Joanna E. Rode

DFT study of vibrational circular dichroism spectra of D-lactic acid-water complexes

This paper presents a discussion of the interaction energies, conformations, vibrational absorption (VA, harmonic and anharmonic) and vibrational circular dichroism (VCD) spectra for conformers of monomeric chiral d(-)-lactic acid and their complexes with water at the DFT(B3LYP)/aug-cc-pVDZ and DFT(B3LYP)/aug-cc-pVTZ levels. A detailed analysis has been performed principally for the two most stable complexes with water, differing by lactic acid conformation. The VCD spectra were found to be sensitive to conformational changes of both free and complexed molecules, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Using the theoretical prediction, we demonstrate that the VCD technique can be used as a powerful tool for structural investigation of intermolecular interactions of chiral molecules and can yield information complementary to data obtained through other molecular spectroscopy methods.

IR Low‐Temperature Matrix and ab Initio Study on β‐Alanine Conformers

For the first time the argon-matrix low-temperature FTIR spectra of beta-alanine are recorded. They reveal a quite complicated spectral pattern which suggests the presence of several beta-alanine conformers in the matrix. To interpret the spectra, the eighteen beta-alanine conformers, stable in the gas phase, are estimated at the B3LYP and MP2 levels combined with the aug-cc-pVDZ. Ten low-energy structures are reoptimized at the QCISD/aug-cc-pVDZ and B3LYP and MP2 levels by using the aug-cc-pVTZ basis sets. Assignment of the experimental spectra is undertaken on the basis of the calculated B3LYP/aug-cc-pVDZ anharmonic IR frequencies as well as careful estimation of the conformer population. The presence of at least three beta-alanine conformers is demonstrated. The detailed analysis of IR spectra points to the possible presence of five additional beta-alanine conformers.

Chirality Measures of α-Amino Acids

To measure molecular chirality, the molecule is treated as a finite set of points in the Euclidean R(3) space supplemented by k properties, p(1)((i)), p(2)((i)), ..., p(k)((i)) assigned to the ith atom, which constitute a point in the Property P(k) space. Chirality measures are described as the distance between a molecule and its mirror image minimized over all its arbitrary orientation-preserving isometries in the R(3) × P(k) Cartesian product space. Following this formalism, different chirality measures can be estimated by taking into consideration different sets of atomic properties. Here, for α-amino acid zwitterionic structures taken from the Cambridge Structural Database and for all 1684 neutral conformers of 19 biogenic α-amino acid molecules, except glycine and cystine, found at the B3LYP/6-31G** level, chirality measures have been calculated by a CHIMEA program written in this project. It is demonstrated that there is a significant correlation between the measures determined for the α-amino acid zwitterions in crystals and the neutral forms in the gas phase. Performance of the studied chirality measures with changes of the basis set and computation method was also checked. An exemplary quantitative structure–activity relationship (QSAR) application of the chirality measures was presented by an introductory model for the benchmark Cramer data set of steroidal ligands of the sex-hormone binding globulin.

On Stability, Chirality Measures, and Theoretical VCD Spectra of the Chiral C58X2 Fullerenes (X = N, B)

The stability of all 23 C(58)N(2) and C(58)B(2) heterofullerenes in the singlet and triplet states was determined at the B3LYP/6-31G** level. In equilibrium mixture the achiral (1,4) C(58)N(2) isomer would be populated in ca. 95.8%, the chiral (1,16) one in ca. 3.3%, and the achiral (1,4) C(58)B(2) in 100%, whereas all triplet state isomers are less stable. Fourteen out of 23 C(58)X(2) are chiral. Four different chirality measures were calculated by our own CHIMEA program: pure geometrical, labeled, mass, and charge. Intercorrelations between the measures for all chiral compounds indicate that the pure geometrical chirality measure is unstable and should not be used in QSAR predictions of the other molecular properties, while the labeled and mass-weighted ones are promising QSAR descriptors. For each chiral C(58)N(2) molecule, some very strong VCD bands, of intensity comparable with that in the IR spectra, can serve in identification and characterization of the isomers.

VCD technique in determining intermolecular H-bond geometry: a DFT study

Abstract Model chiral β -lactam molecules, (3 S )-and (4 R )-fluoro-2-azetidinone, were calculated at the B3PW91/aug-cc-pVTZ level, to be hydrogen bonded with the achiral HX molecule (X=F, Cl, Br). Two stable structures of the complex are possible: a cyclic or a bent H-bond, in which the HX molecule interacts with the CO group and is either close to NH or CH 2 (CHF) moiety, respectively. The VCD effect of these two forms differs in several respects, however, the main difference is the sign of the VCD rotational strength of the ν (HX) stretching vibrations revealing the geometry of the hydrogen bond complex.

