http://precedings.nature.com/subjects/chemistry/ Recently posted documents in Chemistry Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3928/version/1 A systematic and comprehensive semiempirical, Hartree-Fock (HF) ab initio, and B3LYP density functional theory (DFT) study was conducted on the relative thermodynamic properties of various linear and branched perfluorinated and perhydrogenated alkyl compounds. The semiempirical AM1, PM3, and PM6 methods all consistently and accurately predict that branched alkyl compounds will generally be more thermodynamically stable than their linear counterparts. In contrast, HF and B3LYP calculations with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets predict that linear isomers will be more stable than branched analogs. These different linear versus branched perfluoroalkyl/perhydroalkyl thermodynamic property trends between semiempirical and ab initio/DFT methods were evident in both gas and aqueous phase calculations. Comparison of experimentally determined thermodynamic properties for several classes of linear and branched alkanes and alcohols with values calculated at the PM6 and B3LYP/6-311++G(d,p) levels of theory supported the well known findings that such DFT and HF approaches incorrectly predict branched alkyl compounds will be less thermodynamically stable than linear isomers. Calculations at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) and M05-2X/6-311++G(d,p) levels of theory on a representative subset of the linear and branched perfluorinated compounds supported the thermodynamic conclusions from the PM6 method. Strong agreement between PM6 estimated thermodynamic properties and available experimental data supports use of this computational method for accurately calculating the well established higher thermodynamic stability of branched alkyl compounds. Branched perfluoroalkyl compounds are thus expected to be more thermodynamically stable than their linear analogs. http://precedings.nature.com/documents/3928/version/1 Mon, 02 Nov 2009 15:24:31 UTC Comparative semiempirical, ab initio, and DFT study on the thermodynamic properties of linear and branched PFSA/Fs, PFCA/Fs, and perhydroalkyl sulfonic acids, alkanes, and alcohols hdl:10101/npre.2009.3928.1 2009-11-03 Sierra Rayne Nature Precedings 2009-11-02T15:24:31Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3881.1 1. Topological materials: Moebius nanographite and conjugated polymers2. Magnetic domain wall states [1] vs. helical magmetic order in nanographite [2]3. Static polarizability α and the first hyperpolarizability β are studied, comparing three models: Mobius strip cyclacene, ring cyclacene, and linear strip.4. Opening the knot of the Mobius to form the ring leads to the increase of α from 268 to 323 a.u. and β increases about three times from 393 to 1049 a.u.5. Opening the ring to form the linear strip, α increases from 323 to 476 a.u. β as well increases about three times from 1049 to 2814 a.u.[1] K. Wakabayashi and K. Harigaya, J. Phys. Soc. Jpn. 72, 998 (2003).[2] A. Yamashiro, Y. Shimoi, K. Harigaya, and K. Wakabayashi, Physica E 22, 688 (2004). http://dx.doi.org/10.1038/npre.2009.3881.1 Mon, 02 Nov 2009 13:20:47 UTC Theoretical Investigation on Electronic Properties of Topological Materials: Moebius Nanographite *and Conjugated Polymers doi:10.1038/npre.2009.3881.1 2009-11-02 Kikuo Harigaya Nature Precedings 2009-11-02T13:20:47Z Presentation Chemistry http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3909.1 DFT study on the the stability and reactivity of Pt(100) and Pt(111) surfaces modified by nickel UPD monolayer deposition have been carried out. We used the binding energy calculation of bimetallic structures versus the cohesion energy of the bulk adsorbate to quantify the underpotential shift (ΔEupd) to determine the stability of the bimetallic systems. The reactivity of the clean and modified surface was analized by energy levels of the highest occupied molecular orbital (HOMO), softness and local softness. We concluded that the stability of Pt(100)25Ni9 and Pt(111)25Ni10 bimetallic structures cannot be explained by excess of the metal- substrate binding energy but the instability can be explained by structural effects. We found that the modified surfaces are more reactive and the active sites are located in the centre of the cluster which favores the formation of islands of atoms onto these surfaces. http://dx.doi.org/10.1038/npre.2009.3909.1 Wed, 28 Oct 2009 12:41:51 UTC Density Functional Study on the Stability and Reactivity of Pt(100) and Pt(111) Surfaces Modified by Ni Atoms doi:10.1038/npre.2009.3909.1 2009-10-28 María López Nature Precedings 2009-10-28T12:41:51Z Manuscript Chemistry http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3884/version/1 Water is widely assumed to be essential for life 1, although the exact molecular basis of this requirement is unclear 2-4. Water facilitates protein motions 5-9 and although enzyme activity has been demonstrated at low hydrations in organic solvents 10-13, such non-aqueous solvents may allow the necessary motions for catalysis. To examine enzyme function in the absence of solvation and bypass diffusional constraints we have tested the ability of an esterase to catalyse alcoholysis as an anhydrous powder, using a closed reaction system in which the substrates and products of the enzyme reaction are gaseous 14-15, and where the water content can be well defined 16. At hydrations equivalent to 3 (±2) molecules of water per molecule of enzyme, activity is observed that is several orders of magnitude greater than non-enzymatic catalysis. Neutron spectroscopy indicates that the fast (≤nanosecond) global anharmonic dynamics of the anhydrous functional enzyme are heavily suppressed. The results indicate that neither hydration water nor the solvent-activated fast anharmonic dynamics are required for enzyme function. An implication of these results is that one of the essential requirements of water for