Evidence of an odd–even effect on the thermodynamic parameters of odd fluorotelomer alcohols

A phase transition study, including vapour pressure determinations of odd fluorotelomer alcohols {oFTOH; CF₃(CF₂)_nCH₂OH, with n = 5 to 9}, is reported in order to explore the effect of the successive introduction of –CF₂– groups into the molecule on the thermodynamic properties related to (solid + liquid, solid + gas, and liquid + gas) equilibria. An odd–even effect on the thermodynamic parameters of fusion and sublimation was observed in the homologous series of odd fluorotelomer alcohols indicating an increase of the stability in the crystal packing for the members with an odd number of carbon atoms. The vaporization parameters of o-FTOH were compared with the literature data for their alkane analogues and the results showed a higher volatility of liquid fluorotelomer alcohols than their congeners. The higher molecular conformation restriction of perfluorinated alcohols and/or the higher molar mass seems to contribute to their higher entropy of vaporization which drives the volatility of the 1H,1H-perfluorinated alcohols.     

Mean field analysis of four liquid crystalline odd–even ester dimers

A mean field analysis is presented for four liquid crystalline ester dimers, Dn, containing the dimethylbenzalazine mesogen, alkanedioyloxy flexible spacers from 7 to 10 carbon atoms and acetate terminal groups. The conformations of the dimers, in the RIS approximation, were generated from the known crystallographic coordinates of D8 and D9. The energy of each conformer is split into an internal (conformation dependent) part and an external (orientation dependent) part. After proper averaging over all orientations and conformations, the orientation–conformation partition function is evaluated and, from that, the Helmholtz free energy. A qualitative agreement between calculated and observed thermodynamic properties is obtained. In fact, the theoretical analysis correctly predicts strong odd–even fluctuations for the mesogenic group order parameter, S, as well as for transition entropy, ΔS _NI, and transition temperature, T _NI. The distribution of conformers is similar for dimers having the same parity of the spacer. For even dimers, the calculated fraction of linear extended conformers in the nematic phase at the N–I transition is around 47%, whereas it is less than 3.6% for odd dimers.     

Is the mobility of the pore walls and water molecules in the selectivity filter of KcsA channel functionally important?

We performed in-depth analysis of the forces which act on the K(+) ions in the selectivity filter of the KcsA channel in order to estimate the relative importance of static and dynamic influence of the filter wall and water molecules on ion permeation and selectivity. The forces were computed using the trajectories of all-atom molecular dynamics simulations. It is shown that the dynamics of the selectivity filter contributes about 3% to the net force acting on the ions and can be neglected in the studies focused on the macroscopic properties of the channel, such as the current. Among the filter atoms, only the pore-forming carbonyl groups can be considered as dynamic in the studies of microscopic events of conduction, while the dynamic effects from all other atoms are negligible. We also show that the dynamics of the water molecules in the filter can not be neglected. The fluctuating forces from the water molecules can be as strong as net forces from the pore walls and can effectively drive the ions through the local energy barriers in the filter.     

Is glassy carbon a really inert electrode material for the reduction of carbon–halogen bonds?

Dissociative electron transfer (DET) to various organic halides has been investigated at glassy carbon electrodes (GCEs) in acetonitrile. It is shown that the surface composition of GCEs significantly affects the reduction peak potential of RX, an increase of the oxygen-to-carbon ratio apparently causing a positive shift of E_p. This catalytic effect depends on both GCE surface composition and DET mechanism, appreciable catalysis being observed only when the initial electron transfer plays a crucial role in the overall kinetics of the process. The highest observed peak potential difference is of the order of 0.1 V found for some alkyl halides undergoing a concerted DET.     

