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  • 1. Ghobril, Cynthia
    et al.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kodepelly, Sanjeevarao
    Spiess, Bernard
    Wagner, Alain
    Himo, Fahmi
    Baati, Rachid
    Structure-Reactivity Relationship Studies for Guanidine-Organocatalyzed Direct Intramolecular Aldolization of Ketoaldehydes2010In: CHEMCATCHEM, ISSN 1867-3880, Vol. 2, no 12, p. 1573-1581Article in journal (Refereed)
    Abstract [en]

    Structure-reactivity studies are performed to explore the reaction mechanism of the guanidine-catalyzed intramolecular aldol reaction of ketoaldehydes. A large number of guanidine and guanidine-like catalysts are synthesized and their properties studied. Kinetic profiles and pK(a) values of the catalysts are measured and correlated to reaction barriers calculated using density functional theory (DFT). The DFT calculations show that structural rigidity influences the pKa of the guanidines. Although the basicity is a very important factor in the catalysis, it is not sufficient to fully account for its catalytic efficiency. The availability of two aligned nitrogen reaction sites for proton shuttling in the transition state is an essential feature that helps to rationalize the reactivity pattern and the activation mode for this family of organocatalysts.

  • 2. Ghobril, Cynthia
    et al.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kodepelly, Sanjeevarao
    Wagner, Alain
    Spiess, Bernard
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Baati, Rachid
    Structure and reactivity relationship studies for guanidine-organocatalyzed direct intramolecular aldolization of ketoaldehydesManuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    Structure-reactivity studies are performed to explore the reaction mechanism of guanidine-catalyzed intramolecular aldol reaction of ketoaldehydes. A large number of guanidines and guanidine-like catalysts were synthesized and their properties were determined. Kinetic profiles and pKa values of the catalysts were measured and correlated to reaction barriers calculated using density functional theory. The calculations show that the structural rigidity determines the pKa of the guanidines. Although the basicity is a very important factor in the catalyst, it is not sufficient to account for the full catalytic power. The availability of two reaction sites aligned for proton shuttling in the transition states is also an essential feature that helps us rationalize the reactivity pattern observed.

  • 3.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum Chemical Studies of Enantioselective Organocatalytic Reactions2008Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Density Functional Theory is used in order to shed light on the reaction mechanisms and the origins of stereoselectivity in enantioselective organocatalytic reactions. The reactions investigated are the dipeptide-catalyzed aldol reaction, the cinchona thiourea-catalyzed nitroaldol reaction and the prolinol derivative-catalyzed hydrophosphination reaction. We can justify the stereoselectivity in the reactions from the energies arising from different interactions in the transition states. The major contributions to the energy differences are found to be hydrogen bond-type attractions and steric repulsions. This knowledge will be useful in the design of improved catalysts as well as general understanding of the basis of selection in other reactions.

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  • 4.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum Chemical Studies of Mechanisms and Stereoselectivities of Organocatalytic Reactions2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    As the field of organocatalysis is growing, it is becoming more important to understand the specific modes of action of these new organic catalysts. Quantum chemistry, in particular density functional theory, has proven very powerful in exploring reaction mechanisms as well as selectivities in organocatalytic reactions, and is the tool used in this thesis. Different reaction mechanisms of several organocatalytic reactions have been examined, and we have been able to exclude various reaction pathways based on the calculated reaction barriers. The origins of stereoselection in a number of reactions have been rationalized. The computational method has generally reproduced the experimental stereoselectivities satisfactorily.

    The amino acid-catalyzed aldol reaction has previously been established to go through an enamine intermediate. In the first study of this thesis the understanding of this kind of reactions has been expanded to the dipeptide-catalyzed aldol reaction. The factors governing the enantioselection have been studied, showing how the chirality of the amino acids controls the conformation of the transition state, thereby determining the configuration of the product.

    In the cinchona thiourea-catalyzed Henry reaction two reaction modes regarding substrate binding to the two sites of the catalyst have been investigated, showing the optimal arrangement for this reaction. This enabled the rationalization of the observed stereoselectivity.

    The hydrophosphination of α,β-unsaturated aldehydes was studied. The bulky substituent of the chiral prolinol-derived catalyst was shown to effectively shield one face of the reactive iminium intermediate, thereby inducing the stereoselectivity.

    The transfer hydrogenation of imines using Hantzsch esters as hydride source and axially chiral phosphoric acid catalyst has also been explored. A reaction mode where both the Hantzsch ester and the protonated imine are hydrogen bonded to the phosphoric acid is demonstrated to be the preferred mode of action. The different arrangements leading to the two enantiomers of the product are evaluated for several cases, including the hydride transfer step in the reductive amination of α-branched aldehydes via dynamic kinetic resolution.

