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Perrin CL, Agranat I, Bagno A, Braslavsky SE, Fernandes PA, Gal JF, Lloyd-Jones GC, Mayr H, Murdoch JR, Nudelman NS, Radom L, Rappoport Z, Ruasse MF, Siehl HU, Takeuchi Y, Tidwell TT, Uggerud E, Williams IH. Glossary of terms used in physical organic chemistry (IUPAC Recommendations 2021). PURE APPL CHEM 2022. [DOI: 10.1515/pac-2018-1010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.
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Affiliation(s)
- Charles L. Perrin
- Department of Chemistry , University of California , San Diego , La Jolla , CA , USA
| | | | - Alessandro Bagno
- University of Padova Faculty of Mathematics Physics and Natural Sciences , Padova , Veneto , Italy
| | - Silvia E. Braslavsky
- Max Planck Institute for Chemical Energy Conversion , Muelheim an der Ruhr , Germany
| | | | | | | | - Herbert Mayr
- Department Chemie , Ludwig-Maximilians-Universität München , München , Germany
| | | | | | - Leo Radom
- School of Chemistry, University of Sydney , Sydney , NSW , Australia
| | - Zvi Rappoport
- Organic Chemistry, The Hebrew University , Jerusalem , Israel
| | | | | | | | - Thomas T. Tidwell
- Department of Chemistry , University of Toronto , Toronto , ON , Canada
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2
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3
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Radom L. Curriculum Vitae of Leo Radom. J Phys Chem A 2019. [DOI: 10.1021/acs.jpca.9b06511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Radom L. Students and Collaborators of Leo Radom. J Phys Chem A 2019. [DOI: 10.1021/acs.jpca.9b06510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Carroll L, Karton A, Radom L, Davies MJ, Pattison DI. Carnosine and Carcinine Derivatives Rapidly React with Hypochlorous Acid to Form Chloramines and Dichloramines. Chem Res Toxicol 2019; 32:513-525. [DOI: 10.1021/acs.chemrestox.8b00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luke Carroll
- The Heart Research Institute, Newtown, New South Wales 2042, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
- Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - Amir Karton
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michael J. Davies
- The Heart Research Institute, Newtown, New South Wales 2042, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
- Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - David I. Pattison
- The Heart Research Institute, Newtown, New South Wales 2042, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
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Chan B, Radom L. An ONIOM investigation of the effect of conformation on bond dissociation energies in peptides. J Comput Chem 2018; 40:82-88. [DOI: 10.1002/jcc.25538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Bun Chan
- Graduate School of Engineering Nagasaki University Bunkyo 1‐14, Nagasaki‐shi, Nagasaki, 852‐8521 Japan
| | - Leo Radom
- School of Chemistry University of Sydney New South Wales, 2006 Australia
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Abstract
The effect of adding explicit water molecules to the neutral (N) and zwitterionic (Z) forms of the glycyl radical has been examined. The results show that a minimum of three water molecules is required to stabilize the Z radical as a local minimum, with an energy gap of 123 kJ mol-1 between the N and Z forms at this point, in favor of the N form. Increasing the number of water molecules to ∼20 leads to a converged Z-N energy difference of ∼50 kJ mol-1 still in favor of the N form, even though the radical is not considered fully solvated from a structural point of view. Thus, energetic convergence is determined mainly by solvation of the polar functional groups, and a complete coverage of the entire molecule is not necessary. Because aqueous closed-shell glycine exists as a zwitterion while aqueous glycyl radical prefers the neutral form, the conversion between the two necessitates a change along the hydrogen-abstraction reaction pathway. In this regard, the transition structure for α-hydrogen abstraction by the ·OH radical has greater resemblance to glycine than to the glycyl radical. Overall, the barrier for hydrogen abstraction from Z glycine is larger than that from the N isomer, and this might act to provide some protection against radical damage to the free amino acid in the (aqueous) biological environment.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan.,School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Jamie Rintelman
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States
| | - Geoffrey P F Wood
- School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Leo Radom
- School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Mark S Gordon
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States
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Kovačević B, Barić D, Babić D, Bilić L, Hanževački M, Sandala GM, Radom L, Smith DM. Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12. J Am Chem Soc 2018; 140:8487-8496. [DOI: 10.1021/jacs.8b03109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Borislav Kovačević
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Danijela Barić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Darko Babić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Luka Bilić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Marko Hanževački
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Gregory M. Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick E4L 1G8, Canada
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Affiliation(s)
- Bun Chan
- Graduate
School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
- School
of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Christopher J. Easton
- Research
School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2600, Australia
| | - Leo Radom
- School
of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
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Abstract
Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.
