New insights into the stability of alkenes and alkynes, fluoro-substituted or not: a DFT, G4, QTAIM and GVB study

Many undergraduate organic chemistry books do not agree with the order of relative stability of alkenes towards hydrogenation reactions. Although they ascribe the stability of alkenes to the number and spatial position of the alkyl groups attached to the vinyl carbon atoms, results from the quantum theory of atoms in molecules indicate that the influence of an alkyl substituent on the stability of unsaturated hydrocarbons arises from the slight removal of electron density of the π bond, not from donation of their charge density to unsaturated carbon atoms as stated in many text books. There is an inverse relation between delocalization index—the number of shared electrons between two atoms, or Wiberg bond index of C=C bond—and the number of methyl groups attached to the vinyl carbon atoms. Electron withdrawing groups (EWGs) attached to unsaturated carbon atoms of alkenes and alkynes have two different behaviors: slight EWGs (alkyl groups) stabilize unsaturated carbon atoms while the strong EWG destabilizes the unsaturated carbon atoms. Generalized valence bond theory was also used to study the ambiguous behavior of fluorine substituents bonded to vinyl carbon atoms.

Acyl-CoA desaturase ADS4.2 is involved in the formation of characteristic wax alkenes in young Arabidopsis leaves

Monounsaturated alkenes are present in the cuticular waxes of diverse plants and are thought to play important roles in their interactions with abiotic and biotic factors. Arabidopsis (Arabidopsis thaliana) leaf wax has been reported to contain alkenes; however, their biosynthesis has not been investigated to date. Here, we found that these alkenes have mainly ω-7 and ω-9 double bonds in characteristically long hydrocarbon chains ranging from C₃₃ to C₃₇. A screening of desaturase-deficient mutants showed that a single desaturase belonging to the acyl-CoA desaturase (ADS) family, previously reported as ADS4.2, was responsible for introducing double bonds en route to the wax alkenes. ADS4.2 was highly expressed in young leaves, especially in trichomes, where the alkenes are known to accumulate. The enzyme showed strong activity on acyl substrates longer than C₃₂ and ω-7 product regio-specificity when expressed in yeast (Saccharomyces cerevisiae). Its endoplasmic reticulum localization further confirmed that ADS4.2 has access to very-long-chain fatty acyl-CoA substrates. The upstream biosynthesis pathways providing substrates to ADS4.2 and the downstream reactions forming the alkene products in Arabidopsis were further clarified by alkene analysis of mutants deficient in other wax biosynthesis genes. Overall, our results show that Arabidopsis produces wax alkenes through a unique elongation–desaturation pathway, which requires the participation of ADS4.2.

Arabidopsis produces cuticular alkenes through a unique elongation–desaturation pathway requiring the acyl-CoA desaturase ADS4.2.     

Regression and model-building in conservation biology, biogeography and ecology: The distinction between – and reconciliation of – ‘predictive’ and ‘explanatory’ models

In many large-scale conservation or ecological problems where experiments are intractable or unethical, regression methods are used to attempt to gauge the impact of a set of nominally independent variables (X) upon a dependent variable (Y). Workers often want to assert that a given X has a major influence on Y, and so, by using this indirection to infer a probable causal relationship. There are two difficulties apart from the demonstrability issue itself: (1) multiple regression is plagued by collinear relationships in X; and (2) any regression is designed to produce a function that in some way minimizes the overall difference between the observed and predicted Ys, which does not necessarily equate to determining probable influence in a multivariate setting. Problem (1) may be explored by comparing two avenues, one in which a single best regression model is sought and the other where all possible regression models are considered contemporaneously. It is suggested that if the two approaches do not agree upon which of the independent variables are likely to be significant, then the deductions must be subject to doubt.     

Variation in fish growth characteristics along a river course

Variation in the growth patterns of roach, Rutilus rutilus (L.), pike, Esox lucius L., and chub, Leuciscus cephalus (L.) was examined along the upper Warta River, where human impact (mostly pollution) has influenced the longitudinal zonation on the fish assemblage. Significant differences were found in the exponent of weight-length relationships for roach and chub populations occupying different zones of the river, but no such variation was observed in pike. Moreover, pike growth was isometric, whereas roach and chub grew allometrically, with regression coefficients (slope) above 3. Although the length-at-age data were similar for each zone, the von Bertalanffy parameters (L _inf, K and t ₀) suggest that there may exist some inter-zone variation in the overall growth patterns of these species. All the species grew better in the zone where the index of relative abundance (relating dominance of a particular species to its maximum abundance in river system) achieved its highest value. The results suggest that a relative abundance index expressed in this way can be a good index of habitat quality.     

