Density Functional Theory Calculations and Vibrational Circular Dichroism of Aromatic Foldamers

Exploring Geometrical, Electronic and Spectroscopic Properties of 2-Nitroimidazole-Based Radiopharmaceuticals via Computational Chemistry Methods

Tumor hypoxia plays an important role in the clinical management and treatment planning of various cancers. The use of 2-nitroimidazole-based radiopharmaceuticals has been the most successful for positron emission tomography (PET) and single photon emission computed tomography (SPECT) imaging probes, offering noninvasive means to assess tumor hypoxia. In this study we performed detailed computational investigations of the most used compounds for PET imaging, focusing on those derived from 2-nitroimidazole: fluoromisonidazole (FMISO), fluoroazomycin arabinoside (FAZA), fluoroetanidazole (FETA), fluoroerythronitroimidazole (FETNIM) and 2-(2-nitroimidazol-1-yl)-N-(2,2,3,3,3-pentafluoropropyl)acetamide (EF5). Conformational analysis, structural parameters, vibrational IR and Raman properties (within both harmonic and anharmonic approximations), as well as the NMR shielding tensors and spin-spin coupling constants were obtained by density functional theory (DFT) calculations and then correlated with experimental findings, where available. Furthermore, time-dependent DFT computations reveal insight into the excited states of the compounds. Our results predict a significant change in the conformational landscape of most of the investigated compounds when transitioning from the gas phase to aqueous solution. According to computational data, the 2-nitroimidazole moiety determines to a large extent the spectroscopic properties of its derivatives. Due to the limited structural information available in the current literature for the investigated compounds, the findings presented herein deepen the current understanding of the electronic structures of these five radiopharmaceuticals.

Chiroptical Properties in Thin Films of π-Conjugated Systems

Chiral π-conjugated molecules provide new materials with outstanding features for current and perspective applications, especially in the field of optoelectronic devices. In thin films, processes such as charge conduction, light absorption, and emission are governed not only by the structure of the individual molecules but also by their supramolecular structures and intermolecular interactions to a large extent. Electronic circular dichroism, ECD, and its emission counterpart, circularly polarized luminescence, CPL, provide tools for studying aggregated states and the key properties to be sought for designing innovative devices. In this review, we shall present a comprehensive coverage of chiroptical properties measured on thin films of organic π-conjugated molecules. In the first part, we shall discuss some general concepts of ECD, CPL, and other chiroptical spectroscopies, with a focus on their applications to thin film samples. In the following, we will overview the existing literature on chiral π-conjugated systems whose thin films have been characterized by ECD and/or CPL, as well other chiroptical spectroscopies. Special emphasis will be put on systems with large dissymmetry factors (g_abs and g_lum) and on the application of ECD and CPL to derive structural information on aggregated states.

Assignment of Vibrational Circular Dichroism Cross-Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers

Assignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X‐ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)^conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)^conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β‐amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N‐methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.

Effect of puckering motion and hydrogen bond formation on the vibrational circular dichroism spectrum of a flexible molecule: the case of (S)-1-indanol

Vibrational circular dichroism spectra of (S)-1-indanol in DMSO and CCl₄ are described by cluster-in-the-bulk static calculations and first principles molecular dynamics.

Conformational Preference and Spectroscopical Characteristics of the Active Pharmaceutical Ingredient Levetiracetam

The analysis of the possible conformers and the conformational change between solid and liquid states of a particular drug molecule are mandatory not only for describing reliably its spectroscopical properties but also for understanding the interaction with the receptor and its mechanism of action. Therefore, here we investigated the free-energy conformational landscape of levetiracetam (LEV) in gas phase as well as in water and ethanol, aiming to describe the 3-dimensional structure and energetic stability of its conformers. Twenty-two unique conformers were identified, and their energetic stability was determined at density functional theory B3LYP/6-31+G(2d,2p) level of theory. The 6 most stable monomers in water, within a relative free-energy window of 0.71 kcal mol^-1 and clearly separated in energy from the remaining subset of 16 conformers, as well as the 3 most stable dimers were then used to compute the Boltzmann populations-averaged UV-Vis and NMR spectra of LEV. The conformational landscape in solution is distinctly different from that corresponding to gas phase, particularly due to the relative orientations of the butanamide group. Aiming to clarify the stability of the possible dimers of LEV, we also investigated computationally the structure of a set of 11 nonhydrated and hydrated homochiral hydrogen-bonded LEV dimers.

