Petr Malon

Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra

A direct transfer of Cartesian molecular force fields (FF) and electric property tensors is tested on model systems and compared to transfer in internal coordinates with an aim to improve simulation of vibrational spectra for larger molecules. This Cartesian transformation can be implemented easily and offers greater flexibility in practical computations. It can be also applied for transfer of anharmonic derivatives. The results for model calculations of the force field and vibrational frequencies for N‐methylacetamide show that our method removes errors associated with numerical artifacts caused by nonlinearity of the otherwise required Cartesian to internal coordinate transformation. For determination of IR absorption and vibrational circular dichroism intensities, atomic polar and axial tensors were also transferred in the Cartesian representation. For the latter, which are dependent upon the magnetic dipole operator, a distributed origin gauge is used to avoid an origin dependence. Comparison of the results of transferring ab initio FF and intensity parameters from an amide dimer fragment onto a tripeptide with those from a conventionally determined tripeptide FF document some limitations of the transfer method and its possible applications in the vibrational spectroscopy. Finally, application to determination of the FF and spectra for helical heptapeptide are presented and compared to experimental results.

A Solution to the Artifact Problem in Fourier Transform Vibrational Circular Dichroism

Using a newly constructed FT-IR vibrational circular dichroism (VCD) instrument, we have found that elimination of the ellipsoidal collection mirror before the detector and its replacement by a lens leads to a significant improvement in the absorption artifact problem seen previously in FT-IR/VCD. In the mid-IR region, we have been able to measure VCD of a single enantiomer for molecules such as α-pinene, 3-methylcyclohexanone, and dimethyltartrate. More importantly, this reduction in artifact level brings the FT-IR/VCD band shape of some particularly-difficult-to-measure bands, such as carbonyl stretches, into better agreement with those found in dispersive measurements. These results imply that the dispersive results are reliable, though of lower resolution than those obtained with the use of FT-IR/VCD.

Comparison of vibrational circular dichroism instruments: development of a new dispersive VCD.

A dispersive vibrational circular dichroism (VCD) instrument has been designed and optimized for the measurement of mid-infrared (MIR) bands such as the amide I and amide II vibrational modes of peptides and proteins. The major design considerations were to construct a compact VCD instrument for biological molecules, to increase signal-to-noise (S/N) ratio, to simultaneously collect and digitize the sample transmission and polarization modulation signals, and to digitally ratio them to yield a VCD spectrum. These were realized by assembling new components using design factors adapted from previous VCD instruments. A collection of spectra for peptides and proteins having different dominant secondary structures (alpha-helix, beta-sheet, and random coil) measured for identical samples under the same conditions showed that the new instrument had substantially improved S/N as compared with our previous dispersive VCD instrument These instruments both provide protein VCD for the amide I that are comparable to or somewhat better than those measurable with commercial Fourier transform (FT) VCD instruments if just the amide I band in the spectra is obtained at modest resolution (8 cm−1) with the same total data collection time on each type of instrument.

Spinning Quarter-Wave Plate Polarization Modulator: Test of Feasibility for Vibrational Circular Dichroism Measurements

A novel polarization modulator design based on a rotating quarter-wave plate and preliminary results of its application for vibrational circular dichroism (VCD) are presented. The device permits quarter-wave retardation in the infrared with alternating senses so that the resultant components of circular polarization can be modulated at frequencies on the order of 100 Hz. We have been able to apply this device to measure VCD with a step-scan FT-IR spectrometer by incorporating a stressed ZnSe optical element as the rotating quarter-wave plate. VCD of α-pinene and camphor were obtained. While these test spectra were of low signal-to-noise ratio (S/N), they exhibited the correct VCD spectral features for these chiral molecules. While not yet of competitive, practical utility, this design is potentially adaptable to extension into the far-IR with alternative optical elements, permits variable-frequency polarization modulation, and should be capable of improved S/N with modifications to increase rotation frequency.

Vibrational and electronic optical activity of the chiral disulphide group: Implications for disulphide bridge conformation

Using dihydrogendisulphide (H(2)S(2)), dimethyl- ((CH(3))(2)S(2)), and diethyldisulphide ((CH(3)CH(2))(2)S(2))as model molecules, theoretical ECD, VCD, and ROA spectra of nonplanar disulphides were calculated by DFT methods. Most of the calculated electronic and vibrational chiroptical features suffer an equivocal relation between calculatedsigns of ECD, VCD, or ROA and the sense of disulphide nonplanarity as noted earlier for low-lying ECD bands. This is a consequence of local C(2) symmetry of a disulphide group causing most electronic and vibrational transitions to occur as pairs falling to alternative A, B symmetry species, which become degenerate and switch their succession (and consequently the observed chiroptical sign pattern) at the energetically most favorable perpendicular conformation. According to present calculations, the key to resolving this ambiguity may involve the S-S stretching vibrational mode at approximately 500 cm(-1). The relation of signs of the relevant VCD and ROA features to sense of disulphide chirality seems simpler and less ambiguous. The right-handed arrangement of the S-S group (0 < chi(S-S) < 180 degrees) results in mostly negative VCD signals. Although relation to ROA still suffers some ambiguity, it gets clearer along the series H(2)S(2)-(CH(3))(2)S(2)-(CH(3)CH(2))(2)S(2). ROA is also attractive for the analysis of disulphide-containing peptides and proteins, because applying it to aqueous solutions is not problematic.

Vibrational circular dichroism study of [3R,4R]-dideuteriocyclobutane-1,2-dione. Preliminary comparison of experiment and calculations

Abstract The preparation, infrared absorption and vibrational circular dichroism (VCD) spectra of the title compound are presented. The absorption intensities and VCD signs and magnitudes were calculated using an ab initio force field and the a priori theory of Stephens, both carried out with a 6-31G** basis set at the SCF level. Excellent agreement was found between theory and experiment for the single-signed VCD seen in the CH ( + ) and C—D ( − ) stretching regions. As predicted, no VCD was detectable in the CO stretching region. The mid-IR VCD pattern from 1300 to 900 cm−1, consisting of two large negative bands and several weak positive bands, was well represented by the calculations.

Techniques And Application Of FTIR Vibrational Circular Dichroism

Vibrational Circular Dichroism (VCD) has proven to be useful for detecting conformational change and for characterizing secondary structures for a variety of biopolymers. Use of FTIR-based VCD for such problems has been made possible with recent improvements in optical design and S/N. FTIR-VCD and dispersive VCD each have strengths that are optimal for specific problems. A comparison of techniques is presented in this lecture, and selected examples of VCD applications to polypeptides and proteins are given.

Fourier transform vibrational circular dichroism and the artifact problem

FTIR vibrational circular dichroism spectra ofβ-pinene are presented as an example of the artifact reduction capability of our new instrument design. The key to this advance is the incorporation of a lens after the sample to focus onto a relatively large detector. Baseline correction with just solvent becomes possible in some cases.