Impact of Hydrogen Bonding on the Susceptibility of Peptides to Oxidation.

The tendency of peptides to be oxidized is intimately connected with their function and even their ability to exist in an oxidative environment. Here we report high-level theoretical studies that show that hydrogen bonding can alter the susceptibility of peptides to oxidation, with complexation to a hydrogen-bond acceptor facilitating oxidation, and vice versa, impacting the feasibility of a diverse range of biological processes. It can even provide an energetically viable mechanistic alternative to direct hydrogen-atom abstraction. We find that hydrogen bonding to representative reactive groups leads to a broad (≈400 kJ mol-1 ) spectrum of ionization energies in the case of model amide, thiol and phenol systems. While some of the oxidative processes at the extreme ends of the spectrum are energetically prohibitive, subtle environmental and solvent effects could potentially mitigate the situation, leading to a balance between hydrogen bonding and oxidative susceptibility.

The effect of diet, temperature and intermittent low oxygen on the metabolism of rainbow trout.

An automated respirometer system was used to measure VO2, protein catabolism as ammonia quotient and the energy budget to evaluate whether the crude protein content of a standard protein (SP) diet (42·5 %) or a high-protein (HP) diet (49·5 %) influences metabolism in rainbow trout under challenging intermittent, low dissolved oxygen concentrations. In total, three temperature phases (12, 16, 20°C) were tested sequentially, each of which were split into two oxygen periods with 5 d of unmanipulated oxygen levels (50-70 %), followed by a 5d manipulated oxygen period (16.00-08.00 hours) with low oxygen (40-50 %) levels. For both diets, catabolic protein usage was lowest at 16°C and was not altered under challenging oxygen conditions. Low night-time oxygen elevated mean daily VO2 by 3-14 % compared with the unmanipulated oxygen period for both diets at all temperatures. The relative change in VO2 and retained energy during the intermittent low oxygen period was smaller for the HP diet compared with the SP diet. However, in absolute terms, the SP diet was superior to the HP diet as the former demonstrated 30-40 % lower protein fuel use rates, higher retained energy (1-4 % digestible energy) and slightly lowered VO2 (0-8 %) over the range of conditions tested. The decrease in retained energy under low oxygen conditions suggests that there is scope to improve the performance of SP diets under challenging conditions; however, this study suggests that simply increasing the dietary protein content is not a remedy, and other strategies need to be explored.

Life in a dark biosphere: a review of circadian physiology in "arrhythmic" environments.

Most of the life with which humans interact is exposed to highly rhythmic and extremely predictable changes in illumination that occur with the daily events of sunrise and sunset. However, while the influence of the sun feels omnipotent to surface dwellers such as ourselves, life on earth is dominated, in terms of biomass, by organisms isolated from the direct effects of the sun. A limited understanding of what life is like away from the sun can be inferred from our knowledge of physiology and ecology in the light biosphere, but a full understanding can only be gained by studying animals from the dark biosphere, both in the laboratory and in their natural habitats. One of the least understood aspects of life in the dark biosphere is the rhythmicity of physiology and what it means to live in an environment of low or no rhythmicity. Here we describe methods that may be used to understand rhythmic physiology in the dark and summarise some of the studies of rhythmic physiology in "arrhythmic" environments, such as the poles, deep sea and caves. We review what can be understood about the adaptive value of rhythmic physiology on the Earth's surface from studies of animals from arrhythmic environments and what role a circadian clock may play in the dark.

The energetic cost of vision and the evolution of eyeless Mexican cavefish.