Evaluating indices of body condition in two cricket species

Body mass components (dry mass, lean dry mass, water mass, fat mass) in each sex correlate strongly with body mass and pronotum length in Gryllus texensis and Acheta domesticus. Ordinary least squares (OLS) regression underestimates the scaling relationship between body mass and structural size (i.e., pronotum length) in both cricket species compared with standard major axis (SMA) regression. Standardized mass components correlate more strongly with scaled mass index () than with residual body mass (R_i). R_i represents the residuals from an OLS regression of log body mass against log pronotum length. Neither condition index predicts energy stores (i.e., fat content) in G. texensis. R_i is not correlated with energy stores in A. domesticus whereas is negatively correlated. A comparison of condition index methods using published data showed that neither sex nor diet quality affected body condition at adulthood in G. texensis when using the scaled mass index. However, the residual index suggested that sex had a significant effect on body condition. Further, analysis of covariance (ANCOVA) suggested that diet quality significantly affects body mass while statistically controlling for body size (i.e., body condition). We conclude that the statistical assumptions of condition index methods must be met prior to use and urge caution when using methods that are based on least squares in the y‐plane (i.e., residual index ANCOVA).     

Molecular Dynamics Investigation of Bond Ordering of Unsaturated Lipids in Monolayers

Molecular dynamics simulations of three model lipid monolayers of 2,3-diacyl-D-glycerolipids, that contained stearoyl (18:0) in the position 3 and oleoyl (18:9cis), linoleoyl (18:26cis), or linolenoyl (18:33cis) in the position 2, have been carried out. The simulation systems consisted of 24 lipid molecules arranged in a rectangular simulation cell, with periodic boundary conditions in the surface plane. 1 nanosecond simulations were performed at T = 295 K. C-C and C-H bond order parameter profiles and the bond orientation distributions about the monolayer normal have been calculated. The relation of the distributions to the order parameters was analyzed in terms of maxima and widths of the distributions. The cis double bond order parameter is found to be higher than those of adjacent single C-C bonds. The widths of the two distributions of C-H bonds of the cis double bond segment in di- and triunsaturated molecules are much smaller than that obtained for methylene group located between the double bonds. The bond orientation distribution function widths depend on both the segment location in the chain and the segment chemical structure.     

Theoretical study for high-energy-density compounds from cyclophosphazene III. A quantum chemistry study: High nitrogen-contented energetic compound of 1,1,3,3,5,5,7,7-octaazido-cyclo-tetraphosphazene: N4P4(N3)8

Molecular structure, vibrational frequencies and infrared intensities of 1,1,3,3,5,5,7,7-octaazido-cyclo-tetraphosphazene have been studied employing HF, B3LYP and B3PW91 methods using 6-31G¹ basis set. The study showed that this molecule has non-planar structure and there is no imaginary frequency. Furthermore, there exist four sets of special PN bonds in the P₄N₂₈ ring; the PN bonds and the azide groups conjoint to them have special characters. The NBO population analysis was used to help us understand the interactions between donor orbit and acceptor orbit in the nitrogen phosphorus systems. Furthermore, three methods with the same basis set are further employed to calculate the heats of formation for the compound.     

The parabolic pattern of animal growth: determination of equation parameters and their temperature dependencies

