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Liljenberg, M., Halldin Stenlid, J. & Brinck, T. (2018). Mechanism and regioselectivity of electrophilic aromatic nitration in solution: the validity of the transition state approach. Journal of Molecular Modeling, 24(1), Article ID 15.
Open this publication in new window or tab >>Mechanism and regioselectivity of electrophilic aromatic nitration in solution: the validity of the transition state approach
2018 (English)In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 24, no 1, article id 15Article in journal (Refereed) Published
Abstract [en]

The potential energy surfaces in gas phase and in aqueous solution for the nitration of benzene, chlorobenzene, and phenol have been elucidated with density functional theory at theM06-2X/6-311G(d,p) level combined with the polarizable continuum solvent model (PCM). Three reaction intermediates have been identified along both surfaces: the unoriented pi-complex (I), the oriented reaction complex (II), and the sigma-complex (III). In order to obtain quantitatively reliable results for positional selectivity and for modeling the expulsion of the proton, it is crucial to take solvent effects into consideration. The results are in agreement with Olah's conclusion from over 40 years ago that the transition state leading to (II) is the rate-determining step in activated cases, while it is the one leading to (III) for deactivated cases. The simplified reactivity approach of using the free energy for the formation of (III) as a model of the rate-determining transition state has previously been shown to be very successful for halogenations, but problematic for nitrations. These observations are rationalized with the geometric and energetic resemblance, and lack of resemblance respectively, between (III) and the corresponding rate determining transition state. At this level of theory, neither the sigma-complex (III) nor the reaction complex (II) can be used to accurately model the rate-determining transition state for nitrations.

Place, publisher, year, edition, pages
SPRINGER, 2018
Keywords
Nitration, Electrophilic aromatic substitution, Transition state, Regioselectivity, Quantumchemistry
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-222199 (URN)10.1007/s00894-017-3561-z (DOI)000422667900038 ()2-s2.0-85038842979 (Scopus ID)
Note

QC 20180205

Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2018-03-13Bibliographically approved
Liljenberg, M., Halldin Stenlid, J. & Brinck, T. (2018). Theoretical Investigation into Rate-Determining Factors in Electrophilic Aromatic Halogenation. Journal of Physical Chemistry A, 122(12), 3270-3279
Open this publication in new window or tab >>Theoretical Investigation into Rate-Determining Factors in Electrophilic Aromatic Halogenation
2018 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 12, p. 3270-3279Article in journal (Refereed) Published
Abstract [en]

The halogenation of monosubstituted benzenes in aqueous solvent was studied using density functional theory at the PCM-M06-2X/6-311G(d,p) level. The reaction with Cl-2 begins with the formation of C atom coordinated pi-complex and is followed by the formation of the sigma-complex, which is rate-determining. The final part proceeds via the abstraction of the proton by a water molecule or a weak base. We evaluated the use of the sigma-complex as a model for the rate-determining transition state (TS) and found that this model is more accurate the later the TS comes along the reaction coordinate. This explains the higher accuracy of the model for halogenations (late TS) compared to nitrations (early TS); that is, the more deactivated the substrate the later the TS. The halogenation with Br-2 proceeds with a similar mechanism as the corresponding chlorination, but the bromination has a very late rate-determining TS that is similar to the sigma-complex in energy. The iodination with ICl follows a different mechanism than chlorination and bromination. After the formation of the pi-complex, the reaction proceeds in a concerted manner without a sigma-complex. This reaction has a large primary hydrogen kinetic isotope effect in agreement with experimental observations.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-226789 (URN)10.1021/acs.jpca.7b10781 (DOI)000429080300020 ()29505259 (PubMedID)2-s2.0-85044836973 (Scopus ID)
Note

QC 20180504

Available from: 2018-05-04 Created: 2018-05-04 Last updated: 2018-06-04Bibliographically approved
Halldin Stenlid, J., Johansson, A. J., Leygraf, C. & Brinck, T. (2017). Atomic-scale modelling of copper corrosion in anoxic and sulphide containing water. In: EUROCORR 2017 - The Annual Congress of the European Federation of Corrosion, 20th International Corrosion Congress and Process Safety Congress 2017: . Paper presented at Joint European Corrosion Congress 2017, EUROCORR 2017 and 20th International Corrosion Congress and Process Safety Congress 2017. Asociace koroznich inzenyru z.s.- AKI - Czech Association of Corrosion Engineers
Open this publication in new window or tab >>Atomic-scale modelling of copper corrosion in anoxic and sulphide containing water
2017 (English)In: EUROCORR 2017 - The Annual Congress of the European Federation of Corrosion, 20th International Corrosion Congress and Process Safety Congress 2017, Asociace koroznich inzenyru z.s.- AKI - Czech Association of Corrosion Engineers , 2017Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Asociace koroznich inzenyru z.s.- AKI - Czech Association of Corrosion Engineers, 2017
National Category
Other Chemistry Topics
Identifiers
urn:nbn:se:kth:diva-234517 (URN)2-s2.0-85052295357 (Scopus ID)
Conference
Joint European Corrosion Congress 2017, EUROCORR 2017 and 20th International Corrosion Congress and Process Safety Congress 2017
Note

