Now showing 1 - 10 of 84
  • Publication
    An assessment of theoretical procedures for π-conjugation stabilisation energies in enones
    (Taylor & Francis, 2015)
    Yu, Li-Juan
    ;
    Sarrami, Farzaneh
    ;
    ;

    We introduce a representative database of 22α,β-toβ,γ-enecarbonyl isomerisation energies (to be known as the EIE22 data-set). Accurate reaction energies are obtained at the complete basis-set limit CCSD(T) level by means of the high-level W1-F12thermochemical protocol. The isomerisation reactions involve a migration of one double bond that breaks the conjugatedπ-system. The considered enecarbonyls involve a range of common functional groups (e.g., Me, NH2,OMe,F,andCN). Apart from π-conjugation effects, the chemical environments are largely conserved on the two sides of the reactions and therefore the EIE22 data-set allows us to assess the performance of a variety of density functional theory (DFT) procedures for the calculation ofπ-conjugation stabilisation energies in enecarbonyls. We find that, with few exceptions (M05-2X, M06-2X,BMK, and BH&HLYP), all the conventional DFT procedures attain root mean square deviations (RMSDs) between 5.0 and 11.7 kJ mol−1. The range-separated and double-hybrid DFT procedures, on the other hand, show good performance with RMSDs below the 'chemical accuracy' threshold. We also examine the performance of composite and standard ab initio procedures. Of these, SCS-MP2 offers the best performance-to-computational cost ratio with an RMSD of 0.8 kJ mol−1.

  • Publication
    Bond orders for intermolecular interactions in crystals: charge transfer, ionicity and the effect on intramolecular bonds
    (International Union of Crystallography (IUCr), 2018-09)
    Alhameedi, Khidhir
    ;
    ;
    Jayatilaka, Dylan
    ;
    Thomas, Sajesh P

    The question of whether intermolecular interactions in crystals originate from localized atom⋯atom interactions or as a result of holistic molecule⋯molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby-Gould bond indices are reported for intermolecular 'σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom⋯atom and molecule⋯molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the 'conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom⋯atom interactions in the formation of these intermolecular binding motifs.

  • Publication
    Deciphering the exceptional selectivity of semipinacol rearrangements in cis-fused β-lactam diols using high-level quantum chemical methods
    (Royal Society of Chemistry, 2019-03-21)
    Baroudi, Abdulkader
    ;

    The mechanism for the semipinacol rearrangement in cis-fused β-lactam diols has been examined using highly accurate double-hybrid density functional theory methods. This reaction involves a competition between two possible migrating groups (alkyl and acyl), which can undergo a 1,2 C-C bond migration. We find that acyl migration is both kinetically and thermodynamically more favorable. These results are consistent with experimental observations and are rationalized based on conformational, structural, and orbital interaction analysis. We proceed to investigate the semipinacol rearrangement in trans-fused β-lactam diol and propose that this system undergoes a reversed selectivity which favors the alkyl migration.

  • Publication
    Computational insights for the hydride transfer and distinctive roles of key residues in cholesterol oxidase
    (Nature Publishing Group, 2017)
    Yu, Li-Juan
    ;
    Golden, Emily
    ;
    Chen, Nanhao
    ;
    Zhao, Yuan
    ;
    Vrielink, Alice
    ;

    Cholesterol oxidase (ChOx), a member of the glucose-methanol-choline (GMC) family, catalyzes the oxidation of the substrate via a hydride transfer mechanism and concomitant reduction of the FAD cofactor. Unlike other GMC enzymes, the conserved His447 is not the catalytic base that deprotonates the substrate in ChOx. Our QM/MM MD simulations indicate that the Glu361 residue acts as a catalytic base facilitating the hydride transfer from the substrate to the cofactor. We find that two rationally chosen point mutations (His447Gln and His447Asn) cause notable decreases in the catalytic activity. The binding free energy calculations show that the Glu361 and His447 residues are important in substrate binding. We also performed high-level double-hybrid density functional theory simulations using small model systems, which support the QM/MM MD results. Our work provides a basis for unraveling the substrate oxidation mechanism in GMC enzymes in which the conserved histidine does not act as a base.

