Vibrational circular dichroism of adenosine crystals.

Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution.

Induced Chirality in Canthaxanthin Aggregates Reveals Multiple Levels of Supramolecular Organization.

Carotenoids tend to form supramolecular aggregates via non-covalent interactions where the chirality of individual molecules is amplified to the macroscopic level. We show that this can also be achieved for non-chiral carotenoid monomers interacting with polysaccharides. The chirality induction in canthaxanthin (CAX), caused by heparin (HP) and hyaluronic acid (HA), was monitored by chiroptical spectroscopy.

What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments.

Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively).

Vibrational Circular Dichroism Unravels Supramolecular Chirality and Hydration Polymorphism of Nucleoside Crystals.

Invited for the cover of this issue are Valery Andrushchenko, Monika Krupová, and co-workers at the Institute of Organic Chemistry and Biochemistry (IOCB Prague) of the Czech Academy of Sciences. The image depicts a "crystal city" illuminated by "chiral suns" shining left- and right-circularly polarized light (L-CPL and R-CPL), which reveals differences in the structure of the chiral crystalline "skyscrapers". Designed by Tomáš Belloň @ IOCB Prague.

Vibrational Circular Dichroism Unravels Supramolecular Chirality and Hydration Polymorphism of Nucleoside Crystals.

Vibrational circular dichroism (VCD) spectroscopy has been widely used to study (bio)molecules in solution. However, its solid-state applications have been restricted due to experimental limitations and artifacts. Having overcome some of them, the first VCD study of nucleoside crystals is now presented.

Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment.

Chiroptical spectroscopic methods are excellent tools to study structure and interactions of biomolecules. However, their sensitivity to different structural aspects varies. To understand the dependence of absorption, electronic and magnetic circular dichroism (ECD, MCD) intensities on the structure, dynamics and environment, we measured and simulated spectra of nucleosides and other nucleic acid model components.

Origins of Optical Activity in an Oxo-Helicene: Experimental and Computational Studies.

Helicenes are known to provide extremely strong optical activity. Prediction of the properties of helicenes may facilitate their design and synthesis for analytical or materials sciences. On a model 7,12,17-trioxa[11]helicene molecule, experimental results from multiple spectroscopic techniques are analyzed on the basis of density functional theory (DFT) simulations to test computational methodology and analyze the origins of chirality.

Insight into the Mechanism of Action and Peptide-Membrane Interactions of Aib-Rich Peptides: Multitechnique Experimental and Theoretical Analysis.

The increase in resistant bacterial strains necessitates the identification of new antimicrobial molecules. Antimicrobial peptides (AMPs) are an attractive option because of evidence that bacteria cannot easily develop resistance to AMPs. The peptaibols, a class of naturally occurring AMPs, have shown particular promise as antimicrobial drugs, but their development has been hindered by their mechanism of action not being clearly understood.

Complexation and stability of the fungicide penconazole in the presence of zinc and copper ions.

Rationale: For the risk assessment of penconazole in the environment and the evaluation of the possible consequences of its use, it is important to determine how its reactivity and degradation are influenced by metals commonly found in nature, such as copper and zinc.

Methods: Changes in the reactivity of penconazole in the presence of zinc/copper ions were studied using electrospray ionisation mass spectrometry and density functional theory calculations.

Results: Many penconazole complexes with copper and zinc ions were created; a comparison of the elements showed that a few complexes were formed analogously (doubly charged complexes with four penconazole molecules, singly charged complexes with chlorine as a counterion and singly charged complexes with deprotonated penconazole as a counterion).

Characterization of Eight Novel Spiroleptosphols from .

Chemical analyses of grown on banana medium resulted in eight novel spiroleptosphols, T1, T2 and U-Z (-). The structures were elucidated by a combination of high-resolution mass spectrometric data and 1- and 2-D NMR experiments. The relative stereochemistry was assigned by H coupling and NOESY/ROESY experiments.

Influence of the hydrophobic domain on the self-assembly and hydrogen bonding of hydroxy-amphiphiles.

The amphiphiles 1-octadecanol (octadecyl (stearyl) alcohol, ODA) and 1,2-dioleoylglycerol (DOG) were studied by IR spectroscopy and X-ray diffraction combined with multiscale theoretical modeling. The computations allowed us to rationalize the experimental findings and deduce the supramolecular structure of the formed assemblies while providing a fairly detailed insight into their hydrogen-bonding patterns. IR spectra revealed that the amphiphilic assemblies dramatically differ in structural order and hydrogen-bond strength, both being high in ODA and low in DOG.