One hypothesis for the reduction of vision in cave animals, such as the eyeless Mexican cavefish, is the high energetic cost of neural tissue and low food availability in subterranean habitats. However, data on relative brain and eye mass in this species or on any measure of the energetic cost of neural tissue are not available, making it difficult to evaluate the "expensive tissue hypothesis." We show that the eyes and optic tectum represent significant metabolic costs in the eyed phenotype. The cost of vision was calculated to be 15% of resting metabolism for a 1-g fish, decreasing to 5% in an 8.5-g fish as relative eye and brain size declined during growth. Our results demonstrate that the loss of the visual system in the cave phenotype substantially lowered the amount of energy expended on expensive neural tissue during diversification into subterranean rivers, in particular for juvenile fish.

Prolonged SDA and reduced digestive efficiency under elevated CO2 may explain reduced growth in Atlantic cod (Gadus morhua).

Land-based aquaculture systems expose fish to elevated dissolved CO2 levels, a factor that is correlated with reduced growth, feed conversion efficiency and body condition index. The physiological basis underlying the pathological effects of environmental hypercapnia is poorly understood, in particular for marine fish species. We investigated whether changes in energy expenditure and the specific dynamic action (SDA) of digestion and assimilation could account for the lower growth of adult Atlantic cod (Gadus morhua) under environmental hypercapnia. Fish acclimated to a partial pressure of 800 µatm CO2 (0.6 mmHg, 1.5 mg/L) and 9200 µatm CO2 (7 mmHg, 18.7 mg/L) exhibited no difference in maintenance metabolic rates, which concurs with previous research for this species and other fish species. At 9200 µatm CO2 Atlantic cod had a significantly diminished (14%) maximum aerobic capacity. While hypercapnia did not affect the amount of oxygen required for the SDA process, it did prolong the SDA duration by 23%. The longer SDA process time may offer an explanation for the observation of lower feed intake, growth and condition factor in long-term hypercapnia studies. Comparison of aerobic scope and cardiac performance during digestion suggested that reduced oxygen delivery capacity under hypercapnia could be one mechanism by which CO2 prolongs SDA, although our results could not definitively demonstrate this effect.

Eyeless Mexican cavefish save energy by eliminating the circadian rhythm in metabolism.

The eyed surface form and eyeless cave form of the Mexican tetra Astyanax mexicanus experience stark differences in the daily periodicities of light, food and predation, factors which are likely to have a profound influence on metabolism. We measured the metabolic rate of Pachón cave and surface fish at a fixed swimming speed under light/dark and constant dark photoperiods. In constant darkness surface forms exhibited a circadian rhythm in metabolism with an increase in oxygen demand during the subjective daytime, whereas cave forms did not. The lack of circadian rhythm in metabolism leads to a 27% energy savings for Pachón cave fish compared to surface fish when comparing both forms in their natural photoperiods. When surface forms were tested under constant dark conditions they expended 38% more energy than cave forms under equivalent conditions. Elimination of the circadian rhythm in metabolism may be a general feature of animals that live in perpetually dark food-limited environments such as caves or the deep sea.

Stretch to see: lateral tension strongly determines cell survival in long-term cultures of adult porcine retina.

PURPOSE: To explore the effect of lateral tension as a survival factor for retinal explants in vitro. The central nervous system (CNS) resides in a highly mechanical milieu. However, the importance of biomechanical homeostasis for normal CNS function has not been extensively explored. Diseases in which normal mechanical forces are disrupted, such as retinal detachment of the eye, are highly debilitating and the mechanisms underlying disease progression are not fully understood. METHODS: Using a porcine animal model, we developed a novel technique of culturing adult retinal explants under stretch for up to 10 days in vitro (DIV). These were compared with standard (no stretch) and free-floating cultured explants. Cell survival was analyzed using immunohistochemistry, and retinal architecture using hematoxylin and eosin staining. RESULTS: Compared with unstretched specimens, which at 10 DIV degenerated into a gliotic cell mass, stretched retinas displayed a profound preservation of the laminar retinal architecture as well as significantly increased neuronal cell survival, with no signs of impending gliosis. CONCLUSIONS: The results confirm that biomechanical tension is a vital factor in the maintenance of retinal tissue integrity, and suggest that mechanical cues are important components of pathologic responses within the CNS.