Thermal and odd–even behaviour in a homologous series of lithium n-alkanoates

Thermotropic phase transition temperatures, enthalpies and entropies of phase changes and odd–even alternation, in a homologous series of anhydrous lithium n-alkanoates, LiC_nH_2n?1O₂ (LiC_8–19 inclusive), have been investigated by differential scanning calorimetry (d.s.c.), hot stage polarizing microscopy and solid state ¹³C NMR spectroscopy. The number of phases observed, between the room temperature microcrystalline solid and isotropic melt, shows a clear dependence on chain length. For LiC_8–13, only one intermediate lamellar II crystalline phase is observed. For LiC_14–19, a lamellar II and high temperature phase are evident. The high temperature phase is characterized by pre-melting and disordering of hydrocarbon chains as they change from nearly all-trans to one with increased gauche conformers. It is probably a solid rotator phase. Odd–even alternation in melting temperature, density and some thermodynamic data result from the relative distance between methyl groups, from opposite layers in a bi-layer. Molecular models indicate that the methyl groups in odd chains are more favourably orientated which lead to a more energetically favoured staggered conformer. As a consequence, the methyl groups, for odd chains, are in closer proximity than even chains. This subtle change in the molecular lattice could account for the presence of polymorphic structures on cooling from the melt.     

Is the stereomutation of methane possible?

Large basis set ab initio calculations at correlated levels, including MP2, single reference, as well as multireference configuration interaction, carried out on the methane potential energy surface, have located and characterized a transition structure for stereomutation (one imaginary frequency). This structure is best described as a pyramidal complex between singlet methylene and a side-on hydrogen molecule with C_s symmetry. At the single reference CI level, it lies 105 kcal/mol above the methane T_d-ground state but is stable relative to dissociation into CH₂(¹A₁) and H₂ by 13 kcal/mol at 0 K (with harmonic zero point energy (ZPE) corrections for all structures). Dissociation of the transition state into triplet methylene and hydrogen also is endothermic (by 4 kcal/mol), but single bond rupture to give CH and H^. is 3 kcal/mol exothermic. Thus, it does not appear likely that methane can undergo stereomutation classically beneath the dissociation limit. Confirming earlier conclusions, side-on insertion of ¹A₁ CH₂ into H₂ in a perpendicular geometry occurs without activation energy. Planar (D_4h) methane (130.5 kcal/mol) has four imaginary frequencies. Two of these are degenerate and lead to equivalent planar C_2v structures with one three-center, two-electron bond and two two-electron bonds and two imaginary frequencies. The remaining imaginary frequencies of the D_4h form lead to tetrahedral (T_d) and pyramidal (C_4v) methane. The latter has three negative eigenvalues in the force-constant matrix; one of these leads to the T_d global minimum and the other to the C_s (parallel) stereomutation transition structure. Multireference CI calculations with a large atomic natural orbitals basis set produce similar results, with the electronic energy of the C_s stereomutation transition state 0.7 ± 0.5 kcal/mol higher than that of CH + H^. dissociation products, and a ZPE-corrected energy which is 5 ± 1 kcal/mol higher. Also considered are photochemical pathways for stereomutation and the possible effects of nuclear spin, inversion tunneling, and the parity-violating weak nuclear interaction on the possibility of an experimental detection of stereomutation in methane. © 1995 by John Wiley & Sons, Inc.     

Is there computational support for an unprotonated carbon in the E4 state of nitrogenase?

In the key enzyme for nitrogen fixation in nature, nitrogenase, the active site has a metal cluster with seven irons and one molybdenum bound by bridging sulfurs. Surprisingly, there is also a carbon in the center of the cluster, with a role that is not known. A mechanism has been suggested experimentally, where two hydrides leave as a hydrogen molecule in the critical E₄ state. A structure with two hydrides, two protonated sulfurs and an unprotonated carbon has been suggested for this state. Rather recently, DFT calculations supported the experimental mechanism but found an active state where the central carbon is protonated all the way to CH₃. Even more recently, another DFT study was made that instead supported the experimentally suggested structure. To sort out the origin of these quite different computational results, additional calculations have here been performed using different DFT functionals. The conclusion from these calculations is very clear and shows no computational support for an unprotonated carbon in E₄. © 2017 Wiley Periodicals, Inc.     

Is there any group additive rules in the calculation of electron correlation energies of long straight chain alkane molecules?