1. Parabolic (power) growth is characteristic of many aquatic poikilothermic animals for certain stages of their development. The parabolic pattern describing growth in weight (or length) under constant ambient conditions can be expressed in the following general form: where Y is growth rate (or specific growth rate), X is animal size, and Ω and τ are coefficients. The constancy of ambient conditions is of cardinal importance in determining τ. The problem of maintaining a constant level of nutrition can be reliably solved only by the presence of food in excess of demand. Data satisfying these requirements have demonstrated that τ does not depend on factors such as temperature, and can be assumed to be independent of ambient conditions. In the growth rate-weight equation, τ ranges between 0.5 and 0.85 for animals representing a variety of taxonomic groups. 2. The coefficient Ω. is affected by ambient conditions (e. g. temperature, amount of food). Its value reflects the ‘level’ of the growth rate-size relationship under given conditions. For a specific time period, Ω can be computed from the following formula: where X₁ and X₂ are the animal sizes (weights, lengths) at time t₁ and t₂, the beginning and end of the time period. The calculated value of Ω corresponds to the average intensity of the ambient factor (F) affecting the growth during the period between the two observations. If the values of the Ω are calculated for wide range of the factor, the relationship between the Ω. and F, Ω=f(F), can be determined. The function can be then incorporated into the parabolic equation of growth, as 3. Dependence of the development rate (1/D, where D is time interval needed to complete a given stage) on temperature (T), and dependence of Ω on T, are both described by sigmoid-shape curves. The broad intermediate part of these curves, a range to which animals are adapted in nature, can be approximated by straight line functions. For two groups, pan-size sockeye salmon (Oncorhynchus nerka) and different species of chironomid larvae, it was shown that an equation combining parabolic growth and linear temperature patterns describes accurately the variability observed in growth rates under experimental and natural conditions.     

Dependence ofγ-irradiated Y-peak and melting of DNA on concentration and ionic environment

Summary Y-peak is found to be a function of ionic strength and concentrations of DNA. The Y-peak reveals close dynamic interaction between DNA and solvent system. Electronic transitions responsible for Y-peak are not the same transitions that are responsible for X-peak. Y-peak's electronic transitions are indicative of charge transfer complex formation between DNA and solvent system.-irradiation induces hyperchromicity due to strand separation at lower doses. A-T base pairs are first to undergo coiled state as shown byTm spread. Strand chopping and saturation of double bonds of the exposed bases by free radicals (H° and OH°) give rise to hypochromic regions at X-peak. Rise in ionic strength and the concentration of DNA has protective effect against-damage. Y-peak is found to be a function of solvent, whereas, X-peak is independent of solvent nature.     

A novel ene-reductase from Synechococcus sp. PCC 7942 for the asymmetric reduction of alkenes

The increasing demand for enantiopure molecules in the pharmaceutical and fine-chemical industry requires the availability of well-characterized and efficient biocatalysts for asymmetric syntheses. Thereby, asymmetric reduction of alkenes represents one of the most employed reactions for the production of chiral molecules. Here, we present a novel ene-reductase from the cyanobacterium Synechococcus sp. PCC 7942, a member of the old yellow enzyme family, capable of reducing CC bonds in a anti-specific fashion. We evaluated its biocatalytic potential by characterizing the substrate spectrum, cofactor preference, stereoselectivity and biochemical properties. This NADPH-dependent flavoprotein accepted a wide range of activated alkenes and displayed a pH optimum between pH 7.6 and pH 8.6. A C-terminal His₆-tag decreased the enzyme activity 2.7-fold, but did not influence the stereoselectivity. The reduction of (R)-carvone and 2-methylmaleimide yielded (R)-products with high optical purities (98% de and >99% ee, respectively), pointing out the applicability of this new biocatalyst in the stereoselective production of chiral compounds.     

Spectroscopic characterization of cytochrome P450 Compound I

The cytochrome P450 protein-bound porphyrin complex with the iron-coordinated active oxygen atom as Fe(IV)O is called Compound I (Cpd I). Cpd I is the intermediate species proposed to hydroxylate directly the inert carbon–hydrogen bonds of P450 substrates. In the natural reaction cycle of cytochrome P450 Cpd I has not yet been detected, presumably because it is very short-lived. A great variety of experimental approaches has been applied to produce Cpd I artificially aiming to characterize its electronic structure with spectroscopic techniques. In spite of these attempts, none of the spectroscopic studies of the last decades proved capable of univocally identifying the electronic state of P450 Cpd I. Very recently, however, Rittle and Green [9] have shown that Cpd I of CYP119, the thermophillic P450 from Sulfolobus acidocaldarius, is univocally a Fe(IV)O–porphyrin radical with the ferryl iron spin (S = 1) antiferromagnetically coupled to the porphyrin radical spin (S′ = 1/2) yielding a S_tot = 1/2 ground state very similar to Cpd I of chloroperoxidase from Caldariomyces fumago. In this mini-review the efforts to characterize Cpd I of cytochrome P450 by spectroscopic methods are summarized.     

