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<i>l</i> -Stercobilin-HCl and <i>d</i> -Urobilin-HCl. Analysis of Their Chiroptical and Conformational Properties by VCD, ECD, CPL Experiments and MD, DFT Calculations
摘要： Vibrational circular dichroism (VCD) and IR spectra of dichloromethane solutions of l-stercobilin and d-urobilin hydrochlorides have been recorded in the mid-IR region. The spectra are best interpreted by combining molecular dynamics (MD) calculations and DFT calculations within the QM/MM ONIOM-type framework, and the combined predicted results are better and more informative than the more standard analysis provided by DFT calculations. The same approach also sheds light on the Cotton effect sign inversion of room temperature versus low temperature electronic CD (ECD) spectra of the same compounds in methanol-glycerol solution. Finally, circularly polarized luminescence (CPL) spectra for l-stercobilin in chloroform solution provide information on the excited state geometry of this molecule.
关键词： Vibrational circular dichroism,electronic CD,molecular dynamics,IR spectra,QM/MM ONIOM-type framework,Cotton effect,circularly polarized luminescence,DFT calculations
更新于2025-09-23 15:21:21
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Eu3+ as a luminescence probe in DNA studies: Structural and conformational implications
摘要： Lanthanide ions are widely used as luminescent probes for structural studies of various biomolecules, including DNA. Latest developments of circularly polarized luminescence (CPL) methodology further boosted interest to luminescence techniques. However, an effect of the lanthanide probes themselves on the DNA structure and conformation was investigated only partially and not for all lanthanides. In the present work, we performed a detailed spectroscopic study of Eu3+ complexes with native double-stranded DNA and compared them to the relevant complexes with single-stranded DNA. We employed infrared (IR), vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic methods to investigate Eu3+ effect on DNA structure and conformational transitions. It was shown that Eu3+ ions can induce significant alteration of the native DNA structure at the concentrations often used in luminescence studies. While no DNA denaturation was observed at these metal ion concentrations, significant unstacking of the base pairs and disordering of the sugar-phosphate backbone, partial appearance of the A-form backbone geometry, and DNA transition into condensed ψ–type form took place. Eu3+ binding to single-stranded DNA was more pronounced than the binding to double-stranded DNA. We detected the main Eu3+ binding sites and determined the metal ion concentration range in which DNA geometry remains largely unaltered. The results obtained in the current study could be used for tuning the luminescence and CPL structural studies of DNA utilizing Eu3+ ions as probes.
关键词： infrared (IR),DNA condensation,lanthanide ions,DNA structure,luminescence probe,vibrational circular dichroism (VCD)
更新于2025-09-19 17:15:36
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Analysis of Vibrational Circular Dichroism Spectra of Peptides: a Generalised Coupled Oscillator Approach of a Small Peptide Model Using VCDtools
摘要： Vibrational Circular Dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work we study the origin of these VCD signals using the General Coupled Oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and β-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intra-molecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that contributions to the rotational strengths considered to be insignificant in standard VCD models may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies -and in particular the decomposition of the rotational strength made possible by the GCO analysis- it becomes clear that one should be cautious when employing measures of robustness as proposed previously.
关键词： amide I,Vibrational Circular Dichroism,amide II,VCD robustness,peptides,General Coupled Oscillator analysis
更新于2025-09-19 17:13:59
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Chiral Analysis || Raman Optical Activity
摘要： Raman optical activity (ROA) has many advantages over conventional Raman spectroscopy for investigation of chiral molecules, in general, and biological molecules, in particular, on account of their homochirality. Since it is a manifestation of vibrational optical activity [1], being complementary to vibrational circular dichroism (VCD), ROA is more sensitive to the 3D structures of chiral molecules through its dependence on their absolute handedness, which has led to its development as an incisive probe of the structure and behavior of biomolecules in aqueous solution. For example, ROA spectra obtained from proteins can provide detailed information on the secondary and tertiary structures adopted by polypeptide backbones. Additionally, ROA can probe the tautomers of side chains. In common with other vibrational spectroscopies, there is no restriction on the size of molecules, or in their type, that can be investigated by ROA, broadening its application to unfolded proteins, viruses, and carbohydrates.