QC 20180907

Available from: 2018-09-07 Created: 2018-09-07 Last updated: 2018-09-07Bibliographically approved
Halldin Stenlid, J., Johansson, A. J., Leygraf, C. & Brinck, T. (2017). Computational Analysis of the Early Stage of Cuprous Oxide Sulphidation: A Top-Down Process. Corrosion Engineering, Science and Technology, 52(S1), 50-53
Open this publication in new window or tab >>Computational Analysis of the Early Stage of Cuprous Oxide Sulphidation: A Top-Down Process
2017 (English)In: Corrosion Engineering, Science and Technology, ISSN 1478-422X, E-ISSN 1743-2782, Vol. 52, no S1, p. 50-53Article in journal (Refereed) Published
Abstract [en]

The initial steps of Cu2O sulphidation to Cu2S have been studied using plane-wave density functional theory at the PBE-D3+U level of sophistication. Surface adsorption and dissociation of H2S and H2O, as well as the replacement reaction of lattice oxygen with sulphur, have been investigated for the most stable (111) and (100) surface facets under oxygen-lean conditions. We find that the (100) surface is more susceptible to sulphidation than the (111) surface, promoting both H2S adsorption, dissociation and the continued oxygen–sulphur replacement. The results presented in this proceeding bridge previous results from high-vacuum experiments on ideal surface to more realistic corrosion conditions and set the grounds for future mechanistic studies. Potential implications on the long-term final disposal of spent nuclear fuel are discussed.

Keywords
Density functional theory, sulphidation, cuprite (Cu2O), corrosion, water (H2O), hydrogen sulphide (H2S), nuclear waste disposal, chalcocite (Cu2S)
National Category
Chemical Sciences
Research subject
Materials Science and Engineering; Chemistry; Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-212933 (URN)10.1080/1478422X.2017.1284393 (DOI)
Note

QC 20170829

Available from: 2017-08-24 Created: 2017-08-24 Last updated: 2017-08-29Bibliographically approved
Besharat, Z., Halldin Stenlid, J., Soldemo, M., Marks, K., Önsten, A., Johnson, M., . . . Göthelid, M. (2017). Dehydrogenation of methanol on Cu2O(100) and (111). Journal of Chemical Physics, 146(24)
Open this publication in new window or tab >>Dehydrogenation of methanol on Cu2O(100) and (111)
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2017 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 24Article in journal (Refereed) Published
Abstract [en]

Adsorption and desorption of methanol on the (111) and (100) surfaces of  Cu2O have been studied using high-resolution photoelectron spectroscopy in the temperature range 120–620 K, in combination with density functional theorycalculations and sum frequency generation spectroscopy. The bare (100) surfaceexhibits a (3,0; 1,1) reconstruction but restructures during the adsorption process into a Cu-dimer geometry stabilized by methoxy and hydrogen binding in Cu-bridge sites. During the restructuring process, oxygen atoms from the bulk that can host hydrogen appear on the surface. Heating transforms methoxy to formaldehyde, but further dehydrogenation is limited by the stability of the surface and the limited access to surface oxygen. The (√3 × √3)R30°-reconstructed (111) surface is based on ordered surface oxygen and copper ions and vacancies, which offers a palette of adsorption and reaction sites. Already at 140 K, a mixed layer of methoxy, formaldehyde, and CHxOy is formed. Heating to room temperature leaves OCH and CHx. Thus both CH-bond breaking and CO-scission are active on this  surface at low temperature. The higher ability to dehydrogenate methanol on (111) compared to (100) is explained by the multitude of adsorption sites and, in particular, the availability of surfaceoxygen.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2017
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-211786 (URN)10.1063/1.4989472 (DOI)000404302600033 ()2-s2.0-85021446807 (Scopus ID)
Note

QC 20170816

Available from: 2017-08-13 Created: 2017-08-13 Last updated: 2017-11-10Bibliographically approved
Halldin Stenlid, J. & Brinck, T. (2017). Extending the σ-Hole Concept to Metals: An Electrostatic Interpretation of the Nanostructural Effects in Gold and Platinum Catalysis. Journal of the American Chemical Society
Open this publication in new window or tab >>Extending the σ-Hole Concept to Metals: An Electrostatic Interpretation of the Nanostructural Effects in Gold and Platinum Catalysis
2017 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126Article in journal (Refereed) Published
Abstract [en]