According to the definition in the text, the correlation energy of 1s2C of carbon atoms, the primary and secondary C-H bonding electron pairs in some CH3, CH2 fragments and CH3(CH2)mCH3 (m=1-5) linear alkane molecules are calculated and analyzed. The transferability of the correlation energies of these electron pairs in the linear alkanes is investigated. The results indicate that the correlation energy of 1s2C is perfectly transferable in the respective methyl and methylene groups, while the correlation energies of the primary and secondary C-H bonding electron pairs are approximately transferable in methyl and methylene groups. The analysis of the results of group correlation energy shows that both of the correlation energies of methyl and methylene groups are transferable in these linear alkanes. The correlation energies of methylene group in CH3(CH2)mCH3 (m=1-5) molecules are slightly decreasing showing a converging trend to a "standard" methylene group in linear alkanes. The excellent fitting relationship between the total correlation energy and the number of methylene groups of the linear alkanes shows that the total correlation energy is a linear function of the number of methylene groups, which means that the total correlation energies of large linear alkanes can be reproduced and predicted by counting the numbers of methylene groups. In this way, total correlation energy of large linear alkane molecule can be approximately calculated using this simple group additive scheme with substantial saving in computational time.     

What Is the Structure of Pterodonoic Acid?

EudesmaneacidsandeudesmanelactoneshavebeendrawingattentionduetotheirwidespectrUmofbi0l0gicalpr0perties,particularlyantifeedant,cellgrowthinhibitoryandplantgr0wthregulatingactivities.l'2Inl994,Zha0andWeirep0rted'theisolationofpterodonoicacidfromLaggerapterodonta(DC)Benth,whichtheyclaimedasanewcomPoundwiththesthectureof3-oxoeudesma-4,ll-dien-l2-oicacid1.Infact,comPoundlisnotanewcomPoundandithasaPpearedinliteratureseveraltimes.hi1977,lwasfirstisolated4byBohlmannetalfromMexicangenusEuPat0riu…     

Is allylphosphine a carbon or a phosphorus base in the gas phase?

The gas-phase basicity of allylphosphine (2-propenylphosphine) was measured by means of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry techniques. A complete survey of the allylphosphine-H(+) potential energy surface, carried out through the use of high-level G2(MP2) and B3LYP/6-311+G(3df,2p) calculations, allows us to conclude that, under low-pressure, low-energy ICR conditions, the interaction between the protonated reference base, B(ref)H(+), and allylphosphine leads to a complex in which B(ref)H(+) attaches to the phosphorus atom of allylphosphine, where the electrostatic potential is strongly attractive. Hence, in the first step only the phosphorus protonated species should be formed. Its isomerization to yield the C(beta)-protonated form, which is the global minimum of the potential energy surface, implies a very high activation barrier that cannot be overtaken under normal experimental ICR conditions. Therefore, the main conclusion of our study is that allylphosphine behaves as a phosphorus base in the gas phase, even though the C(beta)-protonated structure is the most stable protonated species. We have also shown that both C(beta)- and C(gamma)-protonation triggers a cyclization of the system. An analysis of the bonding of the different protonated species as compared with that of the neutral system is presented.     

How are small ions involved in the compaction of DNA molecules?

DNA is a genetic material found in all life on Earth. DNA is composed of four types of nucleotide subunits, and forms a double-helical one-dimensional polyelectrolyte chain. If we focus on the microscopic molecular structure, DNA is a rigid rod-like molecule. On the other hand, with coarse graining, a long-chain DNA exhibits fluctuating behavior over the whole molecule due to thermal fluctuation. Owe to its semiflexible nature, individual giant DNA molecule undergoes a large discrete transition in the higher-order structure. In this folding transition into a compact state, small ions in the solution have a critical effect, since DNA is highly charged. In the present article, we interpret the characteristic features of DNA compaction while paying special attention to the role of small ions, in relation to a variety of single-chain morphologies generated as a result of compaction.     