  • Publication
    Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles; electrochemical hydrogen storage performance and density functional theory
    (Elsevier Ltd, 2017-12)
    Salehabadi, Ali
    ;
    Salavati-Niasari, Masoud
    ;
    Sarrami, Farzaneh
    ;

    Spinel BaAl2O4 nanopowders were synthesized via an aqueous combustion using stoichiometric amount of cations, Ba2+ and Al3+, in rational fraction of a fuel (maltose). In order to achieve pure crystals, single fuel led to the formation of combustion reaction. The structural analysis indicates that the concentration of the starting materials and annealing temperature directly affect the purity of the product. The Scherrer and Hall-Williamson equation were performed to measure the average crystallite sizes of the BaAl2O4 nanopowders in the range of 26.5 and 40.8 nm, respectively. The microscopic analysis, SEM and TEM, were indicated the morphology and the nanoscale formation of BaAl2O4 ranging from 30 to 40 nm. The Band gap energy was calculated using Tauc method obtained at 3.34 eV. The maximum discharge capacity of BaAl2O4 obtained at 1000 mAh/g after 15 cycles. This result was also confirmed by theoretical calculation.

  • Publication
    A dataset of highly accurate homolytic N-Br bond dissociation energies obtained by Means of W2 theory
    (John Wiley & Sons, Inc, 2016-01-05)
    O'Reilly, Robert J
    ;

    Homolytic N-Br bond dissociation constitutes the initial step of numerous reactions involving N-brominated species. However, little is known about the strength of N-Br bonds toward homolytic cleavage. We herein report accurate bond dissociation energies (BDEs) for a set of 18 molecules using the high-level W2 thermochemical protocol. The BDEs (at 298 K) of the species in this set range from 162.2 kJ mol-1(N-bromopyrrole) to 260.6 kJ mol-1((CHO)2NBr). In order to compute BDEs of larger systems, for which W2 theory is not applicable, we have benchmarked a wide range of more economical theoretical procedures. Of these, G3-B3 offers the best performance (root-mean-square deviations = 2.9 kJ mol-1), and using this method, we have computed N-Br BDEs for four widely used N-brominated compounds. These include (BDEs are given in parentheses):N-bromosuccinimide (281.6),N-bromoglutarimide(263.2),N-bromophthalimide (274.7), and 1,3-dibromo-5,5-dimethylhydantoin (218.2 and 264.8 kJ mol-1).

  • Publication
    Thermochemistry of phosphorus sulfide cages: an extreme challenge for high-level ab initio methods
    (Springer New York LLC, 2019-10)
    Kroeger, Asja A
    ;

    The enthalpies of formation and isomerization energies of P4Sn molecular cages are not experimentally (or theoretically) well known. We obtain accurate enthalpies of formation and isomerization energies for P4Sn cages (n = 3, 4, 5, 6, and 10) by means of explicitly correlated high-level thermochemical procedures approximating the CCSD(T) and CCSDT(Q) energies at the complete basis set (CBS) limit. The atomization reactions have very significant contribution from post-CCSD(T) correlation effects and, due to the presence of many second-row atoms, the CCSD and (T) correlation energies converge exceedingly slowly with the size of the one-particle basis set. As a result, these cage structures are challenging targets for thermochemical procedures approximating the CCSD(T) energy (e.g., W1-F12 and G4). Our best enthalpies of formation at 298 K (∆fH°298) are obtained from thermochemical cycles in which the P4Sn cages are broken down into P2S2 and S2 fragments for which highly accurate ∆fH°298 values are available from W4 theory. For the smaller P4S3 and P4S4 cages, the reaction energies are calculated at the CCSDT(Q)/CBS level and for the larger P4S5, P4S6, and P4S10 cages, they are obtained at the CCSD(T)/CBS level. Our best ∆fH°298 values are - 94.5 (P4S3), - 108.4 (α-P4S4), - 98.7 (β-P4S4), - 126.2 (α-P4S5), - 126.1 (β-P4S5), - 112.7 (γ-P4S5), - 144.7 (α-P4S6), - 153.9 (β-P4S6), - 134.4 (γ-P4S6), - 136.3 (δ-P4S6), - 118.7 (ε-P4S6), and - 215.4 (P4S10) kJ mol-1. Interestingly, we find a linear correlation (R2 = 0.992) between the enthalpies of formation of the most stable isomers of each molecular formula and the number of atoms in the P4Sn cages. We use our best ∆fH°298 values to assess the performance of a number of lower-cost composite ab initio methods. For absolute enthalpies of formation, G4(MP2) and G3(MP2)B3 result in the best overall performance with root-mean-square deviations (RMSDs) of 10.6 and 12.9 kJ mol-1, respectively, whereas G3, G3B3, and CBS-QB3 result in the worst performance with RMSDs of 27.0-38.8 kJ mol-1. In contrast to absolute enthalpies of formation, all of the considered composite procedures give a good-to-excellent performance for the isomerization energies with RMSDs below the 5 kJ mol-1 mark.

