Educational components in the supervision of chemistry postgraduate students: experiences and reflections

This article focuses on the educational aspects of mentoring chemistry postgraduate students, analysing the challenges encountered by students in the transition from undergraduate to postgraduate learning, and throughout the postgraduate projects up to completion of PhD level, and discussing the design of suitable addressing options by the mentor. The mentoring activity is thus viewed within a typical chemistry education paradigm. Some challenges basically continue those encountered at undergraduate level and others are specific to the postgraduate one, thus requiring new approaches. The information presented in the article is mostly based on the author’s long experience at the University of Venda (South Africa). The approach utilised in the study is a suitable adaptation of action research. The analysis aims at being comprehensive, considering the major features influencing students’ performance, and the strategies that can be adopted to counteract negative impacts and to foster the development of scientific modes of thinking and of research independence. It outlines how known major difficulties, such as diffuse poor language mastery (aggravated by second language instruction), complicate both the undergraduate-postgraduate transition—by affecting the speed and extent to which students learn new approaches—and the further stages, including thesis writing. Writing-related difficulties are given particular attention because they have great impact even for students who have acquired good abilities with the design and practical components of research projects, and because the acquisition of adequate skills in scientific writing is an inherent objective of postgraduate training. Most of the reported observations refer to postgraduate studies in computational chemistry; this enables a broad perspective, by including the common challenges of obtaining, organising and analysing data, as well as the challenges related to learning a new area of chemistry, not encountered in undergraduate studies, and those related to specific demands such as adequate mathematics knowledge, visualization abilities and the ability to abstract thinking.

Conformational preferences and intramolecular hydrogen bonding patterns of tetraflavaspidic acid BBBB – a tetrameric acylphloroglucinol

Tetraflavaspidic acid BBBB is a tetrameric acylphloroglucinol of natural origin isolated from Dryopteris aitoniana. Its molecule consists of four acylphloroglucinol units linked by methylene bridges and having the same R = propyl in their R−C=O groups. In one of the terminal monomers, one of the OHs ortho to R−C=O is replaced by a keto O. The paper reports the results of a conformational study performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels; two options are utilised for the latter, without and with the inclusion of the Grimme’s dispersion correction. Given the importance of intramolecular hydrogen bonds (IHBs) for the stabilisation of acylphloroglucinol conformers, only conformers containing the maximum IHBs’ number were calculated. The IHBs comprise an IHB between the sp2 O of R−C=O and a neighbouring OH in each monomeric unit and two inter-monomer IHBs between each pair of units. The single C−C bonds of the methylene bridges enable a variety of mutual orientations of the monomeric units, giving rise to a variety of conformations and IHB patterns. The results indicate greater stability for conformers in which individual monomers take lower energy conformations, and significant influence of the dispersion correction on the estimation of the energetics and of other molecular properties. The inclusion of the dispersion correction also strongly limits the number of low energy conformers. The influence of dispersion effects is consistent with the presence of four aromatic rings.

The spontaneity of chemical reactions: challenges with handling the concept and its implications

The spontaneity concept plays crucial roles in the description of chemical reactions and entails a variety of implications, including the determination of the difference between galvanic and electrolytic cells. Students experience challenges with handling the concept and its implications within chemistry contexts. Everyday-life examples do not provide immediate evidence of chemistry-related spontaneity, and some features may be misinterpreted. The ΔG < 0 spontaneity criterion does not have an everyday-life correspondence and mostly remains abstract. Tendencies to equate exothermic or fast with spontaneous appear frequently. Using the spontaneity or non-spontaneity concepts in the interpretation of observed simple electrochemical phenomena may pose difficulties. The challenges are greatly enhanced by two diffuse contextual features: tendency to rote learning and inadequate language-mastery, with the latter being a major cause of the former and generally hindering conceptual understanding. The paper highlights the main difficulties diagnosed within an action research approach, documenting them with a sufficiently ample selection of illustrative examples. The ways in which diagnoses are utilised as guidelines for in-class interventions aimed at addressing identified challenges are delineated and discussed. The integration of chemistry-concepts analysis and language-analysis is viewed as the most powerful instrument to address identified difficulties in real time.