Bond dissociation energies and radical stabilization energies: an assessment of contemporary theoretical procedures.

Various contemporary theoretical procedures have been tested for their accuracy in predicting the bond dissociation energies (BDEs) and the radical stabilization energies (RSEs) for a test set of 22 monosubstituted methyl radicals. The procedures considered include the high-level W1, W1', CBS-QB3, ROCBS-QB3, G3(MP2)-RAD, and G3X(MP2)-RAD methods, unrestricted and restricted versions of the double-hybrid density functional theory (DFT) procedures B2-PLYP and MPW2-PLYP, and unrestricted and restricted versions of the hybrid DFT procedures BMK and MPWB1K, as well as the unrestricted DFT procedures UM05 and UM05-2X. The high-level composite procedures show very good agreement with experiment and are used to evaluate the performance of the comparatively less expensive DFT procedures. RMPWB1K and both RBMK and UBMK give very promising results for absolute BDEs, while additionally restricted and unrestricted X2-PLYP methods and UM05-2X give excellent RSE values. UM05, UB2-PLYP, UMPW2-PLYP, UM05-2X, and UMPWB1K are among the less well performing methods for BDEs, while UMPWB1K and UM05 perform less well for RSEs. The high-level theoretical results are used to recommend alternative experimental BDEs for propyne, acetaldehyde, and acetic acid.

An evaluation of harmonic vibrational frequency scale factors.

Scale factors for obtaining fundamental vibrational frequencies, low-frequency vibrational frequencies, zero-point vibrational energies (ZPVEs), and thermal contributions to enthalpy and entropy have been derived through a least-squares approach from harmonic frequencies determined at more than 100 levels of theory. Wave function procedures (HF, MP2, QCISD, QCISD(T), CCSD, and CCSD(T)) and a large and representative range of density functional theory (DFT) approaches (B3-LYP, BMK, EDF2, M05-2X, MPWB1K, O3-LYP, PBE, TPSS, etc.) have been examined in conjunction with basis sets such as 6-31G(d), 6-31+G(d,p), 6-31G(2df,p), 6-311+G(d,p), and 6-311+G(2df,p). The vibrational frequency scale factors were determined by a comparison of theoretical harmonic frequencies with the corresponding experimental fundamentals utilizing a standard set of 1066 individual vibrations. ZPVE scale factors were generally obtained from a comparison of the computed ZPVEs with experimental ZPVEs for a smaller standard set of 39 molecules, though the effect of expansion to a 48 molecule data set was also examined. In addition to evaluating the scale factors for a wide range of levels of theory, we have also probed the effect on scale factors of varying the percentage of incorporated exact exchange in hybrid DFT calculations using a modified B3-LYP functional. This has revealed a near-linear relationship between the magnitude of the scale factor and the proportion of exact exchange. Finally, we have investigated the effect of basis set size on HF, MP2, B3-LYP, and BMK scale factors by deriving values with basis sets ranging from 6-31G(d) up to 6-311++G(3df,3pd) as well as with basis sets in the cc-pVnZ and aug-cc-pVnZ series and with the TZV2P basis.

Ontogenetic scaling of fish metabolism in the mouse-to-elephant mass magnitude range.

Intraspecific or ontogenetic analyses of mass-metabolism relationships do not often conform to the same allometric correlations as those seen in interspecific analyses. A commonly cited reason for this discrepancy is that ontogenetic studies examine smaller mass ranges than interspecific studies, and are therefore not statistically comparable. In this study the metabolic rate of yellowtail kingfish was measured from 0.6 mg-2.2 kg, a mass range comparable to that between a mouse and an elephant. Linear regression of the log transformed data resulted in a scaling exponent of 0.90 and high correlation coefficient. Statistical and information theory comparisons of three other models showed that a segmented linear regression and curvilinear quadratic function were an improvement over a simple linear regression. This confirmed previous observations that the metabolic scaling exponent of fish changes during ontogeny. Ammonia excretion rates were also measured and scaled linearly with an exponent of 0.87. The data showed that the metabolism of yellowtail kingfish during ontogeny did not scale with the commonly cited 2/3 or 3/4 mass exponent. This demonstrates that differences between interspecific and ontogenetic allometries are not necessarily statistical artefacts.