life may lie with its role as a diffusion medium rather than any of its more specific properties. http://precedings.nature.com/documents/3884/version/1 Wed, 28 Oct 2009 11:39:56 UTC Enzyme activity and dynamics in near-anhydrous conditions hdl:10101/npre.2009.3884.1 2009-10-28 Murielle Lopez Nature Precedings 2009-10-28T11:39:56Z Manuscript Biotechnology Chemistry http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3902/version/1 Generalizing Landau’s spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to ‘freeze’ the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemistry, in contrast with a recent prediction of a racemic average. http://precedings.nature.com/documents/3902/version/1 Mon, 26 Oct 2009 17:52:17 UTC On biological homochirality hdl:10101/npre.2009.3902.1 2009-10-26 Rodrick Wallace Nature Precedings 2009-10-26T17:52:17Z Manuscript Chemistry Earth & Environment Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3879.1 Exciton effects are studied in single-wall boron-nitride (BN) nanotubes. Linear absorption spectra are calculated with changingthe chiral index of the zigzag nanotubes. We consider the extended Hubbard model with atomic energies at the boron and nitrogen sites.Exciton effects are calculated using the configuration interaction technique. The Coulomb interaction dependence of the band gap,the lowest exciton energy, and the binding energy of the exciton are discussed. The optical gap of the (5,0) nanotube is about 6 eVat the onsite interaction U=2t with the hopping integral t=1.1 eV. The binding energy of the exciton is 0.50 eV for these parameters.This energy agrees well with that of other theoretical investigations. We find that the energy gap and the binding energy are almostindependent of the geometries of the nanotubes. This novel property is in contrast with that of the carbon nanotubes which show metallicand semiconducting properties depending on the chiral index. Comparison with recent experiments will be discussed. http://dx.doi.org/10.1038/npre.2009.3879.1 Mon, 26 Oct 2009 14:39:05 UTC Exciton Effects in Optical Absorption Spectra of Boron-Nitride Nanotubes doi:10.1038/npre.2009.3879.1 2009-10-26 Kikuo Harigaya Nature Precedings 2009-10-26T14:39:05Z Presentation Chemistry http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3880.1 Nanocarbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings. We also study possible magnetic properties in fullerenes with defects and buckybowl molecules. When the number of lattice defects in C60 is even, we obtain magnetic and nonmagnetic solutions. The total energy of the nonmagnetic solution is lower than that of the magnetic solution. The occurrence of the localized spin is reduced for finite onsite Coulomb repulsions. When the number of defects is odd, magnetic solutions are obtained only. The spin density reflects the symmetry of the molecules. We also consider possible magnetic states in buckybowl molecules. We find localized spin order in the sumanene molecule and a part of the C60. http://dx.doi.org/10.1038/npre.2009.3880.1 Thu, 22 Oct 2009 09:52:45 UTC Edge states and possible magnetic states in nanographene and open-shell conjugated systems doi:10.1038/npre.2009.3880.1 2009-10-22 Kikuo Harigaya Nature Precedings 2009-10-22T09:52:45Z Presentation Chemistry http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3882.1 The KOWWIN and ALOGPS octanol-water partition coefficient (Kow) estimation software programs were compared for their capacity to accurately predict log Kow values of 1596 organic compounds on the publicly available Domestic Substances List (DSL) from Environment Canada for which experimental data is available. KOWWIN contained a significantly lower number and magnitude of prediction errors compared to ALOGPS, particularly at experimental log Kow values ow data on the Canadian DSL. Predictive differences of up to 40 log Kow units were found between KOWWIN and ALOGPS, and in some cases, the discrepancies were sufficiently large that strongly opposing hydrophobicity classifications were obtained. http://dx.doi.org/10.1038/npre.2009.3882.1 Wed, 21 Oct 2009 15:02:21 UTC Performance of the ALOGPS 2.1 program for octanol-water partition coefficient prediction with organic chemicals on the Canadian Domestic Substances List doi:10.1038/npre.2009.3882.1 2009-10-21 Sierra Rayne Nature Precedings 2009-10-21T15:02:21Z Manuscript Chemistry Pharmacology Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3878/version/1 Nano-carbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings. http://precedings.nature.com/documents/3878/version/1 Wed, 21 Oct 2009 12:43:19 UTC Persistence of Edge-State in Stacked Graphene and Nano-Graphene Materials hdl:10101/npre.2009.3878.1 2009-10-21 Kikuo Harigaya Nature Precedings 2009-10-21T12:43:19Z Manuscript Chemistry http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3837/version/1 A molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pKa values) for a final converged set of twelve n-PFOA conformers, including the global minimum helical perfluoroalkyl chain geometry and eleven non-helical higher energy conformations. Collectively, the twelve lowest energy conformers appear to encompass 85% of the total conformational space for n-PFOA, indicating no higher energy conformations likely remain that could appreciably influence the observed composite aqueous pKa of this compound. The estimated pKa values of all eleven non-helical n-PFOA conformers were within 0.2 pKa units of the helical conformer pKa. The findings support previous predictions and recent experimental evidence for an aqueous phase n-PFOA monomeric pKa of about zero. http://precedings.nature.com/documents/3837/version/1 Thu, 08 Oct 2009 11:39:32 UTC Theoretical studies on the pKa values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA) hdl:10101/npre.2009.3837.1 2009-10-08 Sierra Rayne Nature Precedings 2009-10-08T11:39:32Z Manuscript Chemistry Earth & Environment http://creativecommons.org/licenses/by/3.0/