Computational studies of biologically active alkaloids of plant origin: an overview

Computational studies nowadays constitute a crucial source of information for drug development, because they provide information on many molecular properties and also enable predictions of the properties of not-yet-synthesized compounds. Alkaloids are a vast group of natural products exhibiting a variety of biological activities, many of which are interesting for drug development. On the other hand, computational studies of biologically active alkaloids have so far mostly focused on few particularly relevant or “popular” molecules, such as quinine, caffeine, or cocaine, with only few works on the other molecules. The present work offers an overview of existing computational studies on alkaloid molecules, from the earliest ones to the most recent, and considering all the theoretical approaches with which studies have been performed (both quantum mechanics and molecular dynamics). The considered studies are grouped according to their objectives and outcomes, such as conformational analysis of alkaloid molecules, effects of selected solvents on their properties, docking studies aimed at better understanding of the interactions between alkaloid molecules and biological targets, studies focusing on structure activity relationships, and computational studies performed to confirm experimental results. It is concluded that it would be important that computational studies on many other alkaloid molecules are performed and their results made available, covering their different classes as well as the variety of their biological activities, to attain better understanding of the properties not only of individual molecules, but also of groups of related molecules and of the overall alkaloids family.

Five- and six-member bowl-shaped structures from acylphloroglucinols: an ab initio and DFT study

Molecular structures containing bowl-shaped cavities are interesting for purposes such as hosting molecules or metal ions. Acylphloroglucinols are derivatives of phloroglucinol (1,3,5-trihydroxybenzene) containing a CRO group. A previous study had considered bowl-shaped structures consisting of 3 or 4 identical acylphloroglucinol units linked by methylene bridges, selecting representative R chains and including also a structure with phloroglucinol units. The presence of three 'binding' levels between neighbouring units (consecutive hydrogen bonds in the lower rim, the methylene bridges at intermediate level, and another set of hydrogen bonds in the upper rim) makes these bowls 'deeper' than bowls from other hydroxybenzenes. The current study considers larger bowls, consisting of 5 and 6 identical units, to investigate how the molecular properties change with the increase in the size of the bowl. The monomeric units are the same as in the previous study, and the levels of theory are the same as in the previous study, to enable meaningful comparisons. Like in the previous study, two conformers are considered for each bowl, differing by the orientation of the OH groups in the lower rim. Calculations were performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry, complemented by single-point MP2/HF/6-31G(d,p) calculations. The results show that the C_nv symmetry (with n being the number of constituting monomers) is maintained for 5-member bowls, while 6-member bowls do not show C_6v symmetry but only C_2v symmetry. The molecular properties of the calculated bowls are analysed in detail and also compared with the properties of the previously calculated 4- and 5-member bowls. Graphical abstract Bowls built from acylphloroglucinol units have three levels of intermonomer linkages: hydrogen bonds in the bottom rim, methylene bridges at intermediate level, and other hydrogen bonds in the upper rim. They are the deepest bowls that can be built from hydroxybenzene units.

Computational study of acylphloroglucinols: an investigation with many branches

Acylphloroglucinols (ACPLs) are a broad class of compounds structurally derived from phloroglucinol and characterised by the presence of a CRO group. They are interesting for their biological activities and their potentialities as lead compounds in drug development. The current review considers a series of works which, altogether, sum up to a systematic computational study of ACPLs in vacuo and in three solvents – chloroform, acetonitrile and water. An initial set of studies, focusing on ACPLs as a class and utilising an adequately representative selection of molecules, identified patterns in the conformational preferences and molecular properties of ACPLs, which appear valid for the whole class or for specific subclasses such as monomeric ACPLs, dimeric ACPLs, ACPLs with substituents containing C=C double bonds, etc. The validity of the identified patterns was further verified through the study of additional and significantly different ACPL molecules, as well as other molecular structures containing ACPL units. Furthermore, the computational study of ACPLs proved interesting for the insights into the factors stabilising their conformers, first of all intramolecular hydrogen bonding, which plays dominant roles in determining conformational preferences and energetics. The current review outlines the objectives, approaches and main results of these studies. The obtained information may be relevant for further studies aimed at a better understanding of the molecular bases of the biological activities of ACPLs.

