Hydrophobicity plays an important role in numerous physico-chemical processes, from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that in the presence of a hydrophobic solute, water forms transient microscopic ‘icebergs’ arising from strengthened water hydrogen bonding, yet there is no experimental evidence for enhanced hydrogen bonding and/or ‘icebergs’ in such solutions. Here we have used the redshifts and line-shapes of the isotopically decoupled infrared O-D stretching mode of small, purely hydrophobic solutes (methane, ethane, krypton, xenon) in water to study hydrophobicity at the most fundamental level. We present the first unequivocal and model free experimental proof for the presence of strengthened water hydrogen bonds near four hydrophobic solutes, matching those in ice and clathrates. The water molecules involved in the enhanced hydrogen bonds display extensive structural ordering resembling that in clathrates. The number of ice-like hydrogen bonds is 10 to 15 per methane molecule. Abinitio molecular dynamics simulations have confirmed that water molecules in the vicinity of methane form stronger, more numerous and more tetrahedrally oriented hydrogen bonds than those in bulk water, and that their mobility is restricted. We demonstrate the absence of intercalating water molecules that cause the electrostatic screening (shielding) of hydrogen bonds in bulk water as the critical element for the enhanced hydrogen bonding around a hydrophobic solute. Our results confirm the classical view of hydrophobic hydration.
COBISS.SI-ID: 6068250
The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations (PII, beta, and alphaR) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either PII or beta for all dipeptides except Gly, whereas the alphaR population is measurable but always minor ((10%) for 18 dipeptides. (The Gly phi-psi map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative beta and PII populations among the 19 dipeptides. Theband frequencies have been assigned as PII, 1,317-1,306 cm-1; alphaR, 1,304-1,294 cm-1; and beta, 1,294-1,270 cm-1. The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both for band frequency and relative population, were obtained by both spectroscopic methods. The beta and PII bands were assigned fromthe dependence of the 3J(HN,Ha) coupling constant (known for all 19 dipeptides) on the relative beta population. The PII band assignment agrees with one made earlier from Raman optical activity data. The temperature dependencesof the relative beta and PII populations fit the standard model with Boltzmann-weighted energies for alanine and leucine between 30 and 60?°C.
COBISS.SI-ID: 4611098
Recent calorimetric measurements of the solvation enthalpies of some dipeptide analogs confirm our earlier prediction that the principle of group additivity is not valid for the interaction of the peptide group with water. We examine the consequences for understanding the properties of peptide solvation. A major consequence is that the current value of the peptide-solvation enthalpy, which is a basic parameter in analyzing the energetics of protein folding, is seriously wrong. Electrostatic calculations of solvation-free energies provide an estimate of the size and nature of the error. Peptide hydrogen exchange rates provide an experimental approach for testing the accuracy of the solvation-free energies of peptide groups found by electrostatic calculations. These calculations emphasize that ignoring electrostatic interactions with neighboring NHCO groups should be a major source of error. Results in 1972 for peptide hydrogen exchange rates demonstrate that peptide-solvation-free energies are strongly affected by adjoining NHCO groups. In the past, the effect of adjoining peptide groups on the exchange rate of a peptide NH proton was treated as an inductive effect. The effect can be calculated, however, by an electrostatic model with fixed partial charges and a continuum solvent.
COBISS.SI-ID: 4103962
Sterol 14alpha-demethylase (CYP51) is the main drug target for the treatment of fungal infections. The discovery of new efficient fungal CYP51 inhibitors requires an understanding of the structural requirements for selectivity for the fungal over the human ortholog. In this study, a binding mode of the pyridylethanol(phenylethyl)amine type CYP51 inhibitor to the human ortholog was determined at the atomic level. We isolated and purified a full-length human CYP51. The inhibitor-specific binding and its conformational and dynamic properties were evaluated using UV-visible and NMR spectroscopy. Considering the experimental data in docking calculations and molecular dynamics simulations, the location of the inhibitor moieties and their interactions with the enzyme active site were determined. The inhibitor binds to the enzyme in two diastereomeric forms, which have common location of aromatic ring moieties, while the less bulky propyl chain can adapt to various hydrophobic regions of the enzyme active site. The halogenated phenyl ring binds in the substrate access channel making numerous contacts with the hydrophobic side chains, and its interactions with the unconserved residues are especially informative. The results reveal the unique binding properties of the investigated inhibitor in comparison to the azoles and provide novel directions for the design of selective fungal inhibitors.