    Finally, the intramolecular aldol reaction of ketoaldehydes catalyzed by guanidinebased triazabicyclodecene (TBD) has been studied. Different mechanistic proposals have been assessed computationally, showing that the favoured reaction pathway is catalyzed by proton shuttling. The ability of a range of guanidines to catalyze this reaction has been investigated. The calculated reaction barriers reproduced the experimental reactivities quite well.

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  • 5.
    Hammar, Peter
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Córdova, Armando
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density Functional Theory Study of the Stereoselectivity in Small Peptide-Catalyzed Intermolecular Aldol Reactions2008In: Tetrahedron: asymmetry, ISSN 0957-4166, E-ISSN 1362-511X, Vol. 19, p. 1617-1621Article in journal (Refereed)
    Abstract [en]

    The origins of the stereoselection of the dipeptide-catalyzed intermolecular aldol reaction are explored by means of hybrid density functional theory. Transition states were located for the (S)-ala-(S)-ala-catalyzed aldol reaction with cyclohexanone as the donor and benzaldehyde as the acceptor. The calculations reproduce the experimental trends very satisfactorily. It is demonstrated that the main Source of stereoselectivity is the interaction of the N-terminal amino acid side chain of the dipeptide with the cyclohexene ring.

  • 6.
    Hammar, Peter
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ghobril, Cynthia
    Wagner, Alain
    Baati, Rachid
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Theoretical Mechanistic Study of the TBD-Catalyzed Intramolecular Aldol Reaction of Ketoaldehydes2010In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 75, no 14, p. 4728-4736Article in journal (Refereed)
    Abstract [en]

    The intramolecular aldol reaction of acyclic ketoaldehydes catalyzed by 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) is investigated using density functional theory calculations. Compared to the aldol reaction catalyzed by proline, the use of TBD provides a unique and unusual complete switch of product selectivity. Three mechanistic pathways are proposed and evaluated. In the favored mechanism TBD catalyzes the reaction through proton transfer in two steps, enolization and C-C bond formation. The computationally predicted stereochemical outcome of the reaction is in agreement with experimental findings. Additionally, these studies provide new insights into the activation mode of bifunctional guanidine catalysts in aldol reactions.

  • 7.
    Hammar, Peter
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Marcelli, Tommaso
    Van't Hoff Institute of Molecular Sciences, University of Amsterdam.
    Hiemstra, Henk
    Van't Hoff Institute of Molecular Sciences, University of Amsterdam.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density Functional Theory Study of the Cinchona Thiourea-Catalyzed Henry reaction: Mechanism and Enantioselectivity2007In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 349, no 17-18, p. 2537-2548Article in journal (Refereed)
    Abstract [en]

    We report a density functional theory investigation of the enantioselective Cinchona thiourea-catalyzed Henry reaction of aromatic aldehydes with nitromethane. We show that two pathways (differing in the binding modes of the reactants to the catalyst) are possible for the formation of the C-C bond, and that they have comparable reaction barriers. The enantioselectivity is investigated, and our results are in agreement with the experimentally observed solvent dependence of the reaction.

  • 8.
    Ibrahem, Ismail
    et al.
    Stockholms Universitet.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vesely, Jan
    Rios, Ramon
    Eriksson, Lars
    Córdova, Armando
    Organocatalytic Asymmetric Addition of Phosphorus Nucleophiles to α,β-Unsaturated Aldehydes: Mechanism and ScopeArticle in journal (Other academic)
  • 9.
    Ibrahem, Ismail
    et al.
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vesely, Jan
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Rios, Ramon
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Eriksson, Lars
    Department of Structural Chemistry, Arrhenius Laboratory, Stockholm University.
    Córdova, Armando
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Organocatalytic asymmetric hydrophosphination of alpha,beta-unsaturated aldehydes: Development, mechanism and DFT calculations2008In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 350, no 11-12, p. 1875-1884Article, review/survey (Refereed)
    Abstract [en]

    The development and mechanism of the highly chemo- and enantioselective organocatalytic hydrophosphination reaction of alpha,beta-unsaturated aldehydes is presented. The reactions are catalyzed by protected chiral diarylprolinol derivatives and give access to optically active phosphine derivatives in high yields with up to 99% ee. The organocatalytic addition of other phosphorus nucleophiles was also investigated. The origin of the high enantioselectivity for the reaction with diphenylphosphine as the nucleophile is investigated by density functional theory calculations.