On the possibility of homolytic addition of N-bromohexamethyldisilazane to the triple carbon–carbon bond

Russian Journal of General Chemistry - By an example of a reaction of N-bromohexamethyldisilazane with phenylacetylene the possibility of its homolytic addition to the triple carbon-carbon bond...     

Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon–carbon interactions

The nonbonded and bonded force field parameters for carbon atoms in single-wall carbon nanotubes (SWNT) are fitted by means of quantum chemistry calculations with considering the periodic boundary conditions. The nonbonded parameters between carbon atoms and hydrogen atoms are fitted as well. All the fitted parameters are verified by comparing to quantum chemistry results and by calculating Young's modulus. Adsorption of Hydrogen molecules are then carried out on a bundle of self-assembled SWNTs. The adsorption isotherms are consistent to the Freundlich equation. Both hydrogen molecules adsorbed outside and inside the SWNTs are counted. According to our result, hydrogen molecules adsorbed inside the SWNTs are more stable at a relatively high temperature and are playing an important part in total amount of the adsorbed molecules. While C(10,10) have the highest adsorption capacities in most of the temperatures, hydrogen molecules inside C(5,5) are the most stable of all the four kinds of SWNTs. Thus, balancing adsorption capacities and strength of interaction can be important in choosing SWNT for gas adsorption. Besides, we deduct an equation that can describe the relation between hydrogen pressure and amount of SWNTs based on our simulation results. The hydrogen pressure may decrease by adding SWNTs in the system. The fitting method in our system is valid to SWNTs and can be tested in further studies of similar systems. © 2018 Wiley Periodicals, Inc.     

Is the Hammett's constant free of steric effects?

In this work, we have explored the validity of the hypotheses on which rest the Hammett's approach to quantify the substituent effect on a reaction center, by applying two DFT energy decomposition schemes. This is performed by studying the change in the total electronic energy, ΔΔE, associated with a proton transfer isodesmic equilibrium. For this reaction, two sets of substituted benzoic acids and their corresponding benzoate anions have been considered. One of these sets contains para- and meta-substitutions, whereas the other one includes ortho-substituted benzoic acids. For each case, the gas phase change in the total electronic energy has been calculated, and two DFT energy decomposition schemes have been applied. The experimental σ(X) was found to be nearly proportional to the computed ΔΔE. The results for the para- and meta-substituted benzoic acids lead to the conclusion that it is possible to treat separately and, in an additive manner, the electrostatic and steric contributions; and also that the Hammett constant depends mainly on the electronic contributions to the free energy, while the steric contribution is negligible. However, the results for the ortho-substituted cases lead to the conclusion, as was assumed by Hammett, that there are significant qualitative differences between the effects on a reaction site of substituents in the meta- and para-positions and those in the ortho-position.     

Is an iodine atom almighty as a leaving group for Bu(3)SnH-mediated radical cyclization? The effect of a halogen atom on the 5-endo-trig radical cyclization of N-vinyl-alpha-halo amides

The effect of a halogen atom as a leaving group on Bu(3)SnH-mediated 5-endo-trig radical cyclization of N-(cyclohex-1-enyl) alpha-halo amides was examined. The cyclization of alpha-chloro amides occurred with a high degree of efficiency, whereas the corresponding alpha-iodo congeners gave only limited quantities of cyclization products. A detailed study revealed that these phenomena could be attributed to the initial conformations of alpha-halo amides. The cyclizing ability of alpha-iodo amides can be restored with Bu(3)SnCl or Bu(3)SnF as an additive. The cyclization of an alpha-iodo amide in the presence of Bu(3)SnF could be applied to a short-step synthesis of lycoranes featuring sequential 5-endo-trig and 6-endo-trig radical cyclizations.     

Recent advances in the application of nanoparticles in the selective reduction of carbon–carbon double bonds

Herein, we present recent advances in the application of metal nanoparticles in the selective hydrogenation of C–C double bonds. The review focuses on reduction methods of alkenes, arenes, and aromatic heterocycles, which were classified according to transition metals used as catalysts. The majority of described systems concern direct hydrogenation, which is of particular importance to industrial processes. Nonetheless, interesting transfer hydrogenation protocols were also developed, which may be incredibly convenient for laboratory purposes. Some of the methods are distinguished with excellent chemoselectivity making them the perfect tool for the synthesis of compounds containing reducible functional groups. Apart from noble metals, the application of earth-abundant ones as catalysts was a subject of studies, and the related methods were highlighted.     