关键词： vibrational circular dichroism,proteins,Raman optical activity,aqueous solution,carbohydrates,vibrational optical activity,biological molecules,biomolecules,viruses,chiral molecules
更新于2025-09-09 09:28:46
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Chiral Analysis || Vibrational Optical Activity in Chiral Analysis
摘要： Chiral analysis encompasses all analytical techniques focused on quantitative measures of the chiral properties of molecules. The properties unique to chiral molecules are absolute configuration (AC) and enantiomeric excess (ee). As will be discussed below, vibrational optical activity (VOA) can provide information on samples of chiral molecules by direct spectroscopic investigation without modifying the molecules by reacting them, sometimes irreversibly, with other chiral molecules or substrates. From a molecular point of view, VOA chiral analysis may be regarded as noninvasive in that the molecule is not changed or altered from its natural solution or solid-state condition in order to carry out the analysis. An important property of VOA is its sensitivity to the conformational states of chiral molecules, both in solution and in the solid state. Apart from the determination of the absolute chirality of a molecule, VOA can be used to specify these states, in conjunction with quantum mechanical calculations, and determine populations of solution-state conformers that are interconverting faster than the nuclear magnetic resonance (NMR) timescale. VOA can also be used to probe the solid-state conformations of chiral molecules as well as their polymorphic crystal forms. Although this information is not strictly chiral in nature, VOA has extraordinary sensitivity to both the absolute structure and the conformation of chiral molecules and this aspect of chiral analysis by VOA should not be overlooked.
关键词： absolute configuration (AC),Raman optical activity (ROA),enantiomeric excess (ee),Chiral analysis,vibrational optical activity (VOA),vibrational circular dichroism (VCD)
更新于2025-09-09 09:28:46
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Complementarity of Electronic and Vibrational Circular Dichroism Spectroscopy in Structure Determination of Vic-Amino Alcohols
摘要： There is no doubt that determination of the absolute configuration of isolated natural products or synthesized compounds remains one of the most important tasks in all fields of chemistry, biochemistry, structural biology and medicinal chemistry. This is unquestionably due to the fact that biological activity is closely related to the stereostructure of bioactive compounds. Therefore, access to methods allowing simple and primarily unequivocal determination of their absolute configuration (AC) and/or conformation is of particular significance. Such a role is at present fulfilled by chiroptical techniques. In the last two decades chiroptical spectroscopy has been one of the most rapidly developing areas of chiral analysis due to the availability of modern, highly specialized and dedicated to particular chiroptical techniques commercial instruments. Recent progress in ab initio simulations of chiroptical properties has also significantly contributed to the increase of the use of chiroptical spectroscopy as a stereochemistry probe [1]. It is generally accepted that combined experimental and theoretical analysis opens much broader application opportunities for chiroptical spectroscopy by giving theoretical basis to experimental results [1-4]. Moreover, utilization of multiple (at least two) chiroptical techniques increases the confidence level of the stereochemical assignment and is nowadays considered by many authors to be the best practice [1-5]. In this Editorial, we will focus on such a combined experimental and theoretical approach of electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) to determine the absolute configuration and conformation. We intend to demonstrate that both these chiroptical techniques are well cooperating and mutually complementary. Moreover, we want to show that the concerted use of the two methods clearly provides more definitive ACs although in many cases stereochemistry can be determined by using only a single chiroptical property. As a model compound for this study (1S,2R)-2-amino-1,2-diphenylethanol (1) with formula shown here below and representing vic-amino alcohols was chosen (Figure 1).
关键词： Electronic Circular Dichroism,Chiroptical Spectroscopy,Absolute Configuration,Vic-Amino Alcohols,Vibrational Circular Dichroism
更新于2025-09-04 15:30:14