Density functional IR, Raman, and VCD spectra of halogen substituted β-lactams

Abstract Halogenoazetidinones are important as synthetic intermediates for preparation of halogen β-lactam (2-azetidinone) antibiotics and as building blocks for carbohydrates and amino acids. In this paper, we consider the influence of the halogen atom, substituted at the C4 position of the 2-azetidinone ring, on the geometry, IR, Raman, and vibrational circular dichroism spectra. The vibrational spectra were calculated for the chiral 4-(R)-X-2-azetidinone (X=F, Cl or Br) molecules at the B3PW91/aug-cc-pVTZ level. It was shown that the geometry of the molecules studied do not change much upon the change of the halogen atom. In case of the vibrational spectra, the position but even more the intensities depend strongly on the kind of halogen substituent.

On Vibrational Circular Dichroism Chirality Transfer in Electron Donor–Acceptor Complexes: A Prediction for the Quinine···BF3 System

Vibrational circular dichroism (VCD) chirality transfer occurs when an achiral molecule interacts with a chiral one and becomes VCD-active. Unlike for H-bonds, for organic electron donor-acceptor (EDA) complexes this phenomenon remains almost unknown. Here, the VCD chirality transfer from chiral quinine to achiral BF3 is studied at the B3LYP/aug-cc-pVDZ level. Accessibility of four quinine electron donor sites changes with conformation. Therefore, the quinine conformational landscape was explored and a considerable agreement between X-ray and the most stable conformer geometries was achieved. The BF3 complex through the aliphatic quinuclidine N atom is definitely dominating and is predicted to be easily recognizable in the VCD spectrum. Out of several VCD chirality transfer modes, the ν(s)(BF3) mode, the most intense in the entire VCD spectrum, satisfies the VCD mode robustness criterion and can be used for monitoring the chirality transfer phenomenon in quinine···BF3 system.

On chirality transfer in electron donor–acceptor complexes. A prediction for the sulfinimine···BF3 system

Stabilization energies of the electron donor-acceptor sulfinimine···BF(3) complexes calculated at either the B3LYP/aug-cc-pVTZ or the MP2/aug-cc-pVTZ level do not allow to judge, whether the N- or O-atom in sulfinimine is stronger electron-donor to BF(3) . The problem seems to be solvable because chirality transfer phenomenon between chiral sulfinimine and achiral BF(3) is expected to be vibrational circular dichroism (VCD) active. Moreover, the bands associated with the achiral BF(3) molecule are predicted to be the most intense in the entire spectrum. However, the VCD band robustness analyses show that most of the chirality transfer modes of BF(3) are unreliable. Conversely, variation of VCD intensity with change of intermolecular distance, angle, and selected dihedrals between the complex partners shows that to establish the robustness of chirality transfer mode. It is also necessary to determine the influence of the potential energy surface (PES) shape on the VCD intensity. At the moment, there is still no universal criterion for the chirality transfer mode robustness and the conclusions formulated based on one system cannot be directly transferred even to a quite similar one. However, it is certain that more attention should be focused on relation of PES shape and the VCD mode robustness problem.

Chiral allenes: theoretical VCD and IR spectra

Abstract The theoretical geometries, rotational constants, VCD, and IR spectra for the chiral ( S )-HXCCCFH (X=F, Cl, Br) allene molecules were calculated at the B3PW91/aug-cc-pVTZ level. We have shown that there is plausible adequacy between IR spectrum of ( S )-1,3-difluoroallene molecule calculated at B3PW91/aug-cc-pVTZ level and experimental spectra of the racemate system. For the other molecules studied, the experimental spectra were not published, yet, although, some results reported earlier for alkilohalogenoallenes are in line with our findings. The halogen influence on the VCD and IR spectra of the studied molecules is discussed.

Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers

AbstractThe conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point. FigurePhenylisoserine (PhIS) is an active side chain of cytotoxic Paclitaxel medicine. The conformational landscape of phenylisoserine was studied. One zwitterionic and one neutralconformer determine the equilibrium in water whereas in the gas phase the MP2 calculations suggest three PhIS structures to be significantly populated.