  • Publication
    Tribute to Leo Radom
    (American Chemical Society, 2019-12-05) ;
    Martin, Jan M L
    ;
    Gill, Peter M W

    It is our pleasure to introduce this Festschrift of The Journal of Physical Chemistry A to honor Professor Leo Radom on the occasion of his 75th birthday and to recognize his many outstanding contributions to the field of theoretical and computational chemistry. Leo was born in Shanghai in 1944. His family moved to Sydney, Australia, in 1947. Following his BSc in Chemistry at the University of Sydney, he obtained his PhD in experimental physical organic chemistry in 1969 with Raymond Le Fevre. Leo then turned to theory during a ̀ postdoctoral period with John Pople at Carnegie-Mellon University in Pittsburgh. He returned to Australia in 1972 to the Research School of Chemistry at the Australian National University and then moved to the University of Sydney in 2003, where he is now an Emeritus Professor of Chemistry.

  • Publication
    Computational investigation into the gas-phase ozonolysis of the conjugated monoterpene α-phellandrene
    (Royal Society of Chemistry, 2016-10-28)
    Mackenzie-Rae, F A
    ;
    ;
    Saunders, S M

    Reaction with ozone is a major atmospheric sink for α-phellandrene, a monoterpene found in both indoor and outdoor environments, however experimental literature concerning the reaction is scarce. In this study, high-level G4(MP2) quantum chemical calculations are used to theoretically characterise the reaction of ozone with both double bonds in α-phellandrene for the first time. Results show that addition of ozone to the least substituted double bond in the conjugated system is preferred. Following addition, thermal and chemically activated unimolecular reactions, including the so-called hydro-peroxide and ester or 'hot' acid channels, and internal cyclisation reactions, are characterised to major first generation products. Conjugation present in α-phellandrene allows two favourable Criegee intermediate reaction pathways to proceed that have not previously been considered in the literature; namely a 1,6-allyl resonance stabilised hydrogen shift and intramolecular dioxirane isomerisation to an epoxide. These channels are expected to play an important role alongside conventional routes in the ozonolysis of a-phellandrene. Computational characterisation of the potential energy surface thus provides insight into this previously unstudied system, and will aid future mechanism development and experimental interpretation involving α-phellandrene and structurally similar species, to which the results are expected to extend.

  • Publication
    Structure-Activity Studies of Semiochemicals from the Spider Orchid Caladenia plicata for Sexual Deception
    (Springer New York LLC, 2018-05)
    Bohman, Bjorn
    ;
    ;
    Flematti, Gavin R
    ;
    Scaffidi, Adrian
    ;
    Peakall, Rod

    Sexually deceptive orchids attract specific pollinators by mimicking insect sex pheromones. Normally this mimicry is very specific and identical compounds have been identified from orchids and matching females of the pollinators. In this study, we conduct a detailed structure-activity investigation on isomers of the semiochemicals involved in the sexual attraction of the male pollinator of the spider orchid Caladenia plicata. This orchid employs an unusual blend of two biosynthetically unrelated compounds, (S)-β-citronellol and 2-hydroxy-6-methylacetophenone, to lure its Zeleboria sp. thynnine wasp pollinator. We show that the blend is barely attractive when (S)-β-citronellol is substituted with its enantiomer, (R)-β-citronellol. Furthermore, none of the nine-possible alternative hydroxy-methylacetophenone regioisomers of the natural semiochemical are active when substituted for the natural 2-hydroxy-6-methylacetophenone. Our results were surprising given the structural similarity between the active compound and some of the analogues tested, and results from previous studies in other sexually deceptive orchid/wasp systems where substitution with analogues was possible. Interestingly, high-level ab initio and density functional theory calculations of the hydroxy-methylacetophenones revealed that the active natural isomer, 2-hydroxy-6-methylacetophenone, has the strongest intramolecular hydrogen bond of all regioisomers, which at least in part may explain the specific activity.