Simplified and enhanced VCD analysis of cyclic peptides guided by artificial intelligence.

Cyclic peptides are privileged structures in medicinal chemistry; however, their solution-state structure characterization is difficult. Vibrational circular dichroism (VCD) spectroscopy is a powerful alternative to NMR, but requires challenging calculations. We present a VCD approach guided by a genetic algorithm, which is simple, more effective, and has a higher conformer resolution.

An Artificial Intelligence Approach for Tackling Conformational Energy Uncertainties in Chiroptical Spectroscopies.

Determination of the absolute configuration of chiral molecules is a prerequisite for obtaining a fundamental understanding in any chirality-related field. The interaction with polarised light has proven to be a powerful means to determine this absolute configuration, but its application rests on the comparison between experimental and computed spectra for which the inherent uncertainty in conformational Boltzmann factors has proven to be extremely hard to tackle. Here we present a novel approach that overcomes this issue by combining a genetic algorithm that identifies the relevant conformers by accounting for the uncertainties in DFT relative energies, and a hierarchical clustering algorithm that analyses the trends in the spectra of the considered conformers and identifies on-the-fly when a given chiroptical technique is not able to make reliable predictions.

Photonically active bowtie nanoassemblies with chirality continuum.

Chirality is a geometrical property described by continuous mathematical functions. However, in chemical disciplines, chirality is often treated as a binary left or right characteristic of molecules rather than a continuity of chiral shapes. Although they are theoretically possible, a family of stable chemical structures with similar shapes and progressively tuneable chirality is yet unknown.

Molecule-like and lattice vibrations in metal clusters.

We report distinct molecule-like and lattice (breathing) vibrational signatures of atomically precise, ligand-protected metal clusters using low-temperature Raman spectroscopy. Our measurements provide fingerprint Raman spectra of a series of noble metal clusters, namely, Au(SR), Ag(SR), AgAu(SR), Ag(SR) and Ag(SR) (-SR = alkyl/arylthiolate, -SR = dithiolate). Distinct, well-defined, low-frequency Raman bands of these clusters result from the vibrations of their metal cores whereas the higher-frequency bands reflect the structure of the metal-ligand interface.

Revisiting an old concept: the coupled oscillator model for VCD. Part 2: implications of the generalised coupled oscillator mechanism for the VCD robustness concept.

Using two illustrative examples it is shown that the generalised coupled oscillator (GCO) mechanism implies that the stability of the VCD sign computed for a given normal mode is not reflected by the magnitude of the ratio ζ between the rotational strength and dipole strength of the respective mode, i.e., the VCD robustness criterium proposed by Góbi and Magyarfalvi.

Revisiting an old concept: the coupled oscillator model for VCD. Part 1: the generalised coupled oscillator mechanism and its intrinsic connection to the strength of VCD signals.

Motivated by the renewed interest in the coupled oscillator (CO) model for VCD, in this work a generalised coupled oscillator (GCO) expression is derived by introducing the concept of a coupled oscillator origin. Unlike the standard CO expression, the GCO expression is exact within the harmonic approximation. Using two illustrative example molecules, the theoretical concepts introduced here are demonstrated by performing a GCO decomposition of the rotational strengths computed using DFT.

The importance of large-amplitude motions for the interpretation of mid-infrared vibrational absorption and circular dichroism spectra: 6,6'-dibromo-[1,1'-binaphthalene]-2,2'-diol in dimethyl sulfoxide.

Using the 6,6'-dibromo-[1,1'-binaphthalene]-2,2'-diol molecule and its vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra measured in deuterated dimethyl sulfoxide as example, we present a first detailed study of the effects induced in VCD spectra by the large-amplitude motions of solvent molecules loosely bound to a solute molecule. We show that this type of perturbation can induce significant effects in the VA and VCD spectra. We also outline a computational procedure that can effectively model the effects induced in the spectra and at the same time provide detailed structural information regarding the relative orientations of moieties involved in a solute-solvent molecular complex.

Importance of C*-H based modes and large amplitude motion effects in vibrational circular dichroism spectra: the case of the chiral adduct of dimethyl fumarate and anthracene.

The role played by the C*-H based modes (C* being the chiral carbon atom) and the large amplitude motions in the vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra is investigated. The example of an adduct of dimethyl fumarate and anthracene, i.e.

On the complementarity of ECD and VCD techniques.

An unprecedented complementarity of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectroscopic techniques is demonstrated by showing that each technique reveals the structure of a different molecular segment. Using a flexible molecule of biological significance we show that the synergetic use of ECD and VCD yields more complete structural characterization as it provides improved and more reliable conformer resolution.