  • 10.
    Ibrahem, Ismail
    et al.
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Rios, Ramon
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Vesely, Jan
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Eriksson, Lars
    Department of Structural Chemistry, Arrhenius Laboratory, Stockholm University.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Córdova, Armando
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Enantioselective Organocatalytic Hydrophosphination of α,β-Unsaturated Aldehydes2007In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 46, no 24, p. 4507-4510Article in journal (Refereed)
    Abstract [en]

    Keeping it simple: Optically active phosphine derivatives can be obtained in high yields and in up to 99% ee by using simple chiral amines to catalyze the hydrophosphination of α,β-unsaturated aldehydes (see scheme, green sphere = chiral group). The synthetic utility of this highly chemo- and enantioselective transformation was exemplified by the one-pot asymmetric synthesis of β-phosphine oxide acids.

  • 11.
    Marcelli, Tommaso
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Origin of Enantioselectivity in the Organocatalytic Reductive Amination of α-Branched Aldehydes2009In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 351, no 4, p. 525-529Article in journal (Refereed)
    Abstract [en]

    The reason for enantioselectivity in thereductive amination of α-branched aldehydes wasinvestigated. The relative energies of all the diastereomeric transition states for hydride transfer of a suitable computational model were calculated at the B3LYP/6-311+(2d,2p) level of theory. Our calculations successfully reproduce and rationalize the experimentally observed stereochemical outcome of the reaction.

  • 12.
    Marcelli, Tommaso
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Phosphoric Acid Catalyzed Enantioselective Transfer Hydrogenationof Imines: A Density Functional Theory Study of Reaction Mechanismand the Origins of Enantioselectivity2008In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 14, p. 8562-8571Article in journal (Refereed)
    Abstract [en]

    The phosphoric acid catalyzedreaction of 1,4-dihydropyridineswith N-arylimines has been investigatedby using density functional theory.We first considered the reaction of acetophenonePMP-imine (PMP=p-methoxyphenyl)with the dimethylHantzsch ester catalyzed by diphenylphosphate. Our study showed that, inagreement with what has previouslybeen postulated for other reactions, diphenylphosphate acts as a Lewis base/Brønsted acid bifunctional catalyst inthis transformation, simultaneously activatingboth reaction partners. The calculationsalso showed that the hydridetransfer transition states for the E andZ isomers of the iminium ion havecomparable energies. This observationturned out to be crucial to the understandingof the enantioselectivity of theprocess. Our results indicate that whenusing a chiral 3,3’-disubstituted biarylphosphoric acid, hydride transfer to theRe face of the (Z)-iminium is energeticallymore favorable and is responsiblefor the enantioselectivity, whereas thecorresponding transition states for nucleophilicattack on the two faces ofthe (E)-iminium are virtually degenerate.Moreover, model calculations predictthe reversal in enantioselectivityobserved in the hydrogenation of 2-arylquinolines,which during the catalyticcycle are converted into (E)-iminiumions that lack the flexibility of thosederived from acyclic N-arylimines. Inthis respect, the conformational rigidityof the dihydroquinolinium cation imposesan unfavorable binding geometryon the transition state for hydridetransfer on the Re face and is thereforeresponsible for the high enantioselectivity.

  • 13. Ullah, Farman
    et al.
    Zhao, Gui-Ling
    Deiana, Luca
    Zhu, Mingzhao
    Dziedzic, Pawel
    Ibrahem, Ismail
    Hammar, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Sun, Junliang
    Cordova, Armando
    Enantioselective Organocatalytic Conjugate Addition of Fluorocarbon Nucleophiles to alpha,beta-Unsaturated Aldehydes2009In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 39, p. 10013-10017Article in journal (Refereed)
    Abstract [en]

    Highly chemo- and enantioselective organocatalytic conjugate additions of fluorocarbon nucleophiles to alpha,beta-unsaturated aldehydes and the construction of a quaternary carbon stereocenter bearing a fluorine atom with high enantioselectivity was reported. After extensive screening of catalysts and conditions, it was found that chiral amines 5-9 catalyzed the conjugate addition of FBSM 2a to enal 1a to form the corresponding bfluorobis(sulfonyl)methyl aldehyde 3a, which was reduced in situ to the alcohol derivative 4a, with enantiomeric excess (ee) values ranging from nearly racemic to 95%. Chiral protected diarylprolinols catalyzed the transformation with the highest stereoselectivity under reaction conditions and mediated the formation of 3a with high chemoselectivity. The highest enantioselectivity was achieved in toluene. The enantioselectivity was improved, possibly due to stabilization of the iminium intermediate, by the addition of an acid additive and performing the transformation in ethanol.

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