Effects of the basis set and of the exchange-correlation functional on the Inelastic Electron Tunneling signatures of 1,4-benzenedithiol

The effects of the atomic basis set and of the exchange-correlation (XC) functional on the Inelastic Electron Tunneling (IET) spectra have been investigated by considering the prototypical 1,4-benzenedithiol molecule. These studies have been completed by tackling the reliability of the same methods for predicting the IR absorption spectrum of the same molecule. The main conclusions are (i) the B3LYP XC functional is suitable to predict the relative vibrational frequencies, (ii) provided a scaling factor is used, the root mean square error on the vibrational frequencies goes down to 18 cm(-1), (iii) triple-ζ basis sets and in particular the cc-pVTZ basis set is a good compromise between accuracy and computational needs, (iv) basis set effects on the IET intensities are larger than those of the XC functional, and (v) the cc-pVTZ, cc-pVQZ, and aug-cc-pVDZ basis sets provide consistent IET intensities.

Determination of the absolute configurations of bicyclo[3.1.0]hexane derivatives via electronic circular dichroism, optical rotation dispersion and vibrational circular dichroism spectroscopy and density functional theory calculations

The electronic circular dichroism (ECD), optical rotation dispersion (ORD), and vibrational circular dichroism (VCD) spectra of a pair of enantiomers, i.e. 3 and 4, of a bicyclo[3.1.0]hexane derivative have been measured in acetonitrile and acetonitrile-d(3), respectively. Extensive conformational searches at the B3LYP/6-311++G** level have been carried out for 3, which has four OH and one N(3) functional groups. For the bicyclo[3.1.0]hexane ring of 3, the boat-like conformers have been found to be much more stable than the chair-like conformers, while the number and the strength of the intramolecular hydrogen bonds have been identified as the dominant factors in the relative stability among the boat-like and among the chair-like conformers. DFT simulations of the ECD, ORD and VCD spectra have been performed for all low energy conformers at the B3LYP/6-311++G** and B3LYP/aug-cc-pVDZ level. Implicit continuum polarization model has been used to account for solvent effects in all these chiroptical measurements. Comparison of the DFT simulations with the experimental data shows that all three chiroptical properties yield the same absolute configuration assignment for . This work demonstrates that using multiple chiroptical spectroscopic methods in combination with DFT calculations allows one to determine absolute configurations with high confidence for chiral carbohydrates and their analogues, which possess a large number of rotatable bonds.

Determination of the absolute configurations of synthetic daunorubicin analogues using vibrational circular dichroism spectroscopy and density functional theory

The absolute configurations of three synthesized anthracycline analogues have been determined using vibrational circular dichroism (VCD) spectroscopy and the density functional theory (DFT) calculations. The experimental VCD spectra of the three compounds have been measured for the first time in the film state, prepared from their CDCl(3) solutions. Conformational searches for the monomers and some dimers of the three compounds have been performed at the DFT level using the B3LYP functional and the 6-311G** and 6-311++G** basis sets. The corresponding vibrational absorption and VCD spectra have been calculated. The good agreement between the experimental and the calculated spectra allows one to assign the absolute configurations of the three compounds with high confidence. In addition, the dominant conformers of the three compounds have also been identified.

Conformational changes in cryptophane having C1-symmetry studied by vibrational circular dichroism

Vibrational circular dichroism (VCD) measurements and density functional theory (DFT) calculations were used to obtain the absolute configuration of a cryptophane molecule having C1-symmetry (labeled cryptophane-H). This molecule exhibits chiroptical properties different from those published for cryptophane-A having D3-symmetry [Brotin et al. J. Am. Chem. Soc. 2006, 128, 5533-5540]. In particular, we have shown that the conformation of the aliphatic linkers is very dependent on the solvent used and its ability to enter (CDCl3 solution) or not (C2D2Cl4 solution) in the cryptophane cavity. Calculations performed at the DFT (B3PW91/6-31G*) level establish, besides the absolute configuration, the preferential anti and gauche conformations of the aliphatic linkers of the chloroform@cryptophane-H complex and the empty cryptophane-H molecule, respectively. Polarimetric measurements performed in several solvents reflect also the change of conformation of the bridges upon guest encapsulation.