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Abstract
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.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Damian Moran
- School of Chemistry, University of Sydney, Sydney, NSW, 2006, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW, 2006, Australia
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Mitchell NJ, Sayers J, Kulkarni SS, Clayton D, Goldys AM, Ripoll-Rozada J, Barbosa Pereira PJ, Chan B, Radom L, Payne RJ. Accelerated Protein Synthesis via One-Pot Ligation-Deselenization Chemistry. Chem 2017. [DOI: 10.1016/j.chempr.2017.04.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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O'Connor GD, Chan B, Sanelli JA, Cergol KM, Dryza V, Payne RJ, Bieske EJ, Radom L, Schmidt TW. Hydrogen-adduction to open-shell graphene fragments: spectroscopy, thermochemistry and astrochemistry. Chem Sci 2017; 8:1186-1194. [PMID: 28451259 PMCID: PMC5369534 DOI: 10.1039/c6sc03787a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/24/2016] [Indexed: 11/25/2022] Open
Abstract
We apply a combination of state-of-the-art experimental and quantum-chemical methods to elucidate the electronic and chemical energetics of hydrogen adduction to a model open-shell graphene fragment. The lowest-energy adduct, 1H-phenalene, is determined to have a bond dissociation energy of 258.1 kJ mol-1, while other isomers exhibit reduced or in some cases negative bond dissociation energies, the metastable species being bound by the emergence of a conical intersection along the high-symmetry dissociation coordinate. The gas-phase excitation spectrum of 1H-phenalene and its radical cation are recorded using laser spectroscopy coupled to mass-spectrometry. Several electronically excited states of both species are observed, allowing the determination of the excited-state bond dissociation energy. The ionization energy of 1H-phenalene is determined to be 7.449(17) eV, consistent with high-level W1X-2 calculations.
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Affiliation(s)
- Gerard D O'Connor
- School of Chemistry , UNSW Sydney , NSW 2052 , Australia . ; Tel: +61 439 386 109
| | - Bun Chan
- School of Chemistry , The University of Sydney , Sydney , New South Wales 2006 , Australia
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan
| | - Julian A Sanelli
- School of Chemistry , The University of Melbourne , Victoria 3010 , Australia
| | - Katie M Cergol
- School of Chemistry , The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Viktoras Dryza
- School of Chemistry , The University of Melbourne , Victoria 3010 , Australia
| | - Richard J Payne
- School of Chemistry , The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Evan J Bieske
- School of Chemistry , The University of Melbourne , Victoria 3010 , Australia
| | - Leo Radom
- School of Chemistry , The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Timothy W Schmidt
- School of Chemistry , UNSW Sydney , NSW 2052 , Australia . ; Tel: +61 439 386 109
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14
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Karimi M, Ignasiak MT, Chan B, Croft AK, Radom L, Schiesser CH, Pattison DI, Davies MJ. Reactivity of disulfide bonds is markedly affected by structure and environment: implications for protein modification and stability. Sci Rep 2016; 6:38572. [PMID: 27941824 PMCID: PMC5150571 DOI: 10.1038/srep38572] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/09/2016] [Indexed: 11/09/2022] Open
Abstract
Disulfide bonds play a key role in stabilizing protein structures, with disruption strongly associated with loss of protein function and activity. Previous data have suggested that disulfides show only modest reactivity with oxidants. In the current study, we report kinetic data indicating that selected disulfides react extremely rapidly, with a variation of 104 in rate constants. Five-membered ring disulfides are particularly reactive compared with acyclic (linear) disulfides or six-membered rings. Particular disulfides in proteins also show enhanced reactivity. This variation occurs with multiple oxidants and is shown to arise from favorable electrostatic stabilization of the incipient positive charge on the sulfur reaction center by remote groups, or by the neighboring sulfur for conformations in which the orbitals are suitably aligned. Controlling these factors should allow the design of efficient scavengers and high-stability proteins. These data are consistent with selective oxidative damage to particular disulfides, including those in some proteins.
