Glossary of terms used in physical organic chemistry (IUPAC Recommendations 2021)

This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.

G-Protein coupled receptors: structure and function in drug discovery

The G-protein coupled receptors (GPCRs) superfamily comprise similar proteins arranged into families or classes thus making it one of the largest in the mammalian genome. GPCRs take part in many vital physiological functions making them targets for numerous novel drugs. GPCRs share some distinctive features, such as the seven transmembrane domains, they also differ in the number of conserved residues in their transmembrane domain. Here we provide an introductory and accessible review detailing the computational advances in GPCR pharmacology and drug discovery. An overview is provided on family A-C GPCRs; their structural differences, GPCR signalling, allosteric binding and cooperativity. The dielectric constant (relative permittivity) of proteins is also discussed in the context of site-specific environmental effects.

Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer

Isotopic partition-function ratios (IPFRs) computed for transition structures (TSs) of the methyl-transfer reaction catalyzed by catechol O-methyltransferase and modeled by hybrid QM/MM methods are analyzed. The ability of smaller Hessians to reproduce trends in α-3H3 and 14Cα IPFRs as obtained using the much larger subset QM/MM Hessians from which they are extracted is investigated critically. A 6-atom-extracted Hessian reproduces perfectly the α-T3 IPFR values from the full-subset Hessians of all the TSs but not the α-14CIPFRs. Average AM1/OPLS-AA harmonic frequencies and mean-square amplitudes are presented for the 12 normal modes of the α-CH3 moiety within the active site of several enzymic transition structures, together with QM/MM potential energy scans along each of these modes to assess the degree of anharmonicity. A novel investigation of ponderal effects upon IPFRs suggests that the value for α-14C tends toward a limiting minimum whereas that for α-T3 tends toward a limiting maximum as the mass of the rest of the system increases. The transition vector is dominated by motions of atoms within the donor and acceptor moieties and is very well described as a simple combination of Walden-inversion "umbrella" bending and asymmetric stretching of the SCα and CαO bonds. The contribution of atoms of the protein residues Met40, Tyr68, and Asp141 to the transition vector is extremely small. Average valence force constants for the COMT TS show significant differences from early BEBOVIB estimates which were used in support of the compression hypothesis for catalysis. There is no correlation between TS IPFRs and the nonbonded distances for close contacts between the S atom of SAM and Tyr68 or between any of the H atoms of the transferring methyl group and either Met40 or Asp141.

Influence of Dielectric Environment upon Isotope Effects on Glycoside Heterolysis: Computational Evaluation and Atomic Hessian Analysis

Isotope effects depend upon the polarity of the bulk medium in which a chemical process occurs. Implicit solvent calculations with molecule-shaped cavities show that the equilibrium isotope effect (EIE) for heterolysis of the glycosidic bonds in 5'-methylthioadenosine and in 2-(p-nitrophenoxy)tetrahydropyran, both in water, are very sensitive in the range 2 ≤ ε ≤ 10 to the relative permittivity of the continuum surrounding the oxacarbenium ion. However, different implementations of nominally the same PCM method can lead to opposite trends being predicted for the same molecule. Computational modeling of the influence of the inhomogeneous effective dielectric surrounding a substrate within the protein environment of an enzymic reaction requires an explicit treatment. The EIE (K_H/K_D) for transfer of cyclopentyl, cyclohexyl, tetrahydrofuranyl and tetrahydropyranyl cations from water to cyclohexane is predicted by B3LYP/6-31+G(d) calculations with implicit solvation and confirmed by B3LYP/6-31+G(d)/OPLS-AA calculations with averaging over many explicit solvation configurations. Atomic Hessian analysis, whereby the full Hessian is reduced to the elements belonging to a single atom at the site of isotopic substitution, reveals a remarkable result for both implicit and explicit solvation: the influence of the solvent environment on these EIEs is essentially captured completely by only a 3 × 3 block of the Hessian, although these values must correctly reflect the influence of the whole environment. QM/MM simulation with ensemble averaging has an important role to play in assisting the meaningful interpretation of observed isotope effects for chemical reactions both in solution and catalyzed by enzymes.