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

A range of ab initio calculations were carried out on the axial and equatorial anomers of the model carbohydrate 2-ethoxy tetrahydropyran to evaluate the level of theory required to accurately evaluate the glycosyl dihedral angle and the anomeric ratio. Vacuum CCSD(T)/CBS extrapolations at the global minimum yield DeltaE = E(equatorial) - E(axial) = 1.42 kcal/mol. When corrected for solvent (by the IEFPCM model), zero-point vibrations and entropy, DeltaG(298) = 0.49 kcal/mol, in excellent agreement with the experimental value of 0.47 +/- 0.3 kcal/mol. A new additivity scheme, the layered composite method (LCM), yields DeltaE to within 0.1 kcal/mol of the CCSD(T)/CBS result at a fraction of the computer requirements. Anomeric ratios and one-dimensional torsional surfaces generated by LCM and the even more efficient MP2/cc-pVTZ level of theory are in excellent agreement, indicating that the latter is suitable for force-field parameterization of carbohydrates. Hartree-Fock and density functional theory differ from CCSD(T)/CBS for DeltaE by approximately 1 kcal/mol; they show similar deviations in torsional surfaces evaluated from LCM. A comparison of vacuum and solvent-corrected one- and two-dimensional torsional surfaces indicates the equatorial form of 2-ethoxy tetrahydropyran is more sensitive to solvent than the axial.

Carbene stabilization by aryl substituents. Is bigger better?

The geometries and relative stabilities of the singlet and triplet states of phenyl- (Cs), diphenyl- (C2), 1-naphthyl- (Cs), di(1-naphthyl)- (C2), and 9-anthryl-substituted (Cs) carbenes were investigated at the B3LYP/6-311+G(d,p) + ZPVE level of density functional theory. The singlet-triplet energy separations (DeltaEST), 2.7, 2.9, 3.4, 3.7, and 5.7 kcal/mol, respectively, after including an empirical correction (2.8 kcal/mol) based on the error in the computed singlet-triplet gap for methylene versus experiment, are in good agreement with available experimental values. Consistent with literature reports, triplet di(9-anthryl)carbene has a linear, D2d symmetrical, allene structure with 1.336 A C=C bond lengths and considerable biradical character. B3LYP favors such cumulene biradical structures and triplet spin states and predicts a large (>15 kcal/mol) "di(9-anthryl)carbene" singlet-triplet (biradical) energy gap. The resonance stabilization of both singlet and triplet carbenes increases modestly with the size of the arene substituent and overall, (di)arylcarbenes, both singlet and triplet, are better stabilized by bigger substituents. For example, methylene is stabilized more by a naphthyl than a phenyl group (singlets, 26.6 versus 24.4; and triplets, 20.9 versus 18.1 kcal/mol, respectively). The carbene geometries are affected by both steric effects and arene-carbene orbital interactions (sigma-p and p-pi). For instance, the central angles at the carbene are widened by a second arene group, which leads to increased s-character and shorter carbene bond lengths (i.e., C-C, C-H). In general, the aromaticity of the substituted rings in triplet carbenes is most affected by the presence of the unpaired electrons.

Thermochemistry and kinetics of hydrogen abstraction by methyl radical from polycyclic aromatic hydrocarbons.