Estimation of the thermal and photochemical stabilities of pheromones

The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value L_мах corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states. The weakest bonds in molecules determined by the kinetic stability method are compared with the bond length variations in molecules in the excited state upon absorption of light by a molecule. Good agreement between the results obtained is demonstrated and the difference between them is discussed. The universality of formulations within both approaches used to estimate the stability of different pheromone molecules containing strained cycles and conjugated, double, and single bonds allows these approaches to be applied for studying other molecules.

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Graphical Abstract Estimation of the thermal and photochemical stabilities of pheromones

     

Novel distance-based atom-type topological indices DAI for QSPR/QSAR studies of alcohols

In this work, we propose a distance-based atom-type topological index (DAI) for quantitative structure-property/activity relationship (QSPR/QSAR) studies. The newly constructed index, which codes the structural environment of each atom type in a molecule, can be calculated simply. These atom-type topological indices, along with our recently proposed Lu index, were used to construct QSPR/QSAR models for several representative physical properties and biological activities of several data sets of alcohols with a range of non-hydrogen atoms by using multiple linear regression (MLR) analysis. The efficiency of these indices is verified by high quality QSPR models. The results indicate that the combined use of Lu and DAI indices promises to be a useful method for QSPR/QSAR analysis of complex compounds.      

How relevant are S=O and P=O Double Bonds for the Description of the Acid Molecules H2SO3, H2SO4, and H3PO4, respectively?

The acid molecules H₂SO₃, H₂SO₄, and H₃PO₄ are usually drawn using "Lewis structures" which exhibit the octet extension by 3d-orbitals on sulfur and phosphorus, respectively. Thus, S=O and P=O double bonds are assumed to be formed. The natural d-orbital occupancies on S and P, however, were calculated to be as low as 0.1 e, and therefore, an octet extension can hardly be expected. After the natural bond orbitals (NBO) search procedure was forced to attempt to form different Lewis structures of bonds and lone pairs, we defined the optimal Lewis structure, if a dominant structure exists at all, by the maximum electronic charge in Lewis orbitals. Indeed, sulfur obeys the octet rule in the optimal zwitterionic Lewis structures and does not form S=O double bonds. No dominant resonance structure could be found for H₃PO₄ where polarized PO ?-bond and zwitterionic PO bond structures exhibit similar weights.     

Entropy Change for Free Polypeptide Chain upon Hydrogen Bonding

Formation probabilities of different hydrogen bonds between carbonyl oxygen and amide hydrogen were determined by Monte Carlo simulations using a computer model in the space of sterically allowable conformations of alanine and glycine oligopeptides, and the corresponding entropy losses for the peptide backbone, TS, were calculated. The model was studied at different criteria of steric interactions. Comparison with the data of other authors showed the values of TSto be mainly determined by overall extent and type of the state space and to be only slightly dependent on its energy profile. Both short-range and long-range steric interactions were shown to prevent hydrogen bonding, especially in alanine peptides. In the model studied, the initiation of (R)-helices is associated with TS= 8–10 kT, and prior formation of a 3/10-turn or one three-center H-bond does not appreciably decrease this entropy barrier. Elongation of the (R)-helix by one residue leads to TS= 3.0–3.7 kT, the helices begin to stabilize after at least three sequential H-bonds are formed. The difference in the probability of insertion of Ala and Gly into the helix is lower than it follows from comparison of their mobility. The results could be explained assuming that factors different from helical H-bonds take part in the stabilization of the helices. One may suppose upon modeling of folding that even three sequential H-bonds are unable to fix the structure of a flexible peptide loop, while the elongation of (R)-helices in the supersecondary helix-loop-helix structure is favorable as long as the loop conformation remains nearly optimal.     

Photophysics of the carotenoids associated with the xanthophyll cycle in photosynthesis

Green plants use the xanthophyll cycle to regulate the flow of energy to chlorophylla within photosynthetic proteins. Under conditions of low light intensity violaxanthin, a carotenoid possessing nine conjugated double bonds, functions as an antenna pigment by transferring energy from its lowest excited singlet state to that of chlorophylla within light-harvesting proteins. When the light intensity increases, violaxanthin is biochemically transformed into zeaxanthin, a carotenoid that possesses eleven conjugated double bonds. The results presented here show that extension of the conjugation of the polyene lowers the energy of the lowest excited singlet state of the carotenoid below that of chlorophylla. As a consequence zeaxanthin can act as a trap for the excess excitation energy on chlorophylla pigments within the protein, thus regulating the flow of energy within photosynthetic light-harvesting proteins.     

