Modeling red coral (Corallium rubrum) and African snail (Helixia aspersa) shell pigments: Raman spectroscopy versus DFT studies

Pigments from red coral (Corallium rubrum) and African snail (Helixia aspersa) shell were studied non‐invasively using Raman spectroscopy with 1064‐nm laser beam. The two observed bands because of organic pigments confined in biomineralized CaCO₃ matrix at about 1500 and 1100 cm⁻¹ were assigned to ν(CC) and ν(C―C), respectively. Both signals originate from polyene(s) of largely unknown structure, containing several conjugated CC bonds. The small peak at 1016 cm⁻¹ in the Raman spectrum of coral pigment was assigned to in‐plane ―CH₃ rocking or structural deformation of polyene chain because of spatial confinement in the mineral matrix. The organic pigments in red coral and snail shell were present in inorganic matrix containing aragonite (shell) and calcite (coral). In addition, using Raman spectroscopy, it was observed that aragonite was replaced by calcite as result of healing damaged parts of snail shell. This is an important finding which indicates a great potential of nondestructive Raman spectroscopy instead of X‐ray technique, as a diagnostic tool in environmental studies. To support analysis of the observed Raman spectra detailed calculations using density functional theory (DFT with B3LYP and BLYP density functionals) on structure and vibrations of model all‐trans polyenes were undertaken. DFT calculated CC and C―C stretching frequencies for all‐trans polyenes containing from 2 to 14 CC units were compared with the observed ν(CC) and ν(C―C) band positions of the studied coral and shell. Individual correction factors were used to better match theoretical wavenumbers with observed band positions in red coral and African snail. It was concluded that all‐trans polyene pigments of red coral and dark parts of African snail shell contain 11–12 and 14 CC double bond units, respectively. However, Raman spectroscopy cannot produce any clear information on the presence and nature of the end‐chain substituents in the studied pigments. Copyright © 2016 John Wiley & Sons, Ltd.     

Identification of naphthoylindoles acting on cannabinoid receptors based on their fragmentation patterns under ESI-QTOFMS

'Herbal highs' have been advertised as legal and natural substitutes to cannabis, but a detailed examination of these products has revealed that the herbal matrix is laced with synthetic substances that mimic the effects of marijuana. Producers select the ingredients based on the results of scientific studies on the affinities of different chemicals to cannabinoid receptors. Naphthoylindoles have turned out to be the most popular class of substances identified in the products. Legal actions taken in order to tackle the problem of uncontrolled access to one substance have usually resulted in the marketing of derivatives or analogues. In the study, the mass spectral behavior of twelve synthetic cannabinoids from the naphthoylindole family under electrospray ionization (ESI) was investigated. LC-QTOFMS experiments were performed in three modes (low fragmentor voltage, high fragmentor voltage with/without collision energy), and they enabled the identification of protonated molecules and main ions. A general fragmentation pattern under this ionization method was proposed, and mechanisms of ion formation were discussed. The developed procedure allowed the determination of substituent groups of the core naphthoylindole structure and distinction between positional isomers. The obtained results were used for the prediction of the ESI-MS spectra for many naphthoylindoles with a high affinity to cannabinoid receptors. Similarities and differences between ESI-MS and electron impact-MS spectra of naphthoylindoles were discussed. The developed identification process was presented on an example of an analysis of an unknown herbal material, in which JWH-007 was finally identified. Knowledge of the fragmentation mechanisms of naphthoylindoles could also be used by other researchers for identification of unknown substances in this chemical family.     

Retrospective correction for T1-weighting bias in T2 values obtained with various spectroscopic spin-echo acquisition schemes

Localized tissue transverse relaxation time (T₂) is obtained by fitting a decaying exponential to the signals from several spin-echo experiments at different echo times (TE). Unfortunately, time constraints in magnetic resonance spectroscopy (MRS) often mandate in vivo acquisition schemes at short repetition times (TR), that is, comparable with the longitudinal relaxation constant (T₁). This leads to different T₁-weighting of the signals at each TE. Unaccounted for, this varying weighting causes systematic underestimation of the T₂'s, sometimes by as mush as 30%. In this article, we (i) analyze the phenomenon for common MRS spin-echo T₂ acquisition schemes; (ii) propose a general post hoc T₁-bias correction for any (TR, TE) combination; (iii) show that approximate knowledge of T₁ is sufficient, since a 20% uncertainty in T₁ leads to under 3% bias in T₂; and consequently, (iv) efficient, precision-optimized short TR spin-echo T₂ measurement protocols can be designed and used without risk of accuracy loss. Tables of correction for single-refocusing (conventional) spin-echo and double refocusing, such as, PRESS acquisitions, are provided.     

Lack of self-averaging in neutral evolution of proteins

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.     

Fluctuation analysis of meteo-marine data

We study long-term behaviour of air temperature, wave heights and wind speed time series recorded for the period 1993–1997 at a meteo-marine station located in the Adriatic Sea. The scaling analysis shows that fluctuations of air temperature display long-range autocorrelations, while those for wave heights show a more complex behaviour, crossing over from a persistent regime at intermediate time scales (up to about 20 days) to an anti-persistence behaviour at longer times. Furthermore, the crosscorrelations of their records are found to be large, with a covariance of about -0.3 (indicating anti-crosscorrelations) within the full 5-years period, giving a quantitative measure of the actual coupling between the two data sets. Wind speed fluctuations are found to be strongly crosscorrelated (about 0.6) with those of wave heights, indicating as expected that wind is the main driving force for wave height fluctuations.     

Umbilic point screening in random optical fields

Umbilic points--singular points of curvature characterized by a fractional topological charge q=+/-1/2--are the most numerous of all special points in the landscape of random optical fields (speckle patterns), outnumbering maxima, minima, saddle points, and optical vortices. To the best of our knowledge, we present the first experimental evidence that positive and negative umbilic points screen one another. Theory predicts that in the absence of screening the charge variance in a bounded region is proportional to the area of the region, whereas in the presence of screening the variance is drastically reduced and is proportional to the perimeter. Our data confirm this latter prediction and provide the first estimates of the screening lengths for umbilic points of the intensity and of the amplitude (field modulus).     

From holes to sponge at irradiated Ge surfaces with increasing ion energy—an effect of defect kinetics?

We show that hole patterns and sponge-like layers at irradiated Ge surfaces originate from the same driving force, namely the kinetics of ion beam induced defects in the amorphous Ge surface layer. Ge hole patterns reported earlier for irradiation with low energy (5 keV) Ga⁺ ions were reproduced for low energy Bi⁺ but also for Ge⁺ self-irradiation, which proves that the dominating driving force for morphology evolution cannot originate from the implanted impurities. At higher ion energies the well-known formation of sponge-like Ge surface layers after heavy ion irradiation was found for Bi⁺ irradiation and Ge⁺ self-irradiation, also. The transition from smooth surfaces via hole patterns to sponge-like morphologies with increasing ion energies was studied in detail. A model based on the kinetics of ion beam induced defects was developed and implemented in 3D kinetic Monte Carlo simulations, which reproduce the transition from hole patterns to sponge-like layers with increasing ion energy.