COBISS.SI-ID: 31710937
Nerve growth factor (NGF) was discovered because of its neurotrophic actions on sympathetic and sensory neurons in the developing chicken embryo. NGF was subsequently found to influence and regulate the function of many neuronal and non neuronal cells in adult organisms. Little is known, however, about the possible actions of NGF during early embryonic stages. However, mRNAs encoding for NGF and its receptors TrkA and p75(NTR) are expressed at very early stages of avian embryo development, before the nervous system is formed. The question, therefore, arises as to what might be the functions of NGF in early chicken embryo development, before its well-established actions on the developing sympathetic and sensory neurons. To investigate possible roles of NGF in the earliest stages of development, stage HH 11-12 chicken embryos were injected with an anti-NGF antibody (mAb ?D11) that binds mature NGF with high affinity. Treatment with anti-NGF, but not with a control antibody, led to a dose-dependent inversion of the direction of axial rotation. This effect of altered rotation after anti NGF injection was associated with an increased cell death in somites. Concurrently, a microarray mRNA expression analysis revealed that NGF neutralization affects the expression of genes linked to the regulation of development or cell proliferation. These results reveal a role for NGF in early chicken embryo development and, in particular, in the regulation of somite survival and axial rotation, a crucial developmental process linked to left-right asymmetry specification.
COBISS.SI-ID: 6278938
In this paper we describe the IR spectroscopic method, which is applicable for in-situ measurements of chemical reaction. A part of described experimental set up (ATR measurements and differential spectroscopy) will be applied also in the proposed project. Organic materials are receiving an increasing amount of attention as electrode materials for future post lithium-ion batteries due to their versatility and sustainability. However, their electrochemical reaction mechanism has seldom been investigated. This is a direct consequence of a lack of straightforward and broadly available analytical techniques. Herein, a straightforward in operando attenuated total reflectance infrared spectroscopy method is developed that allows visualization of changes of all infrared active bands that occur as a consequence of reduction/oxidation processes. In operando infrared spectroscopy is applied to the analysis of three different organic polymer materials in lithium batteries. Moreover, this in operando method is further extended to investigation of redox reaction mechanism of poly (anthraquinonyl sulfide) in a magnesium battery, where a reduction of carbonyl bond is demonstrated as a mechanism of electrochemical activity. Conclusions done by the in operando results are complemented by synthesis of model compound and density functional theory calculation of infrared spectra
COBISS.SI-ID: 6333978
Monte Carlo simulations of a small model solute in an aqueous solution are used to examine the effects of solute polarity on hydration structure. A judicious definition of the orientational order parameter leads to reinterpretation of the conventional picture of hydration. As the solute varies from hydrophobic to hydrophilic the ordered first shell water simultaneously fractionates into a more highly ordered and a more disordered component. The hydrogen-bond network rearranges such that the more ordered component relaxes to configurations of optimal intermolecular angles, the other fraction being released from the network.
COBISS.SI-ID: 4872474
Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N/m. Structural and dynamic order persists unchanged to within 15 K of themelting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.
COBISS.SI-ID: 4758298
The aim of the paper was to find a direct connection between dynamic colour changes, phase changes and chemical interactions in model three-component leuco dye based thermochromic systems. The model systems, containing crystal violet lactone as a colour former, bisphenol A as a developer and 1-tetradecanol as a co-solvent, were analysed by DSC and FTIR spectroscopy and the results were related to the characteristics of the dynamic colour change. The ternary thermochromic systems were also compared with binary mixtures of the co-solvent with the developer and colour former, respectively. The temperatures characterizing the dynamic colour change at decolouration limits were directly related to the solid–liquid transition on heating and liquid–solid transition on cooling, regardless the concentration of bisphenol A. In ternary thermochromic systems, an indistinctive phase transition at the temperatures below the solid–solid (crystal–rotator) transition was observed. The straight connection between the phase transitions and temperatures characterizing the dynamic colour change at colouration limits was not proved. The colour contrast of thermochromic systems was found to be directly related to the ratio of integrated intensity of lactone ring opened (solid) and lactone ring closed (liquid) carbonyl vibration characterized by infrared spectroscopy.
COBISS.SI-ID: 5983514
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the molecular scale HE has an entropic origin. It is believed that hydrophobic particles induce order in the surrounding water by reducing the volume of configuration space available for hydrogen bonding. Here we show with computer simulation results that this traditional picture, based on average structural features of hydration water, configurational properties of single water molecules, and up to pairwise correlations, is not correct. Analyzing collective fluctuations in water clusters we are able to provide a fundamentally new picture of HE based on pronounced many-body correlations affecting the switching of hydrogen bonds (HBs) between molecules. These correlations emerge as a nonlocal compensation of reduced fluctuations of local electrostatic fields in the presence of an apolar solute. We propose an alternative view which may also be formulated as a maximization principle: The electrostatic noise acting on water molecules is maximized under the constraint that each water molecule on average maintains as many HBs as possible. In the presence of the solute the maximized electrostatic noise is a result of nonlocal fluctuations in the labile HB network giving rise to strong correlations among at least up to four water molecules.
COBISS.SI-ID: 5094426