Complexes of arzanol with a Cu2+ ion: a DFT study

Arzanol (C₂₂H₂₆O₇) is a naturally occurring acylphloroglucinol largely responsible for the anti-inflammatory, anti-oxidant, antibiotic and antiviral activities of Helichrysum italicum. Like all acylphloroglucinols, the molecule contains a carboxylic substituent (-COR group); for arzanol, this is a -COCH₃ group. The molecule is further characterized by the presence of an α-pyrone ring bonded in meta to -COR through a methylene bridge, and of a prenyl chain bonded to the other meta position. The molecule can form up to three intramolecular hydrogen bonds (IHB) simultaneously, and their presence and patterns are the major stabilizing factors. This work considers complexes of representative conformers of arzanol with a Cu²⁺ ion, taking into account the different possibilities for the binding of the Cu²⁺ ion to the electron-density rich sites of the molecule and including simultaneous coordination to two geometrically suitable sites. Calculations were performed at the DFT/B3LYP level, using the 6-31+G(d,p) basis set for the C, O and H atoms and the LANL2DZ pseudopotential for the Cu²⁺ ion. Interaction energies show preference for simultaneous binding of Cu²⁺ to two sites. Simultaneous binding to the O of a phenol OH neighboring the prenyl chain and to the π bond of the prenyl chain appears to be the most favorable option, followed by simultaneous binding to the sp² O of the α-pyrone ring and the O of the phenol OH ortho to -COR on the side of the α-pyrone ring. The charge of the Cu²⁺ ion is reduced to +1 or slightly less in the complexes, which is consistent with the molecules' antioxidant (reducing) ability. Graphical abstract The copper ion prefers to attach to two sites of the arzanol molecule simultaneously. The arzanol molecule reduces the charge of the copper ion from +2 to +1 by transferring an electron to it; it becomes a radical molecular cation. The distribution of the unpaired electron in the molecule (as highlighted by the spin density maps) depends on the site/s to which the Cu²⁺ ion binds and on the molecule's conformer.

Intramolecular Hydrogen Bonding and Conformational Preferences of Arzanol-An Antioxidant Acylphloroglucinol

Arzanol is a naturally-occurring prenylated acylphloroglucinol isolated from Helichrysum italicum and exhibiting anti-oxidant, antibiotic and antiviral activities. The molecule contains an α-pyrone moiety attached to the phloroglucinol moiety through a methylene bridge. The presence of several hydrogen bond donor or acceptor sites makes intramolecular hydrogen bonding patterns the dominant stabilising factor. Conformers with all the possible different hydrogen bonding patterns were calculated at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry in vacuo and in three solvents—chloroform, acetonitrile and water (these levels being chosen to enable comparisons with previous studies on acylphloroglucinols). Calculations in solution were performed with the Polarisable Continuum Model. The results show that the lowest energy conformers have the highest number of stronger intramolecular hydrogen bonds. The influence of intramolecular hydrogen bonding patterns on the other molecular properties is also analysed.

Intramolecular Hydrogen Bonds in Conformers of Quinine and Quinidine: An HF, MP2 and DFT Study

Quinine is an alkaloid with powerful antimalarial activity, isolated from the bark of Peru's cinchona trees. Quinidine is an erythro diastereoisomer of quinine also exhibiting antimalarial activity. Conformational studies performed so far had never identified conformers with intramolecular hydrogen bonds (IHB). The current study shows the possibility of conformers with an IHB between the quinuclidine and quinoline moieties of these molecules. The study was performed at different levels of theory: Hartree Fock (HF) with the 6-31G(d,p) basis set, Density Functional Theory (DFT) with the B3LYP functional and the 6-31+G(d,p) basis set and Møller-Plesset Perturbation Theory (MP2) with the 6-31+G(d,p) basis set, to confirm the results. The results suggest that the stabilising effect of this IHB is weaker or comparable with respect to the stabilising effect of the preferred mutual orientation of the two moieties. Although the IHB-containing conformers may not be the lowest energy ones, their relative energy is sufficiently low for them to be included among the possible ones responsible for the compounds' antimalarial activity.

Evaluation of the antiradical activity of hyperjovinol-A utilizing donor-acceptor maps

Hyperjovinol-A ((2-methyl-1-(2,4,6-trihydroxy-3-(3-hydroxy-3,7-dimethyloct-6-enyl)phen yl)propan-1-one) is an acylated phloroglucinol isolated from Hypericum Jovis and exhibiting good antioxidant activity. The study investigates the compound’s antiradical ability on the basis of the electron-donor and electron-acceptor abilities of its conformers, deriving donor and acceptor indexes and mapping them in terms of donor-acceptor maps (DAM). The DAMs of vitamins C and E and of carotene astaxantine are used as comparison references. Calculations were performed at the DFT/BPW91/6-311+G(d,p) level, with optimizations on fully relaxed geometries to obtain the conformers of the neutral molecule in vacuo, and single point calculations to obtain the energies of the cationic and anionic species in vacuo and of the neutral, cationic, and anionic species in water, ethanol, and pentylethanoate. The calculations in solution utilized the polarizable continuum model (PCM). The results indicate that hyperjovinol-A may have better antiradical activity than vitamin C. This is in agreement with experimental results, showing that the antioxidant activity of hyperjovinol-A is comparable with that of the best drugs currently in clinical use. The activity is maintained in solution. The Fukui function f(·) was also calculated for all the conformers of hyperjovinol-A, to identify the regions of highest reactivity.