Understanding solvent effects in vibrational circular dichroism spectra: [1,1'-binaphthalene]-2,2'-diol in dichloromethane, acetonitrile, and dimethyl sulfoxide solvents.

We present a combined experimental and computational investigation of the vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of [1,1'-binaphthalene]-2,2'-diol. First, the sensitive dependence of the experimental VA and VCD spectra on the solvent is demonstrated by comparing the experimental spectra measured in CH(2)Cl(2), CD(3)CN, and DMSO-d(6) solvents. Then, by comparing calculations performed for the isolated solute molecule to calculations performed for molecular complexes formed between solute and solvent molecules, we identify three main types of perturbations that affect the shape of the VA and VCD spectra when going from one solvent to another.

On the equivalence of conformational and enantiomeric changes of atomic configuration for vibrational circular dichroism signs.

We study systematically the vibrational circular dichroism (VCD) spectra of the conformers of a simple chiral molecule, with one chiral carbon and an "achiral" alkyl substituent of varying length. The vibrational modes can be divided into a group involving the chiral center and its direct neighbors and the modes of the achiral substituent. Conformational changes that consist of rotations around the bond from the next-nearest neighbor to the following carbon, and bond rotations further in the chain, do not affect the modes around the chiral center.

On the origin dependence of the angle made by the electric and magnetic vibrational transition dipole moment vectors.

The concept of robustness of rotational strengths of vibrational modes in a VCD spectrum has been introduced as an aid in assignment of the absolute configuration with the help of the VCD spectrum. The criteria for robustness have been based on the distribution around 90° of the angles ξ(i) between electric and magnetic transition dipoles of all the modes i of a molecule. The angles ξ(i) (not, of course, the rotational strengths) are, however, dependent on the choice of origin.

Signatures of counter-ion association and hydrogen bonding in vibrational circular dichroism spectra.

We study the effect of counter-ion complexation on the example of Cl(-) ions interacting with the [Co(en)(3)](3+) complex. The H-bonding of the N-H groups of the ethylenediamine (en) ligands with the Cl(-) ions may lead to giant enhancement of the VCD intensity for the N-H stretches, but may also lead to VCD sign changes in the finger print region of N-H wagging, twisting and scissoring motions. Such sign changes should not be mistaken for signatures of the presence of the other enantiomer.

A VCD robust mode analysis of induced chirality: the case of pulegone in chloroform.

Vibrational modes in an achiral molecule may acquire rotational strength by complexation to a chiral molecule, as happens for achiral solvent molecules complexed to a chiral solute. We investigate this transfer of chirality in vibrational circular dichroism for the pulegone molecule in CDCl(3) solvent from the point of view of the robustness concept introduced recently. It turns out that the transfer of chirality yields nonrobust modes, which means that, although they are observed in vibrational circular dichroism (VCD) experiments, the sign of these modes cannot be predicted reliably with standard (Density Functional Theory) VCD calculations.

Robust normal modes in vibrational circular dichroism spectra.

The use of calculations of the rotational strengths of normal modes in order to determine the absolute configuration (AC) of a molecule, by comparing a calculated vibrational circular dichroism (VCD) spectrum to an experimental one, can be made much more reliable when the vibrational modes are classified as either robust or non-robust. The robust modes are the ones with a robust sign of the rotational strength in the sense that it will not change by small perturbations in either experiment or calculation. The signs of non-robust modes may change.

Enhancement of IR and VCD intensities due to charge transfer.

Donor-acceptor interactions such as the one between the Cl(-) base and the N-H sigma* acceptor orbitals encountered in the complexation of Cl(-) counterions to the [Co(en)(3)](3+) transition metal complex, have been shown to cause huge enhancement (between 1 and 2 orders of magnitude) of the VCD intensities of N-H stretching modes. This effect has been fully analyzed, and could be attributed to increased charge flow from the Cl(-) donors when the N-H bonds become stretched. The transfer of charge counteracts the movement of negative electronic charge that happens along with the motion of the H nuclei, effectively reversing the electronic part of the electric dipole transition moment (EDTM) in the direction of the charge flow (z, say), and of the magnetic transition dipole moment (MDTM) in the perpendicular direction.

Effects of complex formation on vibrational circular dichroism spectra.

The determination of absolute configurations of chiral compounds using VCD is performed by comparing measured vibrational circular dichroism (VCD) spectra with calculated spectra. The process is based on two facts: the two enantiomers have rotational strengths of opposite sign, and the absolute configuration of the molecule used in the calculation is known. However, calculations on isolated molecules very often predict VCD intensities of very different magnitude or even different signs compared to the spectra measured in solution.