Critical evaluation of anharmonicity and configurational averaging in QM/MM modelling of equilibrium isotope effects

Anharmonic and harmonic QM (internal modes only): essentially the same; harmonic QM/MM (including external modes): strongly inverse EIE.

Computational simulation of mechanism and isotope effects on acetal heterolysis as a model for glycoside hydrolysis

DFT calculations for the equilibrium isotope effect for deuterium substitution at the anomeric centre Cα in 2-(p-nitrophenoxy)tetrahydropyran with continuum solvation show significant variation in the range of relative permittivity 2 ≤ ε ≤ 10. One-dimensional scans of potential energy (with implicit solvation by water) or of free energy (from QM/MM potentials of mean force with explicit aqueous solvation with a hybrid AM1/OPLS method) for heterolysis of the bond between Cα and the nucleofuge do not show a transition state. A two-dimensional free-energy surface that considers also the distance between Cα and a nucleophilic water indicates a pre-association DN*ANint ‡ mechanism with a transition state involving nucleophilic attack upon an ion-pair intermediate, and this is supported by good agreement between the mean values of the calculated and experimental α-D KIEs. However, the magnitudes of the standard deviations about the mean values for the making and breaking C–O bonds suggest that the transition state is rather plastic, with Cα–Onu≈2 ± 0.4 Å and Cα–Olg≈3 ± 0.5 Å. Not only is nucleophilic solvent assistance necessary, but there is also evidence for electrophilic assistance through specific hydrogen bonding to the nucleofuge.

Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling

The origin of enzyme catalysis remains a question of debate despite much intense study. We report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine N-methyltransferase (GNMT) and three mutants to test whether recent experimental observations of rate-constant reductions and variations in inverse secondary α-3H kinetic isotope effects (KIEs) should be attributed to changes in the methyl donor-acceptor distance (DAD): Is catalysis due to a compression effect? Semiempirical (AM1) and DFT (M06-2X) methods were used to describe the QM subset of atoms, while OPLS-AA and TIP3P classical force fields were used for the protein and water molecules, respectively. The computed activation free energies and KIEs are in good agreement with experimental data, but the mutations do not meaningfully affect the DAD: Compression cannot explain the experimental variations on KIEs. On the contrary, electrostatic properties in the active site correlate with the catalytic activity of wild type and mutants. The plasticity of the enzyme moderates the effects of the mutations, explaining the rather small degree of variation in KIEs and reactivities.

Nutritional principles, integration, modelling and research management to practical applications: an overview of John Langtree Black’s contribution to animal science

This is the introductory paper for a Festschrift to honour the contribution that John Langtree Black has made so far to animal science over his 50-year career. The paper outlines the extraordinary wide range of topics, disciplines and animal species covered by his research and intellectual thinking. It describes major contributions made to enhancing knowledge in areas of animal science and to the application of knowledge to rural industries through simulation models, risk-control management systems, methods for measuring ingredient and product quality and communication. An important contribution has been through the management, coordination and integration of findings in large interdisciplinary research programs, particularly with an emphasis on adherence to the scientific method and the role of statistics. The discipline of scientific integrity has been extended to his considerable involvement in community service.

A computational study of the influence of methyl substituents on competitive ring closure to α- and β-lactones

gem-Dimethyl substitution at C3 enhances the preference for β-lactone formation from 2-chlorosuccinate but methylation at C2 almost favours α-lactone.

Influence of Equatorial CH⋅⋅⋅O Interactions on Secondary Kinetic Isotope Effects for Methyl Transfer

DFT calculations for methyl cation complexed within a constrained cage of water molecules permit the controlled manipulation of the "axial" donor/acceptor distance and the "equatorial" distance to hydrogen-bond acceptors. The kinetic isotope effect k(CH3)/k(CT3) for methyl transfer within a cage with a short axial distance becomes less inverse for shorter equatorial C⋅⋅⋅O distances: a decrease of 0.5 Å results in a 3 % increase at 298 K. Kinetic isotope effects in AdoMet-dependent methyltransferases may be m∧odulated by CH⋅⋅⋅O hydrogen bonding, and factors other than axial compression may contribute, at least partially, to recently reported isotope-effect variations for catechol-O-methyltransferase and its mutant structures.

