An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes

Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumental techniques that require a lot of time and money. Hence, the development of efficient and effective metal indicators is essential. Several synthetic metal detectors have been made, but due to their risk of harm, the use of natural pigments is considered a potential alternative. Experiments are needed for their development, but they are expensive and time-consuming. This review explores various computational methods and approaches that can be used to investigate metal-pigment interactions because choosing the right methods and approaches will affect the reliability of the results. The results show that quantum mechanical methods (ab initio, density functional theory, and semiempirical approaches) and molecular dynamics simulations have been used. Among the available methods, the density functional theory approach with the B3LYP functional and the LANL2DZ ECP and basis set is the most promising combination due to its good accuracy and cost-effectiveness. Various experimental studies were also in good agreement with the results of computational methods. However, deeper analysis still needs to be carried out to find the best combination of functions and basis sets.

Chemical reactivity theory to analyze possible toxicity of microplastics: Polyethylene and polyester as examples

Micro- and nanoplastics are widespread throughout the world. In particular, polyethylene (PE) and polyethylene terephthalate or polyester (PET) are two of the most common polymers, used as plastic bags and textiles. To analyze the toxicity of these two polymers, oligomers with different numbers of units were used as models. The use of oligomers as polymeric templates has been used previously with success. We started with the monomer and continued with different oligomers until the chain length was greater than two nm. According to the results of quantum chemistry, PET is a better oxidant than PE, since it is a better electron acceptor. Additionally, PET has negatively charged oxygen atoms and can promote stronger interactions than PE with other molecules. We found that PET forms stable complexes and can dissociate the guanine-cytosine nucleobase pair. This could affect DNA replication. These preliminary theoretical results may help elucidate the potential harm of micro- and nanoplastics.

Insights into Molecular Structure of Pterins Suitable for Biomedical Applications

Pterins are an inseparable part of living organisms. Pterins participate in metabolic reactions mostly as tetrahydropterins. Dihydropterins are usually intermediates of these reactions, whereas oxidized pterins can be biomarkers of diseases. In this review, we analyze the available data on the quantum chemistry of unconjugated pterins as well as their photonics. This gives a comprehensive overview about the electronic structure of pterins and offers some benefits for biomedicine applications: (1) one can affect the enzymatic reactions of aromatic amino acid hydroxylases, NO synthases, and alkylglycerol monooxygenase through UV irradiation of H₄pterins since UV provokes electron donor reactions of H₄pterins; (2) the emission properties of H₂pterins and oxidized pterins can be used in fluorescence diagnostics; (3) two-photon absorption (TPA) should be used in such pterin-related infrared therapy because single-photon absorption in the UV range is inefficient and scatters in vivo; (4) one can affect pathogen organisms through TPA excitation of H₄pterin cofactors, such as the molybdenum cofactor, leading to its detachment from proteins and subsequent oxidation; (5) metal nanostructures can be used for the UV-vis, fluorescence, and Raman spectroscopy detection of pterin biomarkers. Therefore, we investigated both the biochemistry and physical chemistry of pterins and suggested some potential prospects for pterin-related biomedicine.

Keto, thione, selone, and tellone carotenoids — Changing antioxidants to antireductants

Heterocarotenoids can be considered as xenobiotic compounds as they are foreign to living organisms. Thione carotenoids are heterocarotenoids that are particularly interesting because the presence of sulfur shifted the absorption to longer wavelengths than the corresponding keto carotenoids. This may be important for further applications such as the development of new pigments. Keto carotenoids are well-known antiradical molecules, however, nothing is known about heterocarotenoids acting as free radical scavengers. Thus, the main goal of this investigation is to study the antiradical properties of some heterocarotenoids, such as thione, selone, and tellone carotenoids. For this purpose, the energy differences between singlets and triplets are used to analyze the singlet oxygen quenching mechanism, and the electron transfer mechanism is investigated, taking into account that these may constitute antiradical molecules either donating or accepting electrons (antioxidants or antireductants). To analyze these mechanisms, vertical ionization energy (I), vertical electron affinity (A), and electrodonating (χ−) and electroaccepting (χ+) electronegativities were evaluated by applying density functional theory calculations. The investigated heterocarotenoids are as effective as keto carotenoids in terms of being either electron donors or acceptors, and therefore, they have a similar capacity for scavenging free radicals. Changing the C=O group to C=S, C=Se, or C=Te converts an antioxidant to an antireductant.

A folate independent role for cytosolic HPPK/DHPS upon stress in Arabidopsis thaliana

Cytosolic HPPK/DHPS (cytHPPK/DHPS) in Arabidopsis is a functional enzyme with activity similar to its mitochondrial isoform. Genomic complementation of the cytHPPK/DHPS knockout mutant with the wild type gene led to a complete rescue of the stress sensitive mutant phenotype in seed germination tests under abiotic stress conditions. Moreover, over-expression of the gene resulted in higher germination rate under stress as compared to the wild-type, confirming its role in stress resistance. Analysis of folates in seedlings, inflorescence and dry seeds showed unchanged levels in the wild-type, mutant and over-expressor line, upon stress and normal conditions, suggesting a role for cytHPPK/DHPS distinct from folate biosynthesis and a folate-independent stress resistance mechanism. This apparently folate-independent mechanism of stress resistance points towards a possible role of pterins, since the product of HPPK/DHPS is dihydropteroate.