Thermodynamic and kinetic properties relating to hydrogen abstraction by methyl radical from various sites in polycyclic aromatic hydrocarbons (PAHs) have been investigated. The reaction enthalpies (298 K), barriers (0 K), and activation energies and pre-exponential factors (700-1100 K), have been calculated by means of density functional theory, specifically with B3-LYP/6-311G(d,p) geometries, followed by BMK/6-311+G(3df,2p) single-point energy calculations. For uncongested sites in the PAHs, a reasonable correlation is obtained between reactivities (as characterized by the reaction barriers) and reaction enthalpies. This is reflected in a Bell-Evans-Polanyi (BEP) relationship. However, for congested sites, abstraction is accompanied both by lower reaction enthalpies (due to relief of steric strain) and also by reduced reactivities (due to significantly increased steric hindrance effects in the transition structures), so that the BEP relationship does not hold. In addition, the reaction enthalpies and kinetic parameters for the series of linear acenes indicate that abstraction is more difficult from the central rings.

Gas-phase regiocontrolled generation of charged amino acid and peptide radicals.

The combined use of advanced mass spectrometry experiments, condensed-phase synthesis of serine and homoserine nitrate ester radical precursors, and high-level ab initio calculations provides a powerful way of examining the fundamental reactivity of radicals derived from peptides.

Popular theoretical methods predict benzene and arenes to be nonplanar.

Planar (D6h) benzene has one (1181i cm-1, b2g) and three (1844i cm-1, b2g; 462i cm-1, e2u) imaginary vibrational frequencies at the MP2/6-311++G(d,p) and MP2/6-311++G levels of theory, respectively! The spurious frequencies correspond to D3d chair (b2g) and C2v boat (e2u) out-of-plane distortions. Numerous, similar examples where planar benzene is not a minimum are documented at the MP2, MP3, and CISD levels with popular Pople-type basis sets, while the RHF, B3LYP, and BLYP methods exhibit no such problems. We show that, in the sp and spd atomic-orbital limits of MP2 theory, benzene is nonplanar. The observed failure of electron correlation methods with unbalanced basis sets to predict planar minima is not unique to benzene but is also found for other pi-delocalized molecules, including pyridine, naphthalene, anthracene, the cyclopentadienyl and indenyl anions, and the tropylium cation. Detailed mathematical analysis reveals that an insidious, geometry-dependent, two-electron basis set incompleteness error (BSIE) is responsible for the problem and that balanced, correlation-consistent constructions of basis sets are generally required to ensure reliable predictions for arenes with correlated wave functions.

An assessment of theoretical procedures for predicting the thermochemistry and kinetics of hydrogen abstraction by methyl radical from benzene.

The reaction enthalpy (298 K), barrier (0 K), and activation energy and preexponential factor (600-800 K) have been examined computationally for the abstraction of hydrogen from benzene by the methyl radical, to assess their sensitivity to the applied level of theory. The computational methods considered include high-level composite procedures, including W1, G3-RAD, G3(MP2)-RAD, and CBS-QB3, as well as conventional ab initio and density functional theory (DFT) methods, with the latter two classes employing the 6-31G(d), 6-31+G(d,p) and/or 6-311+G(3df,2p) basis sets, and including ZPVE/thermal corrections obtained from 6-31G(d) or 6-31+G(d,p) calculations. Virtually all the theoretical procedures except UMP2 are found to give geometries that are suitable for subsequent calculation of the reaction enthalpy and barrier. For the reaction enthalpy, W1, G3-RAD, and URCCSD(T) give best agreement with experiment, while the large-basis-set DFT procedures slightly underestimate the endothermicity. The reaction barrier is slightly more sensitive to the choice of basis set and/or correlation level, with URCCSD(T) and the low-cost BMK method providing values in close agreement with the benchmark G3-RAD value. Inspection of the theoretically calculated rate parameters reveals a minor dependence on the level of theory for the preexponential factor. There is more sensitivity for the activation energy, with a reasonable agreement with experiment being obtained for the G3 methods and the hybrid functionals BMK, BB1K, and MPW1K, especially in combination with the 6-311+G(3df,2p) basis set. Overall, the high-level G3-RAD composite procedure, URCCSD(T), and the cost-effective DFT methods BMK, BB1K, and MPW1K give the best results among the methods assessed for calculating the thermochemistry and kinetics of hydrogen abstraction by the methyl radical from benzene.

