes, 2-23, of well-established Absolute Configuration. The average absolute deviation of calculated and experimental [alpha](D) values for molecules 2-22 is 24.8. In two of the molecules 2-23, trans-pinane, 10, and endo-isocamphane, 13, the sign of [alpha](D) is incorrectly predicted. Our results demonstrate that absolute configurations of alkanes can be reliably assigned by using B3LYP/aug-cc-pVDZ TDDFT/GIAO calculations if, but only if, [alpha](D) is significantly greater than 25. In the case of (-)-anti-trans-anti-trans-anti-trans-perhydrotriphenylene, 1, [alpha](D) is -93 and TDDFT/GIAO calculations reliably lead to the absolute configuration R(-).

Journal Article↗
PubMed2005

Optical rotation calculation of a highly flexible molecule: the case of paraconic acid.

The absolute configuration of (S)-(-)-paraconic acid is correctly assigned on the basis of ab initio calculations of the specific optical rotation (OR) at the sodium D line, carried out both in vacuum and in methanol. Density functional theory (DFT) and Møller-Plesset second-order perturbation theory (MP2) are used to determine the most stable conformational structures, whose OR values are then calculated using DFT linear response theory and London atomic orbitals. The total OR is obtained by averaging these values using the population fractions determined from Boltzmann's statistics. The total OR of the MP2 structures has the correct sign both in vacuum and in solution, whereas only the solvent-relaxed DFT structures correctly reproduce the experimental sign. The strong solvent effect on the total OR is shown to arise primarily due to the variations in the relative energies of the various conformations.

Journal Article↗
PubMed2000

Case of enantiomer impurity identification by normal-phase chiral high-performance liquid chromatography with optical rotation and mass spectrometric detection.

An impurity produced in the synthesis of compound I is separated and identified as its enantiomer II using normal-phase chiral high-performance liquid chromatography (HPLC) with UV absorbance, optical rotation (OR) and mass spectrometric (MS) detection. The results show that the impurity II and compound I have equal and opposite specific rotations, identical MS spectra and the same MS-MS fragmentation pattern, as required for enantiomers. The procedures presented demonstrate a novel combination of methods for enantiomer identification and characterization that do not require the preparation of individual enantiomer markers or even the racemic mixture, thus reducing the need for additional synthetic work.

Chromatography, High Pressure Liquid↗
PubMed1974

A statistical study of optical rotation for synthetic d,l-copolypeptide solutions.

The right-handed helical fraction H(L) in a D,L-copolypeptide chain is evaluated by a simple probability theory for each L-fraction, p. The curves of optical rotation at a single wavelength against p for poly(gamma-benzyl-D,L-glutamate) and D,L-copolyleucine of a series of different D:L ratios in several positive helix-solvents are calculated with a modified semi-empirical Moffitt equation. From the comparison between the rotations calculated by us and observed by Downie et al., it is shown that to reproduce the observed rotations, the minimum number of right-handed helical nuclei or sequences of L-residues appropriate to the Moffitt equation are eight and four for degrees of polymerization 320 and 1860, respectively.

Journal Article↗