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Affiliation(s)
- Maryam Karimi
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia.,Faculty of Medicine, University of Sydney, NSW, 2006, Australia
| | - Marta T Ignasiak
- Department of Biomedical Science, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Bun Chan
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, Great Britain
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Carl H Schiesser
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - David I Pattison
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia.,Faculty of Medicine, University of Sydney, NSW, 2006, Australia
| | - Michael J Davies
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia.,Faculty of Medicine, University of Sydney, NSW, 2006, Australia.,Department of Biomedical Science, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
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Wetmore S, Radom L. Introduction / Introduction. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Affiliation(s)
- Bun Chan
- Graduate
School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
| | - Amir Karton
- School
of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Krishnan Raghavachari
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Leo Radom
- School
of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
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17
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Osburn S, Chan B, Ryzhov V, Radom L, O'Hair RAJ. Role of Hydrogen Bonding on the Reactivity of Thiyl Radicals: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach. J Phys Chem A 2016; 120:8184-8189. [PMID: 27726360 DOI: 10.1021/acs.jpca.6b08544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Experimental and computational quantum chemistry investigations of the gas-phase ion-molecule reactions between the distonic ions +H3N(CH2)nS• (n = 2-4) and the reagents dimethyl disulfide, allyl bromide, and allyl iodide demonstrate that intramolecular hydrogen bonding can modulate the reactivity of thiyl radicals. Thus, the 3-ammonium-1-propanethiyl radical (n = 3) exhibits the lowest reactivity of these distonic ions toward all substrates. Theoretical calculations on this distonic ion highlight that its most stable conformation involves a six-membered ring configuration, and that it has the strongest intramolecular hydrogen bond. In addition, the calculations indicate that the barrier heights for radical abstraction by this hydrogen-bond-stabilized 3-ammonium-1-propanethiyl radical are the highest among the systems examined, consistent with the experimental observations.
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Affiliation(s)
- Sandra Osburn
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , 30 Flemington Rd, Parkville, Victoria 3010, Australia
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University , Bunkyo 1-14, Nagasaki 852-8521, Japan
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry and Center for Biochemical and Biophysical studies, Northern Illinois University , Dekalb, Illinois 60115, United States
| | - Leo Radom
- School of Chemistry, University of Sydney , Sydney, NSW 2006, Australia
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , 30 Flemington Rd, Parkville, Victoria 3010, Australia
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Poad BLJ, Reed ND, Hansen CS, Trevitt AJ, Blanksby SJ, Mackay EG, Sherburn MS, Chan B, Radom L. Preparation of an ion with the highest calculated proton affinity: ortho-diethynylbenzene dianion. Chem Sci 2016; 7:6245-6250. [PMID: 30034765 PMCID: PMC6024202 DOI: 10.1039/c6sc01726f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 11/23/2022] Open
Abstract
Owing to the increased proton affinity that results from additional negative charges, multiply-charged anions are shown as a route to preparing powerful ‘superbases’.
Owing to the increased proton affinity that results from additional negative charges, multiply-charged anions have been proposed as one route to prepare and access a range of new and powerful “superbases”. Paradoxically, while the additional electrons in polyanions increase basicity they serve to diminish the electron binding energy and thus, it had been thought, hinder experimental synthesis. We report the synthesis and isolation of the ortho-diethynylbenzene dianion (ortho-DEB2–) and present observations of this novel species undergoing gas-phase proton-abstraction reactions. Using a theoretical model based on Marcus–Hush theory, we attribute the stability of ortho-DEB2– to the presence of a barrier that prevents spontaneous electron detachment. The proton affinity of 1843 kJ mol–1 calculated for this dianion superbase using high-level quantum chemistry calculations significantly exceeds that of the lithium monoxide anion, the most basic system previously prepared. The ortho-diethynylbenzene dianion is therefore the strongest base that has been experimentally observed to date.
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Affiliation(s)
- Berwyck L J Poad
- Central Analytical Research Facility , Institute for Future Environments , Queensland University of Technology , Brisbane , QLD 4001 , Australia . .,School of Chemistry , University of Wollongong , Gwynneville , NSW 2522 , Australia
| | - Nicholas D Reed
- School of Chemistry , University of Wollongong , Gwynneville , NSW 2522 , Australia
| | - Christopher S Hansen
- School of Chemistry , University of Wollongong , Gwynneville , NSW 2522 , Australia
| | - Adam J Trevitt
- School of Chemistry , University of Wollongong , Gwynneville , NSW 2522 , Australia
| | - Stephen J Blanksby
- Central Analytical Research Facility , Institute for Future Environments , Queensland University of Technology , Brisbane , QLD 4001 , Australia .
| | - Emily G Mackay
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Michael S Sherburn
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Bun Chan
- School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Leo Radom
- School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
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Easton ME, Ward AJ, Chan B, Radom L, Masters AF, Maschmeyer T. Factors influencing the formation of polybromide monoanions in solutions of ionic liquid bromide salts. Phys Chem Chem Phys 2016; 18:7251-60. [PMID: 26890026 DOI: 10.1039/c5cp06913k] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Six different bromide salts - tetraethylammonium bromide ([N2,2,2,2]Br, Br), 1-ethyl-1-methylpiperidinium bromide ([C2MPip]Br, Br), 1-ethyl-1-methylpyrrolidinium bromide ([C2MPyrr]Br, Br), 1-ethyl-3-methylimidazolium bromide ([C2MIm]Br, Br), 1-ethylpyridinium bromide ([C2Py]Br, Br), and 1-(2-hydroxyethyl)pyridinium bromide ([C2OHPy]Br, Br) - were studied in regards to their capacity to form polybromide monoanion products on addition of molecular bromine in acetonitrile solutions. Using complementary spectroscopic and computational methods for the examination of tribromide and pentabromide anion formation, key factors influencing polybromide sequestration were identified. Here, we present criteria for the targeted synthesis of highly efficient bromine sequestration agents.
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Affiliation(s)
- Max E Easton
- School of Chemistry F11, University of Sydney, New South Wales, Australia.
| | - Antony J Ward
- School of Chemistry F11, University of Sydney, New South Wales, Australia.
| | - Bun Chan
- School of Chemistry F11, University of Sydney, New South Wales, Australia.
| | - Leo Radom
- School of Chemistry F11, University of Sydney, New South Wales, Australia.
| | - Anthony F Masters
- School of Chemistry F11, University of Sydney, New South Wales, Australia.
| | - Thomas Maschmeyer
- School of Chemistry F11, University of Sydney, New South Wales, Australia.
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Chan B, Radom L. Frequency Scale Factors for Some Double-Hybrid Density Functional Theory Procedures: Accurate Thermochemical Components for High-Level Composite Protocols. J Chem Theory Comput 2016; 12:3774-80. [DOI: 10.1021/acs.jctc.6b00554] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bun Chan
- School
of Chemistry and ARC Centre of Excellence for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Leo Radom
- School
of Chemistry and ARC Centre of Excellence for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
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21
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Krechkivska O, Wilcox CM, Troy TP, Nauta K, Chan B, Jacob R, Reid SA, Radom L, Schmidt TW, Kable SH. Hydrogen-atom attack on phenol and toluene is ortho-directed. Phys Chem Chem Phys 2016; 18:8625-36. [PMID: 26948897 DOI: 10.1039/c5cp07619f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of H + phenol and H/D + toluene has been studied in a supersonic expansion after electric discharge. The (1 + 1') resonance-enhanced multiphoton ionization (REMPI) spectra of the reaction products, at m/z = parent + 1, or parent + 2 amu, were measured by scanning the first (resonance) laser. The resulting spectra are highly structured. Ionization energies were measured by scanning the second (ionization) laser, while the first laser was tuned to a specific transition. Theoretical calculations, benchmarked to the well-studied H + benzene → cyclohexadienyl radical reaction, were performed. The spectrum arising from the reaction of H + phenol is attributed solely to the ortho-hydroxy-cyclohexadienyl radical, which was found in two conformers (syn and anti). Similarly, the reaction of H/D + toluene formed solely the ortho isomer. The preference for the ortho isomer at 100-200 K in the molecular beam is attributed to kinetic, not thermodynamic effects, caused by an entrance channel barrier that is ∼5 kJ mol(-1) lower for ortho than for other isomers. Based on these results, we predict that the reaction of H + phenol and H + toluene should still favour the ortho isomer under elevated temperature conditions in the early stages of combustion (200-400 °C).