Neighborhood predictors of plant performance

Summary We developed models of inter-individual interference to predict the fecundity of individuals in populations of the annual plant species, Arabidopsis thaliana. An individual plant is modeled as having a neighborhood which is a circular area of fixed radius with the plant at its center. Other plants which share the circle with the focal plant are termed neighbors of the focal plant. We developed an index of neighborhood interference which is the independent variable in a non-linear regression model that predicts individual plant fecundity. We present methods of exploratory data analysis that are useful in determining a best neighborhood radius, defined as that radius which minimizes residual sum of squares, and in deciding on the functional form of the interference index. In developing the interference index for Arabidopsis, we focus on aspects of the spatial distribution of neighbors: their number, distance and angular dispersion.We found that a best (or optimal) neighborhood radius can be resolved, which provides the best predictor of plant performance. Fecundity predictors based on adult neighbors were noticeably better than those based on neighbors at the seedling stage. Rosettes of Arabidopsis may change location during development (they fall over) and the new fallen positions do provide some improvement in the predictor. Taking into account distance to neighbors within the neighborhood provided only negligible improvement in the model. Finally, the incorporation of angular dispersion in the crowding index produced a considerably better fit. The fecundity predictor that included number of neighbors and angular dispersion in the crowding index explained about 70% of the variation in individual seed set.     

Moose and snowshoe hare competition and a mechanistic explanation from foraging theory

Summary Moose (Alces alces) and snowshoe hare (Lepus americanus) appear to compete with each other. This was determined using the natural experiments of populations found in sympatry and allopatry on islands at Isle Royale National Park, Michigan, and manipulated exclosures. The population densities from these areas are fit to a series of competition models based upon different competitive mechanisms (Schoener 1974a), using non-linear regression techniques. A model of competition for food where the food can be separated into exclusively used and shared categories is found to predict observed densities of moose and hare best. Finally, the competition model's parameters (fraction of food shared and competition coefficients) are shown to agree with values predicted independently from a foraging model.     

Non-aromatic stabilised form of 3,4-difluoropyrrole at triosmium clusters: N-H and C-H versus C-F activation

Reaction of 3,4-difluoropyrrole with the labile triosmium cluster [Os₃(CO)₁₀(CH₃CN)₂] affords products in which C-H, N-H and C-F bonds are cleaved under mild conditions. C-H and N-H bonds are cleaved to give [Os₃H(NCCFCFCH₂)(CO)₁₀] (1) a non-aromatic stabilised form of 3,4-difluoropyrrole. Thermolysis of 1 affords in moderate yields the compounds [Os₃H₂(CCCFCHNH)(CO)₉] (2) and [Os₃H₂(NCHCFCFC)(CO)₉] (3). For compound 3, C-H and N-H bonds are cleaved with concomitant migration of H atoms to the metal framework. In contrast, for compound 2 activation of C-H and C-F bonds leads to coordination of the ligand through the carbon atoms, acting as a four-electron donating species.     

Evolutionary relationship and secondary structure predictions in four transport proteins ofSaccharomyces cerevisiae

Summary The comparison of the amino acid sequences of four yeast transport proteins indicates that there is a questionable relatedness between the uracil permease (FUR4) and the purine-cytosine permease (FCY2), whereas the arginine permease (CAN1) and the histidine permease (HIP1) clearly originated from a common molecular ancestor. The analysis of the primary structure of these transport proteins by two methods of secondary structure predictions suggests the presence of 9–12 membrane-spanning -helices in each polypeptide chain. These results are concordant in that 90% of the -helices were determined by both methods to be at the same positions. In the aligned sequencesHIP1 andCAN1, the postulated membrane-spanning -helices often start at corresponding sites, even though the overall sequence similarity of the two proteins is only 30%. In the aligned DNA coding sequences ofCAN1 andHIP1, synonymous nucleotide substitutions occur with very similar frequencies in regions where the replacement substitution (changing the amino acids) frequencies are widely different. Moreover, our data suggest that the replacement substitutions can be considered as neutral in the N-terminal segment, whereas the other regions are subject to a conservative selective pressure because, if compared to a random drift, the replacement substitutions are underrepresented.