Raman Optical Activity of a Cyclic Dipeptide Analyzed by Quantum Chemical Calculations Combined with Molecular Dynamics Simulations

Raman optical activity of tetra-alanine in the poly(l-proline) II type peptide conformation

The poly(l-proline) II (PPII) helix is considered to be a major conformation in disordered polypeptides and unfolded proteins in aqueous solution. The PPII conformation can be identified by using Raman optical activity (ROA), which measures the different intensities of right- and left-circularly polarized Raman scattered light from chiral molecules and provides information on stereochemistry associated with vibrational motions. In the present study, we used tetra-alanine (Ala₄) as a model system, since its central amide bond adopts the PPII conformation. The predominance of the PPII conformation was supported by 11 ns molecular dynamics (MD) simulations at 300 K. The MD snapshots were used for subsequent quantum mechanical/molecular mechanical (QM/MM) calculations to compute the Raman and ROA spectra. The present MD + QM/MM analysis leads to a good agreement between the observed and simulated spectra, allowing us to assign most of the spectral features including the ROA band near 1320 cm^-1, which has been used as a marker for the PPII conformation. This positive ROA band has three components. The lower frequency component near 1310 cm^-1 arises from an internal peptide bond, whereas the higher frequency components around 1320-1335 cm^-1 appear due to N- and C-terminal peptide groups. The MD + QM/MM calculations also reproduced the electronic circular dichroism spectra of Ala₄. The present results provide a satisfactory framework for future investigations of unfolded/disordered proteins as well as peptides in solutions by chiral spectroscopic methods.

Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly

Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.

Conformational dynamics of carbohydrates: Raman optical activity of D-glucuronic acid and N-acetyl-D-glucosamine using a combined molecular dynamics and quantum chemical approach

As two biologically and medically relevant monosaccharides, the constituents of hyaluronic acid, d-glucuronic acid and N-acetyl-d-glucosamine, constitute perfect test cases for the development of carbohydrate-specific structural methods. These two molecules have been analysed by Raman optical activity (ROA), a spectroscopic technique exhibiting exquisite sensitivity to stereochemistry. We show that it is possible to support the experiment with a simulation approach combining density functional theory (DFT) and molecular dynamics (MD), both using explicit solvation. Thus, we have gained new insight into the crucial hydration effects that contribute to the conformational dynamics of carbohydrates and managed to characterize in detail the poorly understood vibrational nature of this class of biomolecules. Experimental and calculated ROA spectra of these two molecules are reported and excellent agreement has been found. More specifically, comparison has been made with the more commonly used gas phase and implicitly solvated calculation approaches, which offer poor or zero modelling of solvent interactions. The calculated spectra have been used to resolve the structural origins of the observed bands, a current challenge in the study of carbohydrates due to a lack of definitive vibrational assignments. We report and analyse major features in the fingerprint region of the ROA spectra, with recurrent structural and spectral features between the two monosaccharides observed.

The Raman optical activity of β-D-xylose: where experiment and computation meet

Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure-spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved.

Calculation of Raman optical activity spectra for vibrational analysis

This review provides the necessary knowledge to accurately model ROA spectra of solvated systems and interpret their vibrational characteristics.