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Affiliation(s)
- Olha Krechkivska
- School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia.
| | - Callan M Wilcox
- School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia.
| | - Tyler P Troy
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Klaas Nauta
- School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia.
| | - Bun Chan
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Rebecca Jacob
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott A Reid
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Timothy W Schmidt
- School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia.
| | - Scott H Kable
- School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia.
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22
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Chan B, Karton A, Easton CJ, Radom L. α-Hydrogen Abstraction by •OH and •SH Radicals from Amino Acids and Their Peptide Derivatives. J Chem Theory Comput 2016; 12:1606-13. [DOI: 10.1021/acs.jctc.6b00007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Bun Chan
- School
of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Australia
| | - Amir Karton
- School
of Chemistry and Biochemistry, University of Western Australia, Perth, Washington 6009, Australia
| | - Christopher J. Easton
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Australia
- Research
School of Chemistry, Australian National University, Canberra, ACT 2600, Australia
| | - Leo Radom
- School
of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Australia
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23
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Easton ME, Chan B, Masters AF, Radom L, Maschmeyer T. Beyond the Halogen Bond: Examining the Limits of Extended Polybromide Networks through Quantum‐Chemical Investigations. Chem Asian J 2016; 11:682-6. [DOI: 10.1002/asia.201501316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Max E. Easton
- School of Chemistry F11 University of Sydney Eastern Ave NSW 2006 Australia
| | - Bun Chan
- School of Chemistry F11 University of Sydney Eastern Ave NSW 2006 Australia
| | - Anthony F. Masters
- School of Chemistry F11 University of Sydney Eastern Ave NSW 2006 Australia
| | - Leo Radom
- School of Chemistry F11 University of Sydney Eastern Ave NSW 2006 Australia
| | - Thomas Maschmeyer
- School of Chemistry F11 University of Sydney Eastern Ave NSW 2006 Australia
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25
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Abstract
To model the C-C β-scission reactions of backbone peptide alkoxy radicals, enthalpies and barriers for the fragmentation of four substituted alkoxy radicals have been calculated with a variety of ab initio molecular orbital theory and density functional theory procedures. The high-level methods examined include CBS-QB3, variants of the G3 family, and W1. Simpler methods include HF, MP2, QCISD, B3-LYP, BMK, and MPW1K with a range of basis sets. We find that good accuracy can be achieved with the G3(MP2)//B3-LYP and G3X(MP2)-RAD methods. Lower-cost methods producing reasonable results are single-point energy calculations with UB3-LYP/6-311+G(3df,2p), RB3-LYP/6-311+G(3df,2p), UBMK/6-311+G(3df,2p), and RBMK/6-311+G(3df,2p) on geometries optimized with UB3-LYP/6-31G(d) or UBMK/6-31G(d). Heats of formation at 0 K for the alkoxy radicals and their fragmentation products were also calculated. We predict ΔfH0 values for the alkoxy radicals of -71.4 ((•)OCH2CH [Formula: see text] O), -102.5 ((•)OCH(CH3)CH [Formula: see text] O), -176.6 ((•)OCH(CH3)C(NH2) [Formula: see text] O), and -264.6 ((•)OC(CH3)(NHCH [Formula: see text] O)CH [Formula: see text] O) kJ mol(-)(1). For the fragmentation products NH2C((•)) [Formula: see text] O and CH( [Formula: see text] O)NHC(CH3) [Formula: see text] O, we predict ΔfH0 values of -5.9 kJ mol(-)(1) and -352.8 kJ mol(-)(1).
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Affiliation(s)
- Geoffrey P F Wood
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and Department of Chemistry, University of Calgary, Calgary, Alberta T2N IN4, Canada
| | - Arvi Rauk
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and Department of Chemistry, University of Calgary, Calgary, Alberta T2N IN4, Canada
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and Department of Chemistry, University of Calgary, Calgary, Alberta T2N IN4, Canada
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26
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Mitchell NJ, Malins LR, Liu X, Thompson RE, Chan B, Radom L, Payne RJ. Rapid Additive-Free Selenocystine–Selenoester Peptide Ligation. J Am Chem Soc 2015; 137:14011-4. [DOI: 10.1021/jacs.5b07237] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Lara R. Malins
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Xuyu Liu
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robert E. Thompson
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bun Chan
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Radom
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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27
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Chan B, Goerigk L, Radom L. On the inclusion of post-MP2 contributions to double-Hybrid density functionals. J Comput Chem 2015; 37:183-93. [DOI: 10.1002/jcc.23972] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Bun Chan
- School of Chemistry; The University of Sydney and Centre of Excellence for Free Radical Chemistry and Biotechnology; Sydney New South Wales 2006 Australia
| | - Lars Goerigk
- School of Chemistry; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Leo Radom
- School of Chemistry; The University of Sydney and Centre of Excellence for Free Radical Chemistry and Biotechnology; Sydney New South Wales 2006 Australia
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28
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Amos RIJ, Heinroth F, Chan B, Ward AJ, Zheng S, Haynes BS, Easton CJ, Masters AF, Maschmeyer T, Radom L. Hydrogen from Formic Acid via Its Selective Disproportionation over Nanodomain-Modified Zeolites. ACS Catal 2015. [DOI: 10.1021/cs501677b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ruth I. J. Amos
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Falk Heinroth
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bun Chan
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Antony J. Ward
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sisi Zheng
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Brian S. Haynes
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Christopher J. Easton
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anthony F. Masters
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Thomas Maschmeyer
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Leo Radom
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Energy Transformed Cluster
on Biofuels ⊥ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology ∥Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
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29
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Affiliation(s)
- Bun Chan
- School of Chemistry and ARC Centre
of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Leo Radom
- School of Chemistry and ARC Centre
of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
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30
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Abstract
We have examined hydrogen-atom-abstraction reactions for combinations of electrophilic/nucleophilic radicals with electrophilic/nucleophilic substrates. We find that reaction between an electrophilic radical and a nucleophilic substrate is relatively favorable, and vice versa, but the reactions between a radical and a substrate that are both electrophilic or both nucleophilic are relatively unfavorable, consistent with the literature reports of Roberts. As a result, the regioselectivity for the abstraction from a polar substrate can be reversed by reversing the polarity of the attacking radical. Our calculations support Roberts' polarity-reversal-catalysis concept and suggest that addition of a catalyst of appropriate electrophilicity/nucleophilicity can lead to an enhancement of the reaction rate of approximately 5 orders of magnitude. By exploiting the control over regioselectivity associated with the polar nature of the radical and the substrate, we demonstrate the possibility of directing the regioselectivity of hydrogen abstraction from amino acid derivatives and simultaneously providing a significant rate acceleration.
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Affiliation(s)
- Bun Chan
- †School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia.,§ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Christopher J Easton
- ‡Research School of Chemistry, The Australian National University, Canberra, ACT 2600, Australia.,§ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Leo Radom
- †School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia.,§ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
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Krechkivska O, Wilcox CM, Chan B, Jacob R, Liu Y, Nauta K, Kable SH, Radom L, Schmidt TW. H and D Attachment to Naphthalene: Spectra and Thermochemistry of Cold Gas-Phase 1-C10H9 and 1-C10H8D Radicals and Cations. J Phys Chem A 2015; 119:3225-32. [DOI: 10.1021/acs.jpca.5b01652] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olha Krechkivska
- School
of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Callan M. Wilcox
- School
of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Bun Chan
- School
of Chemistry and Centre of Excellence for Free Radical Chemistry and
Biotechnology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rebecca Jacob
- School
of Chemistry and Centre of Excellence for Free Radical Chemistry and
Biotechnology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yu Liu
- School
of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Klaas Nauta
- School
of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Scott H. Kable
- School
of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Leo Radom
- School
of Chemistry and Centre of Excellence for Free Radical Chemistry and
Biotechnology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Timothy W. Schmidt
- School
of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
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Feketeová L, Chan B, Khairallah GN, Steinmetz V, Maître P, Radom L, O'Hair RAJ. Gas-phase structure and reactivity of the keto tautomer of the deoxyguanosine radical cation. Phys Chem Chem Phys 2015; 17:25837-44. [DOI: 10.1039/c5cp01573a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas-phase IR spectroscopy, ion–molecule reactions, collision-induced dissociation and computational chemistry in combination form a powerful tool to gain insights into the structure of one-electron oxidised guanine in DNA and its resultant chemistry.
