Spectroscopic and structural elucidation of amino acid derivatives and small peptides: experimental and theoretical tools

Abstract

This mini review deals with the modern aspects of the spectroscopy and structural elucidation of amino acid derivatives and small biologically active compounds. Free peptide bond rotation in these systems yields various conformers, which possess differing biological activities. Another phenomenon is the intermolecular or intramolecular stacking observed in aromatic small peptides. Specifically, the main aim is to illustrate the successful application of the "complex tool", consisting of a combination of the theoretical approximation methods with experimental linear polarized infrared (IR-LD) and/or Raman spectroscopy of oriented colloid suspensions in a nematic host. The possibilities and limitations of the approach for detailed vibrational assignment and structural elucidation of small peptides are discussed. Having in mind that physical and chemical properties of these systems can be precisely calculated by means of ab initio and DFT methods at Hartee-Fock, MP2 and B3LYP level of theory, varying basis sets, the results obtained allow a precise assignment of many vibrational bands to the corresponding normal modes, electronic structures and conformational state. The validity of the conclusions about the structure or vibrational properties of these systems have been supported, compared and/or additionally proved by the results from independent physical methods. In this respect (1)H and (13)C-NMR, single crystal X-ray diffraction, HPLC tandem mass spectrometry as well as thermal methods are all employed. A well ordered crystal must first be grown in order to determine the molecular structure by the absolute method of single crystal X-ray diffraction. Although the 3D structures of peptides have been determined over the past decades, peptide crystallization is still a major obstacle to X-ray diffraction work, the presence of chiral centre/s makes for this difficulty. For this reason the "complex tool" presented can be regarded as an alternative method for obtaining of structural information in the solid-state. It is obviously that only absolute crystallographic method can yield geometric parameters, bond lengths and angles, but the spectroscopic method presented can provide information about the dihedral angles for cis- and trans-configurated amide groups, mutual disposition of the aromatic fragments in peptides. Its validity is illustrated by comparing the theoretical and spectroscopic results obtained with available crystallographic data. The mini review can serve as a useful source of information not only for specialists in IR spectroscopy but, also, for other scientists, working in the field of structural analysis of amino acid derivatives and other small biologically active systems.

Aggregation Processes in Hybrid Nanosystem Polymer/Nanosilver/Cisplatin

“…For D70-g-PAA(PE), the characteristic peaks are observed in the region of amide 1 (1650-1660 cm −1 , СО stretching vibrations) and amide 2 (1615 cm −1 , NH bending vibrations (40-60%); C-N stretching vibrations (18-40%)). An additional peak at 1570 cm −1 (COO-, stretching vibrations) appears [35]. The complex formation of cisPt with the copolymer carboxyl groups is evident (Fig.…”

Structural, spectroscopic and theoretical study of novel ephedrinum salt

“…The theoretical approach, experimental technique for preparing the samples, procedures for polarized IR spectra interpretation and the validation of this new linear-dichroic infrared (IR-LD) orientation solid-state method for accuracy and precision have been presented. The influence of the liquid crystal medium on peak positions and integral absorbances of the guest molecule bands, the rheological model, the nature and balance of the forces in the nematic liquid crystal suspension system and the morphology of the suspended particles have also been discussed [12][13][14][15][16][17][18][19][20].…”

“…As far as the IR spectroscopy, it is one of the powerful methods for the elucidation of the relationship between structure and properties, the detailed analysis in this respect is reasonable. That is why we present an IR spectroscopic and structural elucidation of the neutral ephedrine hemihydrate (1) and its violurate salt dihydrate (2), depicted in Scheme 1, using the powerful technique for amino acid analysis and small biologically active molecules [12][13][14][15][16][17][18][19][20], linear polarized IR spectroscopy of oriented colloid suspensions as well as single crystal X-ray diffraction. The quantum chemical calculations were also performed with a view to obtain the preferable conformations of the protonated ephedrine molecule and its vibrational properties.…”

Crystal Structure of the N-Benzyloxycarbonyl-alanyl-phenylalanyl-methyl Ester: The Importance of the H-Bonding Pattern

“…These structural patterns are normally stabilized by the synergic action of weak, non-covalent interactions such as H-bonds, electrostatic, aromatic face to face or edge to face and van der Waals contacts [10,11]. The advantages of using small model peptides are the ease of preparation at large scale through well described synthetic methodologies [12], as well as the possibility of using a broader set of crystallization conditions, not suitable for more elaborate peptides and proteins [13,14]. Moreover, an understanding of the forces ruling the formation of supramolecular aggregates in the solid state is extremely useful for the controlled assembly of simple peptidic sequences at the nanometric scale, with important applications in the preparation of nanomaterials [15][16][17].…”