Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-H..Se and C-H..S interactions (∼80%), notably less numerous are structures with Se..Se and S..S interactions (∼5%), and Se..π and S..π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-H..Se (∼-0.8 kcal mol-1) and C-H..S interactions are weaker than the most stable parallel interaction (∼-3.3 kcal mol-1) and electrostatic interactions of σ/π type (∼-2.6 kcal mol-1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-H..Se (∼-4.4 kcal mol-1) and N-H..Se interactions (∼-2.2 kcal mol-1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand. © 2020 International Union of Crystallography

Fluorination of aliphatic compounds. Driving force in crystal structures

Statistical analysis of crystal structures from CSD (Crystallographic database) has shown the F...F contacts are the second group of interactions (23050 structures), immediately after the hydrogen bonds (43397 structures), that are mainly of aliphatic C−H...F type. There is no clear tendency of F...F contacts toward some certain values of d parameter, but it is possible to notice noticeable clear tendency of numerous structures to d values greater than 2.9 Å. There is a pronounced maximum in the range of torsion angle T from 160 to 180° corresponding to trans orientation of interacting C−F and X−Y fragments.На основу анализе кристалних структура преузетих из Кембричке базе кристалографских података (CSD) показано је да се алифтичне C−H...F водоничне везе издвајају као најбројније интеракције флуорованих алифатичних група (43397 стуктура). Далеко испод (23050 структура), на другом месту су F...F интеракције. Уочљиво је да су вредности F...F растојања (d параметар) претежно изнад 2,9 Å. Међутим, не постоји јасно изражена тенденција према одређеној вредности d параметра. Пошто се за највећи број структура вредности торзионог угла C-F-X-Y (Т параметар) крећу између 160 и 180° може се закључити да интерагујуће C−F и X−Y групе међусобно заузимају trans оријентациј

Fluorination of aromatic groups. The effects of coordination on fluorine interactions

Statistical analysis of crystal structures obtained from Cambridge Structural Database (CSD) showed that the most numerous are structures in which carbon atom is bound to interacting fluorine atom.Statistička analiza kristalnih struktura iz Kembričke baze strukturnih podataka pokazuje da su najbrojnije one strukture kod kojih je ugljenikov atom vezan za interagujući atom fluora. One u kojima je fluor vezan za aromatičnu grupu su malo manje zastupljene

Influence of halogenation of aromatic ring on the conformation of spirohydantoin compounds

Kristalografska i kvantnohemijska studija, koja je usmerena na proučavanje efekata fluorovanja benzoil-grupe vezane za cikloheksan-5-spirohidantoin, pokazala je da aromatični prsten ima najveći afinitet prema cikloheksanskom prstenu (nepolarnim grupama), sa kojim gradi C–H∙∙∙π i paralelne interakcije sa velikim pomakom. Uvođenje atoma fluora na aromatični prsten dovodi do povećanog afiniteta, usled stvaranja dodatnih C–H∙∙∙F interakcija. Dodatno, ova studija je proširena na hlorovane i bromovane derivate. Analizom kristalnog pakovanja četiri derivata spirohidantoina (slika) pokazano je da orijentacija aromatičnog prstena, koja je preko rotabilne C(aromatični)–C(karbonilni) veze odvojena od rigidnog spirohidantoinskog jezgra, određuje trodimenzionalnu supramolekulsku arhitekturu. Energijski profil rotabilne veze (slika) jako zavisi od vrste halogenog atoma vezanog za aromatični prsten (X). Najvišu barijeru (najmanju rotacionu slobodu) ima aromatični prsten sa Br atomom (oko 36 kcal/mol), dok najnižu barijeru imaju prstenovi sa vezanim Cl ili F atomom (oko 7 kcal/mol). Izmerene vrednosti torzionog ugla T (slika) u kristalnim stukturama, koji definiše rotabilnost ove veze, odgovaraju minimumima energije na energijskim profilima. Kod ovih orijentacija aromatični prstenovi istovremeno grade C– H...π interakcije sa hidantoinskim prstenom i C–H...O interakciju sa karbonilnom grupom koja premošćuje dva prstena. Na osnovu ovih rezultata može se zaključiti da su orijentacije aromatičnog prstena određene unutarmolekulskim interakcijama, a ne međumolekulskim interakcijama, kao i da su konformacione razlike uzrok razlika u kristalnom pakovanju ovih jedinjenja.The crystallographic and quantum chemical study, focused on the effects of fluorination of the benzoyl group bound to the spirohydantoin moiety, showed that the aromatic ring has the highest affinity towards the cyclohexene ring (nonpolar groups), thus forming C–H∙∙∙π and parallel interactions at large offset. Introduction of a fluorine atom into the aromatic ring leads to higher affinity, due to formation of additional C–H∙∙∙F interactions. Subsequently, the present study has been extended to chlorinated and brominated derivatives. An analysis of the crystal packaging of four spirohydantoin derivatives has shown that the orientation of the aromatic ring, bound to the rigid spirohydantoin moiety by the rotatable C(aromatic)–C(carbonyl) bond, determines the three-dimensional supramolecular architecture. The energy profile of the rotatable bond (Figure) strongly depends on the halogen atom bound to the aromatic ring (X). The highest barrier (the lowest rotational freedom) has been found for the aromatic ring with the Br atom (36 kcal/mol), while the rings with the Cl or F atom have the lowest barrier (7 kcal/mol). The measured values of the torsion angle T in the crystal structures which defines the rotability of the mentioned bond, correspond to the energy minima on the energy profiles. In these orientations, the aromatic ring simultaneously forms C–H...π interactions with the hydantoin ring and C–H...O interaction with the carbonyl spacer group. Based on these results, one can conclude that the orientation of the aromatic ring is defined by intramolecular interactions, not by intermolecular interactions, as well as that the conformational differences further cause differences in the crystal packaging of these compounds