Dynamics of the thumb-finger regions in a GH11 xylanase Bacillus circulans: comparison between the Michaelis and covalent intermediate

The structure and dynamics of B. circulans β-1,4-xylanase (BCX) were comparatively studied utilizing molecular dynamics.

C-H functionalization of sp(3) centers with aluminum: a computational and mechanistic study of the Baddeley reaction of decalin

Decalin undergoes reaction with aluminum trichloride and acetyl chloride to form a tricyclic enol ether in good yield, as first reported by Baddeley. This eye-catching transformation, which may be considered to be an aliphatic Friedel-Crafts reaction, has not previously been studied mechanistically. Here we report experimental and computational studies to elucidate the mechanism of this reaction. We give supporting evidence for the proposition that, in the absence of unsaturation, an acylium ion acts as a hydride acceptor, forming a tertiary carbocation. Loss of a proton introduces an alkene, which reacts with a further acylium ion. A concerted 1,2-hydride shift/oxonium formation, followed by elimination, leads to formation of the observed product.

Solvent effects on isotope effects: methyl cation as a model system

The isotopic sensitivity (CH3(+) vs CD3(+)) of the equilibrium between the methyl cation in vacuum and in solution has been investigated. Two alternative options for describing the shape of the solute cavity within the widely used polarized continuum model for implicit solvation were compared; the UFF and UA0 methods give equilibrium isotope effects (EIEs) that vary as a function of the dielectric constant in opposite directions. The same isotope effect was also obtained as the average over 40 structures from a hybrid quantum mechanical/molecular mechanical molecular dynamics simulation for the methyl cation explicitly solvated by many water molecules; the inverse value of the EIE agrees with UFF but not UA0. The opposing trends may be satisfactorily explained in terms of the different degrees of exposure of the atomic charges to the dielectric continuum in cavities of different shapes.

The Nasonov pheromone of the honeybeeApis mellifera L. (Hymenoptera, Apidae). Part II. Bioassay of the components using foragers

The Nasonov pheromone of the honeybee comprises seven components, (Z)-citral, nerol, geraniol, nerolic acid, geranic acid, and (E,E)-farnesol. Bioassay of individual components showed each attracted foraging bees. A mixture of components in proportions present in the honeybee was as attractive as the natural secretion, and each component contributed to the attractiveness of the mixture. Honeybees responded anemotactically to the source of Nasonov odor. The presence of footprint pheromone enhanced the attractiveness of the synthetic Nasonov mixture. Nasonov and footprint pheromones may prove useful in attracting honeybees to crops needing pollination.

Nasonov pheromone of the honey bee,Apis mellifera L. (Hymenoptera, Apidae). part III. : Regulation of pheromone composition and production

GC and GC-MS analyses of the multicomponent Nasonov pheromone of the honey bee, and of the air above insects releasing the pheromone, show that constant composition is maintained during release, despite differing volatilities of the components. The regulating mechanism may involve a specific enzyme process, detected in excised Nasonov glands, which converts the major component geraniol into the more volatile (E)-citral. Analysis of honey bees of known ages and at different times of year shows that maximum secretion occurs when foraging is most likely.

Nasonov pheromone of the honeybee.Apis mellifera L. (Hymenoptera, Apidae) : IV. Comparative electroantennogram responses

Electroantennogram (EAG) responses from worker honeybee antennae were obtained for each Nasonov component. Response amplitudes to 10 μg of components correlated well with reported relative abilities to attract foragers in the field. EAG responses of worker, queen, and drone antennae to natural pheromone were consistently greater than to synthetic pheromone, a difference only partly explained by enzymic conversion of geraniol to (E)-citral during preparation of natural extracts.

Kinetic Isotope Effects from QM/MM Subset Hessians: "Cut-Off" Analysis for SN2 Methyl Transfer in Solution

Isotopic partition-function ratios and kinetic isotope effects for reaction of S-adenosylmethionine with catecholate in water are evaluated using a subset of 324 atoms within its surrounding aqueous environment at the AM1/TIP3P level. Two alternative methods for treating motion in the six librational degrees of freedom of the subset atoms relative to their environment are compared. A series of successively smaller subset Hessians are generated by cumulative deletion of rows and columns from the initial 972 × 972 Hessian. We find that it is better to treat these librations as vibrations than as translations and rotations and that there is no need to invoke the Teller-Redlich product rule. The validity of "cut-off" procedures for computation of isotope effects with truncated atomic subsets is assessed: to ensure errors in ln(KIE) < 1% (or 2% for the quantum-corrected KIE) for all isotopic substitutions considered, it is necessary to use a less-restrictive procedure than is suggested by the familiar two-bond cutoff rule.

Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water

2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of 1030 classical solvent water molecules at 300 K. This provides a simple model for glycosyl transfer in water. The AM1/TIP3P surfaces with 2D-spline corrections at either MPWB1K/6-31+G(d,p) or MP2/6-31+G(d,p) contain a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a DN*AN mechanism. MD analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections for vibrational zero-point energy are included, the lifetime is estimated to be about 1 ps, in agreement with the best experimental estimate. This suggests that computational simulation, with appropriate high-level correction, is a reliable tool to obtain detailed and reliable mechanistic descriptions for glycosidases. In view of the importance of developing improved anti-influenza drugs, simulations of sialidases that considered both sialyl oxacarbenium ion and covalent sialyl-enzyme as possible intermediates could provide particular insight.

Catalysis: transition-state molecular recognition?

THE KEY TO UNDERSTANDING THE FUNDAMENTAL PROCESSES OF CATALYSIS IS THE TRANSITION STATE (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for S(N)2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.

Gas exchange patterns of bumble bee foragers before and after exposing to lowered temperature

The gas exchange patterns are known to vary between insect species, individuals and even intra-individually. Using volumetric-manometric and flow-through respirometry combined with IR-actography we studied how periods of low temperature affect the respiratory patterns of bumble bee Bombus terrestris foragers. We have shown, in this study, that there is a change in the respiratory patterns of individual B. terrestris foragers after exposing to low temperatures. The bumble bees seemed to become more inactive. The different respiratory patterns appeared in succession and the transition from one pattern to another was associated with the change from an active to a resting state. Typical patterns after exposition to low temperature were discontinuous gas exchange cycles (DGCs).

Relationships between faecal dry matter, worm burdens and inflammatory mediators and cells in parasite-resistant Merino rams

Immune-mediated scouring due to ingested parasite larvae is a major concern for sheep producers in Mediterranean climates. We investigated immune-mediated scouring in parasite-resistant Merino sheep in Australia. Forty-adult, parasite-resistant Merino rams were judged to be either susceptible or non-susceptible to immune-mediated scouring on the basis of dag scores taken under field conditions. We hypothesised that the susceptible rams would have lower faecal dry matter during larval challenge than non-susceptible rams and that, at post-mortem examination, inflammatory mediators and granulocytes would be negatively correlated with both faecal dry matter and worm numbers. In pens, the rams received a dose of 500 Teladorsagia circumcincta L(3) and 500 Trichostrongylus colubriformis L(3) each day for 6 weeks before euthanasia. Ten rams acted as unchallenged controls. Challenging sheep with larvae reduced faecal dry matter at 2, 3 and 4 weeks after challenge began and the greatest reductions were with the sheep susceptible to scouring. The sheep showed good resistance to the parasite challenge as evidenced by low faecal worm egg counts and low total worm counts at post-mortem, with the numbers of T. colubriformis particularly low. Sheep with low faecal dry matter had significantly higher numbers of eosinophils in small intestine tissue. Sheep with low total worm counts had significantly higher levels of bradykinin in abomasum mucus. Sheep with more granulocytes in tissue and inflammatory mediators in mucus tended to have fewer numbers of T. circumcincta but there was little relationship with numbers of T. colubriformis. Our results show that dag scores are correlated to a reduction in faecal dry matter, which can be attributed to the challenge with infective parasite larvae. Inflammation during worm infection is associated with rejection of the worm challenge and may result in more fluid faeces and consequently diarrhoea. Therefore, sheep breeders should focus on breeding for both low worm egg counts and also low dag scores.