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Affiliation(s)
- Linda Feketeová
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology
- The University of Melbourne
- Parkville
- Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Bun Chan
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry
- University of Sydney
- Australia
| | - George N. Khairallah
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology
- The University of Melbourne
- Parkville
- Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | | | - Philippe Maître
- Laboratoire de Chimie Physique
- Université Paris Sud
- Orsay Cedex
- France
| | - Leo Radom
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry
- University of Sydney
- Australia
| | - Richard A. J. O'Hair
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology
- The University of Melbourne
- Parkville
- Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
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Amos RIJ, Heinroth F, Chan B, Zheng S, Haynes BS, Easton CJ, Masters AF, Radom L, Maschmeyer T. Hydrogen from formic acid through its selective disproportionation over sodium germanate--a non-transition-metal catalysis system. Angew Chem Int Ed Engl 2014; 53:11275-9. [PMID: 25169798 DOI: 10.1002/anie.201405360] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Indexed: 11/08/2022]
Abstract
A robust catalyst for the selective dehydrogenation of formic acid to liberate hydrogen gas has been designed computationally, and also successfully demonstrated experimentally. This is the first such catalyst not based on transition metals, and it exhibits very encouraging performance. It represents an important step towards the use of renewable formic acid as a hydrogen-storage and transport vector in fuel and energy applications.
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Affiliation(s)
- Ruth I J Amos
- School of Chemistry, The University of Sydney, Sydney, NSW 2006 (Australia); CSIRO Energy Transformed Cluster on Biofuels and Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia); ARC Centre of Excellence for Free Radical Chemistry and Biotechnology (Australia).
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Amos RIJ, Heinroth F, Chan B, Zheng S, Haynes BS, Easton CJ, Masters AF, Radom L, Maschmeyer T. Hydrogen from Formic Acid through Its Selective Disproportionation over Sodium Germanate-A Non-Transition-Metal Catalysis System. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Amos RIJ, Chan B, Easton CJ, Radom L. Hydrogen-Atom Abstraction from a Model Amino Acid: Dependence on the Attacking Radical. J Phys Chem B 2014; 119:783-8. [DOI: 10.1021/jp505217q] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ruth I. J. Amos
- School
of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Bun Chan
- School
of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Christopher J. Easton
- Research
School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Leo Radom
- School
of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
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36
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Chan B, Gilbert ATB, Gill PMW, Radom L. Performance of Density Functional Theory Procedures for the Calculation of Proton-Exchange Barriers: Unusual Behavior of M06-Type Functionals. J Chem Theory Comput 2014; 10:3777-83. [DOI: 10.1021/ct500506t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Bun Chan
- School
of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | | | | | - Leo Radom
- School
of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
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37
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Morris M, Chan B, Radom L. Effect of Protonation State and Interposed Connector Groups on Bond Dissociation Enthalpies of Alcohols and Related Systems. J Phys Chem A 2014; 118:2810-9. [DOI: 10.1021/jp501256f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michael Morris
- School of Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bun Chan
- School of Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Leo Radom
- School of Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, New South Wales 2006, Australia
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38
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Pople JA, Scott AP, Wong MW, Radom L. Scaling Factors for Obtaining Fundamental Vibrational Frequencies and Zero-Point Energies from HF/6-31G* and MP2/6-31G* Harmonic Frequencies. Isr J Chem 2013. [DOI: 10.1002/ijch.199300041] [Citation(s) in RCA: 742] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Abstract
We have formulated the W3X procedure by incorporating cost-effective post-CCSD(T) components (up to the CCSDT(Q) level) into the W1X-1 protocol, the latter representing a recently reported economical yet accurate approximation to CCSD(T)/CBS. For medium-sized systems, W3X is moderately more computationally demanding than W1X-1, but it is significantly less costly than the W3.2lite and (especially) W3.2 procedures. Because of the use of the cost-effective W1X-1 method as the underlying CCSD(T) component, W3X is also less expensive than the W2.2 protocol, which does not incorporate post-CCSD(T) excitations. We find that, for single-reference systems (the G2/97 set and most of the W4-11 set), W3X is comparable in accuracy to the underlying W1X-1 protocol, as might have been expected. For the more challenging cases of the multireference systems within the W4-11 set, the dissociation of F2 and the automerization of cyclobutadiene, W3X provides improved performance compared with the CCSD(T)-based procedures (W1X-1 and W2.2). Highly multireference chromium oxides CrO, CrO2, and CrO3 are still somewhat challenging for W3X (and even for the higher-level W3.2lite and W3.2 procedures), but the inclusion of the economical post-CCSD(T) terms in W3X already leads to a significant improvement over W1X-1. Thus, W3X provides a cost-effective means for treating systems with significant (but perhaps not excessive) multireference character that are otherwise not well-described by CCSD(T)-based methods.