Crystalline surfaces of gold are chemically inert, whereas nanoparticles of gold are excellent catalysts for many reactions. The catalytic properties of nanostructured gold have been connected to increased binding affinities of reactant molecules to low-coordinated Au atoms. Here we show that the high reactivity at these sites is a consequence of the formation of σ-holes, i.e. maxima in the surface electrostatic potential (Vs,max) due to the overlap of mainly the valence s-orbitals when forming the bonding σ-orbitals. The σ-holes are binding sites for Lewis bases, and binding energies correlate with magnitudes of the Vs,max. For symmetrical Au clusters, of varying size, the most positive Vs,max are found at corners, edges, and surfaces (facets) and decreasing in that order. This is in agreement with the experimentally and theoretically observed dependence of catalytic activity on local structure. The density of σ-holes can explain the increasing catalytic activity with decreasing particle size also for other transition metal catalysts, such as platinum.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Physical Chemistry Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-211788 (URN)10.1021/jacs.7b05987 (DOI)000408074800019 ()2-s2.0-85026319771 (Scopus ID)
Note

QC 20170816

Available from: 2017-08-13 Created: 2017-08-13 Last updated: 2017-09-26Bibliographically approved
Stenlid, J. H., Johansson, A. J. & Brinck, T. (2017). Local Lewis Acidity of (TiO2)(n) (n=7-10) Nanoparticles Characterized by DFT-Based Descriptors: Tools for Catalyst Design. The Journal of Physical Chemistry C, 121(49), 27483-27492
Open this publication in new window or tab >>Local Lewis Acidity of (TiO2)(n) (n=7-10) Nanoparticles Characterized by DFT-Based Descriptors: Tools for Catalyst Design
2017 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 121, no 49, p. 27483-27492Article in journal (Refereed) Published
Abstract [en]

Transition metal oxide nanoparticles are common materials in a multitude of applications including heterogeneous catalysis, solar energy harvesting, and energy storage. Understanding the particles' interplay with their surroundings is key to their efficient usage and design. Herein two DFT-based descriptors are used to study local reactivity on (TiO2)(n) (n = 7-10) nanoparticles. The local electron attraction energy [E(r)] and the electrostatic potential [V(r)], evaluated on isodensity surfaces, are able to identify and rank Lewis acidic sites on the particles with high accuracy when compared to the interaction energies of the Lewis bases H2O, H2S, NH3, and CO. These interactions are characterized as mainly electrostatically controlled. Given the local character, low computational cost, and excellent performance of the E-s(r) and V-s(r) descriptors, they are anticipated to find widespread use in nanoparticle research and development.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2017
National Category
Materials Chemistry
Identifiers
urn:nbn:se:kth:diva-220830 (URN)10.1021/acs.jpcc.7b09311 (DOI)000418393900027 ()2-s2.0-85038397134 (Scopus ID)
Note

QC 20180111

Available from: 2018-01-11 Created: 2018-01-11 Last updated: 2018-03-12Bibliographically approved
Gustafsson, C., Vassiliev, S., Kürten, C., Syrén, P.-O. & Brinck, T. (2017). MD Simulations Reveal Complex Water Paths in Squalene–Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site. ACS Omega, 2(11), 8495-8506
Open this publication in new window or tab >>MD Simulations Reveal Complex Water Paths in Squalene–Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site
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2017 (English)In: ACS Omega, ISSN 2470-1343, Vol. 2, no 11, p. 8495-8506Article in journal (Refereed) Published
Abstract [en]

Squalene–hopene cyclase catalyzes the cyclization of squalene to hopanoids. A previous study has identified a network of tunnels in the protein, where water molecules have been indicated to move. Blocking these tunnels by site-directed mutagenesis was found to change the activation entropy of the catalytic reaction from positive to negative with a concomitant lowering of the activation enthalpy. As a consequence, some variants are faster and others are slower than the wild type (wt) in vitro under optimal reaction conditions for the wt. In this study, molecular dynamics (MD) simulations have been performed for the wt and the variants to investigate how the mutations affect the protein structure and the water flow in the enzyme, hypothetically influencing the activation parameters. Interestingly, the tunnel-obstructing variants are associated with an increased flow of water in the active site, particularly close to the catalytic residue Asp376. MD simulations with the substrate present in the active site indicate that the distance for the rate-determining proton transfer between Asp376 and the substrate is longer in the tunnel-obstructing protein variants than in the wt. On the basis of the previous experimental results and the current MD results, we propose that the tunnel-obstructing variants, at least partly, could operate by a different catalytic mechanism, where the proton transfer may have contributions from a Grotthuss-like mechanism.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Biocatalysis and Enzyme Technology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-234939 (URN)10.1021/acsomega.7b01084 (DOI)000418744100113 ()
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180914