Is spin-component scaled second-order Møller-Plesset perturbation theory an appropriate method for the study of noncovalent interactions in molecules?

Testing of the spin-component scaled second-order M?ller-Plesset (SCS-MP2) method for the computation of noncovalent interaction energies is done with a database of 165 biologically relevant complexes. The effects of the spin-scaling procedure (i.e., MP2 vs SCS-MP2), the basis set size, and the corrections for basis set superposition error (BSSE) are systematically examined. When using two-point basis set extrapolations for the correlation energy, augmentation of the atomic orbital basis with computationally costly diffuse functions is found to be obsolete. In general, SCS-MP2 also improves results for noncovalent interactions statistically on MP2, and significant outliers are removed. Moreover, it is shown that effects of BSSE and one-particle basis set incompleteness almost cancel each other in the case of triple-zeta sets (SCS-MP2/TZVPP or SCS-MP2/cc-pVTZ without counterpoise correction), which opens a practical route to efficient computations for large systems. We recommend SCS-MP2 as the preferred quantum chemical wave function based method for the noncovalent interactions in large biologically relevant systems when reasonable coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) calculations cannot be performed anymore. A comparison to MP2 and CCSD(T) interaction energies for n-alkane dimers, however, indicates (and this also holds to a lesser extent for hydrogen-bonded systems) limitations of SCS-MP2 when treating chemically "saturated" interactions. The different behavior of second-order perturbation theory for saturated and for stacked pi-systems is discussed.     

How does the mobility of phospholipid molecules at a water/oil interface reflect the viscosity of the surrounding oil?

The mobility of phospholipid molecules at a water/oil interface on cell-sized phospholipid-coated microdroplets was investigated through the measurement of diffusion constants by fluorescence recovery after photobleaching. It is found that the diffusion constant of phospholipids showed the relation D approximately (eta water + eta oil) -0.85, where D is the diffusion constant, eta water is the viscosity of water, and eta oil is the viscosity of oil. This observation indicates that the viscosity of the surrounding oil is the primary factor that determines the diffusibility of phospholipids at a water/oil interface.     

Is the trend of the polarizability per atom for all small 3d transition metal clusters the same? The case of Nin (n< or =5) clusters

The first theoretical study on static polarizability and polarizability anisotropy of small nickel clusters up to the pentamer is presented. All-electron-type calculations were performed using a finite field approach as implemented in the density functional program deMon2K. A newly developed first-order field-induced basis set for density functional calculations was employed. For the static polarizability per atom of these clusters, a different trend to the one reported in the literature for other transition metal cluster systems of similar size, is observed.     

How does surface modification aid in the dispersion of carbon nanofibers?

Small-angle light scattering is used to assess the dispersion behavior of vapor-grown carbon nanofibers suspended in water. These data provide the first insights into the mechanism by which surface treatment promotes dispersion. Both acid-treated and untreated nanofibers exhibit hierarchical morphology consisting of small-scale aggregates (small bundles) that agglomerate to form fractal clusters that eventually precipitate. Although the morphology of the aggregates and agglomerates is nearly independent of surface treatment, their time evolution is quite different. The time evolution of the small-scale bundles is studied by extracting the size distribution from the angle-dependence of the scattered intensity, using the maximum entropy method in conjunction with a simplified tube form factor. The bundles consist of multiple tubes possibly aggregated side-by-side. Acid oxidation has little effect on this bundle morphology. Rather acid treatment inhibits agglomeration of the bundles. The time evolution of agglomeration is followed by fitting the scattering data to a generalized fractal model. Agglomerates appear immediately after cessation of sonication for untreated fibers but only after hours for treated fibers. Eventually, however, both systems precipitate.