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Affiliation(s)
- Bun Chan
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney , Sydney, NSW 2006, Australia
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney , Sydney, NSW 2006, Australia
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42
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Thompson RE, Chan B, Radom L, Jolliffe KA, Payne RJ. Chemoselective peptide ligation-desulfurization at aspartate. Angew Chem Int Ed Engl 2013; 52:9723-7. [PMID: 23893778 DOI: 10.1002/anie.201304793] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Indexed: 11/07/2022]
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44
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Chan B, Radom L. Hierarchy of Relative Bond Dissociation Enthalpies and Their Use to Efficiently Compute Accurate Absolute Bond Dissociation Enthalpies for C–H, C–C, and C–F Bonds. J Phys Chem A 2013; 117:3666-75. [DOI: 10.1021/jp401248r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bun Chan
- School of Chemistry and ARC Center
of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, NSW 2006 Australia
| | - Leo Radom
- School of Chemistry and ARC Center
of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, NSW 2006 Australia
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45
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Karton A, Chan B, Raghavachari K, Radom L. Evaluation of the Heats of Formation of Corannulene and C60 by Means of High-Level Theoretical Procedures. J Phys Chem A 2013; 117:1834-42. [DOI: 10.1021/jp312585r] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Amir Karton
- School of
Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Bun Chan
- School of
Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47408, United
States
| | - Leo Radom
- School of
Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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46
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O’Reilly RJ, Karton A, Radom L. Effect of Substituents on the Preferred Modes of One-Electron Reductive Cleavage of N–Cl and N–Br Bonds. J Phys Chem A 2013; 117:460-72. [DOI: 10.1021/jp310048f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Robert J. O’Reilly
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- School of Chemistry, University of Tasmania, Private Bag
75, Hobart, TAS 7001, Australia
| | - Amir Karton
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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47
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Goerigk L, Karton A, Martin JML, Radom L. Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution. Phys Chem Chem Phys 2013; 15:7028-31. [DOI: 10.1039/c3cp00057e] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Feketeová L, Khairallah GN, Chan B, Steinmetz V, Maître P, Radom L, O'Hair RAJ. Gas-phase infrared spectrum and acidity of the radical cation of 9-methylguanine. Chem Commun (Camb) 2013; 49:7343-5. [DOI: 10.1039/c3cc43244k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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49
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Morris M, Chan B, Radom L. Heteroatomic Deprotonation of Substituted Methanes and Methyl Radicals: Theoretical Insights into Structure, Stability, and Thermochemistry. J Phys Chem A 2012; 116:12381-7. [DOI: 10.1021/jp3101927] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Morris
- School of Chemistry and
ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Bun Chan
- School of Chemistry and
ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Radom
- School of Chemistry and
ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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50
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Karton A, O’Reilly RJ, Pattison DI, Davies MJ, Radom L. Computational Design of Effective, Bioinspired HOCl Antioxidants: The Role of Intramolecular Cl+ and H+ Shifts. J Am Chem Soc 2012; 134:19240-5. [DOI: 10.1021/ja309273n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Amir Karton
- School of Chemistry, University of Sydney, Sydney, NSW 2006,
Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - Robert J. O’Reilly
- School of Chemistry, University of Sydney, Sydney, NSW 2006,
Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
| | - David I. Pattison
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia
- Faculty of Medicine, University of Sydney, Sydney, NSW 2006,
Australia
| | - Michael J. Davies
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia
- Faculty of Medicine, University of Sydney, Sydney, NSW 2006,
Australia
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006,
Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
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