Metal-mediated formation of gas-phase amino acid radical cations.

The results from an investigation of the collision-induced dissociation (CID) of the ternary complexes [Cu(II)(terpy)(AA)](2+) are presented (terpy = 2,2':6',2' '-terpyridine; AA = one of the twenty common amino acids). These complexes show a rich gas-phase chemistry, which depends on the identity of the amino acid. For the histidine-, lysine- and tryptophan-containing complexes, oxidative dissociation of the amino acid is observed, yielding the amino acid radical cation. The results of further mass selection and CID of these amino acid radical cations are presented. The CID of the series [Fe(III)(salen)(AA)](+) (where salen = N,N'-ethylenebis(salicylideneaminato)) is also examined. These complexes undergo loss of the neutral amino acid in all cases, although the radical cation of arginine is also produced and its subsequent fragmentation examined. B3-LYP/6-31G(d) computations were carried out to test aspects of the proposed fragmentation mechanism of the histidine and arginine radical cations.

An experimental and theoretical investigation of gas-phase reactions of Ca2+ with glycine.

The gas-phase reactions between Ca(2+) and glycine ([Ca(gly)](2+)) have been investigated through the use of mass spectrometry techniques and B3-LYP/cc-pWCVTZ density functional theory computations. The major peaks observed in the electrospray MS/MS spectrum of [Ca(gly)](2+) correspond to the formation of the [Ca,C,O(2),H](+), NH(2)CH(2) (+), CaOH(+), and NH(2)CH(2)CO(+) fragment ions, which are produced in Coulomb explosion processes. The computed potential energy surface (PES) shows that not only are these species the most stable product ions from a thermodynamic point of view, but they may be produced with barriers lower than for competing processes. Carbon monoxide is a secondary product, derived from the unimolecular decomposition of some of the primary ions formed in the Coulomb explosions. In contrast to what is found for the reactions of Ca(2+) with urea ([Ca(urea)](2+)), minimal unimolecular losses of neutral fragments are observed for the gas-phase fragmentation processes of [Ca(gly)](2+), which is readily explained in terms of the topological differences between their respective PESs.

On the origin of cis/trans stereoselectivity in intramolecular Diels-Alder reactions of substituted pentadienyl acrylates: a comprehensive density functional study.

[structures: see text] A gas-phase B3LYP/6-31+G(d) study of substituent effects on the stereochemistry of both intramolecular Diels-Alder (IMDA) reactions of 9-E- and 9-Z-substituted pentadienyl acrylates and intermolecular Diels-Alder (DA) reactions between butadiene and monosubstituted alkenes and 3-substituted acrylates is reported and involves the calculation of 230 transition structures. It was found that, although exo ("anti-Alder") addition of monosubstituted ethenes to butadiene is the norm, Alder endo selectivity is more widely predicted for 3-substituted methyl acrylate dienophiles, and this was explained in terms of secondary orbital interactions (SOIs). Whereas cis/trans selectivity for IMDA reactions involving 9-E-substituted pentadienyl acrylates generally follows the normal pattern found for the corresponding intermolecular DA reactions, the 9-Z-substituted stereoisomers generally displayed trans selectivity that was much stronger than can be attributed to effects of the isolated substituent. This is strikingly so with unsaturated electron-withdrawing substituents whose endo selectivities, displayed in intermolecular DA reactions, are reversed in the IMDA reactions of pentadienyl acrylates. The origin of this anomalous Z-effect is explained in terms of the twist-mode asynchronicity concept of Brown and Houk. These ideas are used to explain the stereochemical outcomes of IMDA reactions of other triene systems.