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A potential role of optical technologies in medicine including micro-Raman spectroscopy is diagnosis of bacteria, cells and tissues which is covered in this chapter. The main advantage of Raman-based methods to complement and augment diagnostic tools is that unsurpassed molecular specificity is achieved without labels and in a nondestructive way. Principles and applications of micro-Raman spectroscopy in the context of medicine will be described. First, Raman spectra of biomolecules representing proteins, nucleic acids, lipids and carbohydrates are introduced. Second, microbial applications are summarized with the focus on typing on species and strain level, detection of infections, antibiotic resistance and biofilms. Third, cytological applications are presented to classify single cells and study cell metabolism and drug–cell interaction. Fourth, applications to tissue characterization start with discussion of lateral resolution for Raman imaging followed by Raman-based detection of pathologies and combination with other modalities. Finally, an outlook is given to translate micro-Raman spectroscopy as a clinical tool to solve unmet needs in point-of-care applications and personalized treatment of diseases.

The field of computational prediction of various toxicity end-points has evolved over last two decades significantly. Availability of newer modelling techniques, powerful computational resources and good-quality data have made it possible to generate reliable predictions for new chemical entities, impurities, chemicals, natural products and a lot of other substances. The field is still undergoing metamorphosis to take into account molecular complexities underlying toxicity end-points such as teratogenicity, mutagenicity, carcinogenicity, etc. Expansion of the applicability domain of these predictive models into areas other than life sciences, such as environmental and materials sciences have received a great deal of attention from all walks of life, fuelling further development and growth of the field. The present chapter discusses the state-of-the-art computational prediction of toxicity end-points of small organic molecules to balance the trade-off between the molecular complexity and the quality of such predictions, without compromising their immense utility in many fields.

Phthalocyanines (Pcs) and their derivatives have attracted a lot of attention because of their both biological importance and technological applications. The properties of Pcs can be tuned by replacing the central atom, by modifying the periphery of phthalocyanine ring, and by changing the meso -atoms. One more promising pathway for modifying Pcs and their derivatives can be the core-modification , or substitution of the core isoindole nitrogen(s) by other elements. Motivated by the results obtained for some core-modified porphyrins, we investigated computationally complete core-modification of regular Zn phthalocyanine (ZnPc) with P and S. We performed density functional theory studies of the structures, charges, and frontier molecular orbitals of P-core-modified and S-core-modified ZnPcs, ZnPc(P) 4 and ZnPc(S) 4 , using both B3LYP and two dispersion-corrected functionals. Also, we studied computationally formation of complexes between the fullerene C 60 and ZnPc(P) 4 and ZnPc(S) 4 . Both ZnPc(P) 4 and ZnPc(S) 4 show strong bowl-like distortions similar to the results obtained earlier for ZnP(P) 4 and ZnP(S) 4 . The size of the “bowl” cavity of the both core-modified Pcs is essentially the same, showing no dependence on the core-modifying element. For ZnPc(S) 4 , the HOMO is quite different from those of ZnPc and ZnPc(P) 4 . When the fullerene C 60 forms complexes with the ZnPc(P) 4 and ZnPc(S) 4 species in the gas phase, it is located relatively far (4.30–5.72 Å) from the one of the P-centers and from the Zn-center of ZnPc(P) 4 , whereas with ZnPc(S) 4 C 60 forms relatively short bonds with the Zn-center, varying from ca. 2.0 to ca. 3.0 Å. The very strong deformations of both the ZnPc(P) 4 and ZnPc(S) 4 structures are observed. The calculated binding energy at the B3LYP/6-31G* level for the C 60 -ZnPc(P) 4 complex is quite low, 1.2 kcal/mol, which agrees with the quite long distances fullerene - ZnPc(P) 4 , whereas it is noticeably larger, 13.6 kcal/mol, for the C 60 -ZnPc(S) 4 complex which again agrees with the structural features of this complex. The binding energies of the complexes optimized using the dispersion-corrected functionals, CAM-B3LYP and wB97XD, are significantly larger, varying from ca. 14 till 52 kcal/mol which corresponds with the shorter distances between the fullerene and ZnPc(X) 4 species.

Combining a stylistic approach with chemical analyses and focusing not only on composition but also on production technology, this research aims to identify possible centres of post-medieval production of glass as well as decorative production techniques used in stained glass, in particular the grisaille. The use of several combined analytical techniques allowed for the unveiling of the composition of glass and the structure of grisailles. Sorting out the grisaille structure sheds light on the processes employed to produce paints, while compositions of glass objects are used to propose production provenances. Both contribute to the study and critical analysis of how glass heritage has developed over time, including materials and technical practices, uncovering the transfer of technology and movement of people and goods.

Structure elucidation is an important and sometimes time-consuming step for natural products research. This step has evolved in the past few years to a faster and more automated process due to the development of several computational programs and analytical techniques. In this paper, the topics of NMR prediction and CASE programs are addressed. Furthermore, the elucidation of natural peptides is discussed.

Methadone is a morphine-substitute drug in methadone maintenance treatment (MMT) program to treat patients with opioid dependency. However, the methadone clinical effects are depending on the methadone metabolism rates that vary among the patients with genetic polymorphism of cytochrome P450s (CYPs). Our previous study showed methadone has different binding affinity due to the polymorphisms in CYP2B6, CYP2D6 and CYP3A4 that could contribute to the methadone metabolism rate. In this work, the conformation and interactions of R - and S -methadone in wild type CYP2B6, CYP2D6 and CYP3A4 were further studied in order to understand behaviour of R - and S -methadone at the CYP binding site. Clustering analysis showed that the conformation of R - and S -methadone in CYP2B6 are most stable, thus could lead to a higher efficiency of methadone metabolism. The conformation fluctuation of methadone in CYP2D6 could due to relatively smaller binding pocket compared with CYP2B6 and CYP3A4. The binding sites volumes of the studied CYPs were also found to be increased upon the binding with methadone. Therefore, this might contributed to the interactions of both R - and S -methadone in CYPs were mainly by hydrophobic contacts, van der Waals and electrostatic interactions. In the future, should an inhibitor for CYP is to be designed to prolong the prolonged opioid effect, the inhibitor should cater for single CYP isozyme as this study observed the behavioural differences of methadone in CYP isozymes. Graphical Abstract :

While there are many techniques to study phenomena that occur in chemical engineering applications, magnetic resonance imaging (MRI) receives increasing scientific interest. Its non-invasive nature and wealth of parameters with the ability to generate functional images and contrast favors the use of MRI for many purposes, in particular investigations of dynamic phenomena, since it is very sensitive to motion. Recent progress in flow-MRI has led to shorter acquisition times and enabled studies of transient phenomena. Reactive systems can easily be imaged if NMR parameters such as relaxation change along the reaction coordinate. Moreover, materials and devices can be examined, such as batteries by mapping the magnetic field around them.

With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins , and metal containing proteins . Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.