INFLUENCE OF HALOGENATION OF AROMATIC RING ON THE CONFORMATION OF SPIROHYDANTOIN COMPOUNDS

Kristalografska i kvantnohemijska studija, koja je usmerena na proučavanje efekata fluorovan-ja benzoil-grupe vezane za cikloheksan-5-spirohidantoin, pokazala je da aromatični prsten ima najveći afinitet prema cikloheksanskom prstenu (nepolarnim grupama), sa kojim gradi C–H∙∙∙π i paralelne interakcije sa velikim pomakom. Uvođenje atoma fluora na aromatični prsten dovodi do povećanog afiniteta, usled stvaranja dodatnih C–H∙∙∙F interakcija [1]. Dodatno, ova studija je proširena na hlorovane i bromovane derivate. Analizom kristalnog pakovanja četiri derivata spiro-hidantoina (slika) pokazano je da orijentacija aromatičnog prstena, koja je preko rotabilne C(aromatični)–C(karbonilni) veze odvojena od rigidnog spirohidantoinskog jezgra, određuje trodimenzionalnu supramolekulsku arhitekturu. Energijski profil rotabilne veze (slika) jako zavisi od vrste halogenog atoma vezanog za aromatični prsten (X). Najvišu barijeru (najmanju rotacionu slobodu) ima aromatični prsten sa Br atomom (oko 36 kcal/mol), dok najnižu barijeru imaju prstenovi sa vezanim Cl ili F atomom (oko 7 kcal/mol). Izmerene vrednosti torzionog ugla T (slika) u kristalnim stukturama, koji definiše rotabilnost ove veze, odgovaraju minimumima ener-gije na energijskim profilima. Kod ovih orijentacija aromatični prstenovi istovremeno grade C–H...π interakcije sa hidantoinskim prstenom i C–H...O interakciju sa karbonilnom grupom koja premošćuje dva prstena. Na osnovu ovih rezultata može se zaključiti da su orijentacije aro-matičnog prstena određene unutarmolekulskim interakcijama, a ne međumolekulskim interakcija-ma, kao i da su konformacione razlike uzrok razlika u kristalnom pakovanju ovih jedinjenja.The crystallographic and quantum chemical study, focused on the effects of fluorination of the benzoyl group bound to the spirohydantoin moiety, showed that the aromatic ring has the highest affinity towards the cyclohexene ring (nonpolar groups), thus forming C–H∙∙∙π and parallel interac-tions at large offset. Introduction of a fluorine atom into the aromatic ring leads to higher affinity, due to formation of additional C–H∙∙∙F interactions [1]. Subsequently, the present study has been extended to chlorinated and brominated derivatives. An analysis of the crystal packaging of four spirohydantoin derivatives (Figure) has shown that the orientation of the aromatic ring, bound to the rigid spirohydantoin moiety by the rotatable C(aromatic)–C(carbonyl) bond, determines the three-dimensional supramolecular architecture. The energy profile of the rotatable bond (Figure) strongly depends on the halogen atom bound to the aromatic ring (X). The highest barrier (the lowest rotational freedom) has been found for the aro-matic ring with the Br atom (36 kcal/mol), while the rings with the Cl or F atom have the lowest barrier (7 kcal/mol). The measured values of the torsion angle T in the crystal structures (Figure), which defines the rotability of the mentioned bond, correspond to the energy minima on the energy profiles. In these orientations, the aromatic ring simultaneously forms C–H...π interactions with the hydantoin ring and C–H...O interaction with the carbonyl spacer group. Based on these results, one can conclude that the orientation of the aromatic ring is defined by intramolecular interactions, not by intermolecular interactions, as well as that the conformational differences further cause differ-ences in the crystal packaging of these compounds

Nondestructive optical method for plant overall health evaluation

In vivo measurements of the optical properties of plant leaves, by spectrophotometric methods, could potentially provide very useful information for the assessment of the plant’s health. This paper describes a novel experimental set-up that enables continuous measurements of the optical reflection and transmission coefficients of broad-leaved plants. The optical spectral characteristics of leaves, in the broad wavelength range, are often a discussed topic in the scientific literature. Nevertheless, to the best of our knowledge, the real-time spectral analyses of the leaf haven’t been reported so far. Monitoring the evolution of the plant activity in real-time has resulted in the graph of the spectral Circadian rhythm as a function of time. The set-up was tested on Phaseolus vulgaris and the results of the measurements are presented and discussed