Probing synergy between two catalytic strategies in the glycoside hydrolase O-GlcNAcase using multiple linear free energy relationships

Human O-GlcNAcase plays an important role in regulating the post-translational modification of serine and threonine residues with beta-O-linked N-acetylglucosamine monosaccharide unit (O-GlcNAc). The mechanism of O-GlcNAcase involves nucleophilic participation of the 2-acetamido group of the substrate to displace a glycosidically linked leaving group. The tolerance of this enzyme for variation in substrate structure has enabled us to characterize O-GlcNAcase transition states using several series of substrates to generate multiple simultaneous free-energy relationships. Patterns revealing changes in mechanism, transition state, and rate-determining step upon concomitant variation of both nucleophilic strength and leaving group abilities are observed. The observed changes in mechanism reflect the roles played by the enzymic general acid and the catalytic nucleophile. Significantly, these results illustrate how the enzyme synergistically harnesses both modes of catalysis; a feature that eludes many small molecule models of catalysis. These studies also suggest the kinetic significance of an oxocarbenium ion intermediate in the O-GlcNAcase-catalyzed hydrolysis of glucosaminides, probing the limits of what may be learned using nonatomistic investigations of enzymic transition-state structure and offering general insights into how the superfamily of retaining glycoside hydrolases act as efficient catalysts.

Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase

Molecular simulations based on the use of hybrid quantum mechanics/molecular mechanics methods are able to provide detailed information about the complex enzymatic reactions and the consequences of specific mutations on the activity of the enzyme. In this work, the reduction of pyruvate to lactate catalysed by wild-type and Asp168Ala mutant lactate dehydrogenase (LDH) has been studied by means of simulations using a very flexible molecular model consisting of the full tetramer of the enzyme, together with the cofactor NADH, the substrate and solvent water molecules. Our results indicate that the Asp168Ala mutation provokes a shift in the pKa value of Glu199 that becomes unprotonated at neutral pH in the mutant enzyme. This change compensates the loss of the negative charge of Asp168, rendering a still active enzyme. Thus, our methodology gives a calculated barrier height for the Asp168Ala mutant 3 kcal mol-1 higher than that for wild-type LDH, which is in very good agreement with the experiment. The computed potential energy surfaces reveal the reaction pathways and transition structures for the wild-type and mutant enzymes. Hydride transfer is less advanced and the proton transfer is more advanced in the Asp168Ala mutant than in the wild type. This approach provides a very powerful tool for the analysis of the roles of key active-site residues.

Links between de novo fatty acid synthesis and leptin secretion in bovine adipocytes

Leptin secretion by adipose tissue is involved in many physiological control systems, including those that determine growth, development, body composition, milk production, and reproductive function. In the adipocyte of monogastric animals, malonyl CoA (coenzyme A) seems to link the flux of energy substrates to the control of leptin production. In this study, we tested this for ruminants by examining the effect of cerulenin, an inhibitor of de novo fatty acid synthesis at the step from malonyl CoA to palmitate, on leptin production by cultured bovine adipocytes derived from intermuscular fat. Purified preadipocytes were obtained by the ceiling culture method, and adipogenic media were used to induce their differentiation into adipocytes. We found that leptin concentrations increased significantly with time in culture, and with increases in glucose concentration. Addition of 2-deoxy-D-glucose to the medium, a competitive inhibitor of glucose transport and metabolism, suppressed leptin secretion. In media with high glucose concentrations, cerulenin enhanced leptin secretion. We conclude that, as in monogastrics, malonyl CoA may play a key role in the control of leptin secretion in ruminants.

High-level ab initio studies of the structure, vibrational spectra, and energetics of S3

Observation of mass-dependent and non-mass-dependent sulfur isotope fractionations in elemental sulfur is providing new insight into the nature of the sulfur cycle in the atmosphere. Interpretation of the experimental isotope data requires estimation of the energetics for the reaction S+S2-->S3 (isoelectronic with O+O2-->O3). Key molecular properties of the S3 potential-energy surface, such as vibrational frequencies and isotopic shifts, are presented that can be used to assess the mass-dependent fractionation effect. Ab initio results are compared to the available experimental results for S2 to evaluate the reliability of the computational results for S3. The S-S bond dissociation energy for S3 is determined to be 60.9+/-1 kcal mol(-1).

Glycosidase inhibitors as conformational transition state analogues

A method for estimating the conformational similarity between hexopyranose rings is presented and used to probe the behaviour of various glycosyl hydrolase inhibitors as conformational transition state analogues.