Available from: 2018-09-13 Created: 2018-09-13 Last updated: 2018-09-18Bibliographically approved
Stenlid, J. H. & Brinck, T. (2017). Nucleophilic Aromatic Substitution Reactions Described by the Local Electron Attachment Energy. Journal of Organic Chemistry, 82(6), 3072-3083
Open this publication in new window or tab >>Nucleophilic Aromatic Substitution Reactions Described by the Local Electron Attachment Energy
2017 (English)In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 6, p. 3072-3083Article in journal (Refereed) Published
Abstract [en]

A local multiorbital electrophilicity descriptor, the local electron attachment energy [E(r)], is used to study the nucleophilic aromatic substitution reactions of SNAr and VNS (vicarious nucleophilic substitution). E(r) considers all virtual orbitals below the free electron limit and is determined on the molecular isodensity contour of 0.004 atomic units. Good (R-2 = 0.83) to excellent (R-2 = 0.98) correlations are found between descriptor values and experimental reactivity data for six series of electron deficient arenes. These include homo- and heteroarenes, rings of five to six atoms, and a variety of fluorine, bromine, and hydride leaving groups. The solvent, temperature, and nucleophile are in addition varied across the series. The surface E(r) [E-s(r)] is shown to provide reactivity predictions better than those of transition-state calculations for a concerted SNAr reaction with a bromine substantially stronger than those of LUMO energies, and is overall more reliable than the molecular electrostatic potential. With the use of E-s(r), one can identify the various electrophilic sites within a molecule and correctly predict isomeric distributions. Since the calculations of E-s(r) are computationally inexpensive, the descriptor offers fast but accurate reactivity predictions for the important nucleophilic aromatic substitution class of reactions. Applications in, e.g., drug discovery, synthesis, and toxicology studies are envisaged.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-205458 (URN)10.1021/acs.joc.7b00059 (DOI)000397077500027 ()28195731 (PubMedID)2-s2.0-85015645472 (Scopus ID)
Note

QC 20170522

Available from: 2017-05-22 Created: 2017-05-22 Last updated: 2017-08-28Bibliographically approved
Koefoed, L., Vase, K. H., Halldin Stenlid, J., Brinck, T., Yoshimura, Y., Lund, H., . . . Daasbjerg, K. (2017). On the Kinetic and Thermodynamic Properties of Aryl Radicals Using Electrochemical and Theoretical Approaches. CHEMELECTROCHEM, 4(12), 3212-3221
Open this publication in new window or tab >>On the Kinetic and Thermodynamic Properties of Aryl Radicals Using Electrochemical and Theoretical Approaches
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2017 (English)In: CHEMELECTROCHEM, ISSN 2196-0216, Vol. 4, no 12, p. 3212-3221Article in journal (Refereed) Published
Abstract [en]

In this work, sampled-current voltammetry performed on a series of aryldiazonium, diaryliodonium, and triarylsulfonium salts allows the determination of the reduction potential of aryl radicals in acetonitrile. Specifically, this is accomplished by measuring the number of electrons consumed in the reduction process as a function of the applied potential. For the phenyl, 4-bromophenyl, and 4-nitrophenyl radicals, the reduction potential is found to be -0.91 +/- 0.06, -0.90 +/- 0.10, and -0.98 +/- 0.06 V vs. SCE, respectively. Furthermore, from measurements on an extended series of substituted compounds, it is concluded that the substituent effect on the reduction potential is small, which can be explained by the sigma nature of the aryl radical as evidenced from theoretical calculations. At the same time this yields a mean value for the reduction potential of the aryl radical of -0.87 V +/- 0.03 V vs. SCE. Determination of the intrinsic barrier and the standard potential from the data obtained are more uncertain since it is unknown to which extent the competing reference reaction, the electrochemical grafting reaction, is affected by the applied potential. From calculations using density functional theory, the intrinsic barrier for the reduction of the phenyl radical is determined to be 0.32 eV.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2017
Keywords
aryldiazonium salts, density functional calculations, phenyl radicals, reduction potential, sampled-current voltammetry
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-221876 (URN)10.1002/celc.201700772 (DOI)000419269000025 ()2-s2.0-85032256466 (Scopus ID)
Note

QC 20180130

Available from: 2018-01-30 Created: 2018-01-30 Last updated: 2018-01-30Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-2673-075X

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