Eu as a luminescence probe in DNA studies: Structural and conformational implications.

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.

Europium (III) as a Circularly Polarized Luminescence Probe of DNA Structure.

We report as a proof-of-concept the first application of circularly polarized luminescence (CPL) measured with a Raman optical activity (ROA) spectrometer to differentiate several DNA structures without need of sensitizing complexes. The ROA/CPL approach provides sufficiently high CPL intensity to use hydrated Eu ions, thus avoiding DNA structural changes associated with binding of sensitizers and overcoming the sensitizer quenching issue. We showed that deoxyguanosine monophosphate (dGMP), single- and double-stranded DNA provide different CPL spectra, which could be used for their discrimination.

Optically Active Vibrational Spectroscopy of α-Aminoisobutyric Acid Foldamers in Organic Solvents and Phospholipid Bilayers.

Helical α-aminoisobutyric acid (Aib) foldamers show great potential as devices for the communication of conformational information across phospholipid bilayers, but determining their conformation in bilayers remains a challenge. In the present study, Raman, Raman optical activity (ROA), infrared (IR) and vibrational circular dichroism (VCD) spectroscopies have been used to analyze the conformational preferences of Aib foldamers in solution and when interacting with bilayers. A 3 -helix marker band at 1665-1668 cm in Raman spectra was used to show that net helical content increased strongly with oligomer length.

Insight into vibrational circular dichroism of proteins by density functional modeling.

Vibrational circular dichroism (VCD) spectroscopy is an excellent method to determine the secondary structure of proteins in solution. Comparison of experimental spectra with quantum-chemical simulations represents a convenient and objective way to extract information on the structure. This has been difficult for such large molecules where approximate theoretical models have to be used.

Identification of Lanthanide(III) Luminophores in Magnetic Circularly Polarized Luminescence Using Raman Optical Activity Instrumentation.

Luminescence of lanthanide(III) ions sensitively reflects atomic environment. However, the signal may be weak and covered by Raman scattering. In the present study magnetic circularly polarized luminescence (MCPL) is explored as a more sensitive tool to recognize the lanthanide signal and assign underlying electronic transitions.

Dipolar molecules inside C: an electric field-driven room-temperature single-molecule switch.

We propose a two-state electric field-driven room-temperature single-molecule switch based on a dipolar molecule enclosed inside ellipsoidal fullerene C. We show that the two low-energy minima of the molecular dipole inside the C cage provide distinguishable molecular states of the system that can be switched by application of an external electric field.

Vibrational Properties of the Phosphate Group Investigated by Molecular Dynamics and Density Functional Theory.

The phosphate group (PO2(-)) is an important building block occurring in many components of living matter including nucleic acids. It provides distinct features in vibrational spectra and is useful as a local probe of NA conformation and interactions with the environment. For this purpose, it is desirable to explore in detail various factors influencing spectral shapes of characteristic phosphate vibrations.

Metallization of single-stranded polyI by Zn(2+) ions in neutral solutions.

Metallization of single-stranded polyinosinic acid (polyI) by Zn(2+) ions at pH 7.0 was studied by differential UV spectroscopy at different temperatures. It was found that polyI is metallized at N7 and N1 atoms of hypoxanthine.

Magnetic circular dichroism of porphyrin lanthanide M3+ complexes.

Lanthanide complexes exhibit interesting spectroscopic properties yielding many applications as imaging probes, natural chirality amplifiers, and therapeutic agents. However, many properties are not fully understood yet. Therefore, we applied magnetic circular dichroism (MCD) spectroscopy, which provides enhanced information about the underlying electronic structure to a series of lanthanide compounds.

Communication: fullerene resolution by the magnetic circular dichroism.

The similarity in shape makes separation and identification of fullerenes difficult. In this work, the magnetic circular dichroism (MCD) spectroscopy is presented as a useful tool for this purpose. Experimental C60 and C70 spectra were obtained and reproduced with the aid of density functional computations and the complex polarization propagator method.

Porphyrin protonation studied by magnetic circular dichroism.

Magnetic circular dichroism (MCD) spectroscopy provides valuable information about electronic excited states in molecules. The interpretation of spectra is however difficult, often requiring additional theoretical calculations to rationalize the observed signal. Recent developments in time-dependent density functional theory (TDDFT) bring hope that the applicability of MCD spectroscopy for chemical problems may be significantly extended.

Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism.

The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling.

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides.

The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms.