: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.

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Analyzing Reaction Rates with the Distortion/Interaction‐Activation Strain Model

Cellular Incorporation of Unnatural Amino Acids and Bioorthogonal Labeling of Proteins

Chemical modification of proteins is an important tool for probing natural systems, creating therapeutic conjugates and generating novel protein constructs. Site-selective reactions require exquisite control over both chemo- and regioselectivity, under ambient, aqueous conditions. There are now various methods for achieving selective modification of both natural and unnatural amino acids--each with merits and limitations--providing a 'toolkit' that until 20 years ago was largely limited to reactions at nucleophilic cysteine and lysine residues. If applied in a biologically benign manner, this chemistry could form the basis of true Synthetic Biology.

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Selective chemical protein modification

The research on 1,2,3-triazoles has been lively and ever-growing since its stimulation by the advent of click chemistry The attractiveness of 1H-1,2,3-triazoles and their derivatives originates from their unique combination of facile accessibility via click chemistry and truly diverse supramolecular interactions, which enabled myriads of applications in supramolecular and coordination chemistry The nitrogen-rich triazole features a highly polarized carbon atom allowing the complexation of anions by hydrogen and halogen bonding or, in the case of the triazolium salts, via charge-assisted hydrogen and halogen bonds On the other hand, the triazole offers several N-coordination modes including coordination via anionic and cationic nitrogen donors of triazolate and triazolium ions, respectively After CH-deprotonation of the triazole and the triazolium, powerful carbanionic and mesoionic carbene donors, respectively, are available The latter coordination mode even features non-innocent ligand behavior Moreover, these supramolecular interactions can be combined, eg, in ion-pair recognition, preorganization by intramolecular hydrogen bond donation and acceptance, and in bimetallic complexes Ultimately, by clicking two building blocks into place, the triazole emerges as a most versatile functional unit allowing very successful applications, eg, in anion recognition, catalysis, and photochemistry, thus going far beyond the original purpose of click chemistry It is the intention of this review to provide a detailed analysis of the various supramolecular interactions of triazoles in comparison to established functional units, which may serve as guidelines for further applications

Beyond click chemistry - supramolecular interactions of 1,2,3-triazoles.

The 1,3-dipolar cycloaddition of cyclooctynes with azides, also called "copper-free click chemistry", is a bioorthogonal reaction with widespread applications in biological discovery. The kinetics of this reaction are of paramount importance for studies of dynamic processes, particularly in living subjects. Here we performed a systematic analysis of the effects of strain and electronics on the reactivity of cyclooctynes with azides through both experimental measurements and computational studies using a density functional theory (DFT) distortion/interaction transition state model. In particular, we focused on biarylazacyclooctynone (BARAC) because it reacts with azides faster than any other reported cyclooctyne and its modular synthesis facilitated rapid access to analogues. We found that substituents on BARAC's aryl rings can alter the calculated transition state interaction energy of the cycloaddition through electronic effects or the calculated distortion energy through steric effects. Experimental data confirmed that electronic perturbation of BARAC's aryl rings has a modest effect on reaction rate, whereas steric hindrance in the transition state can significantly retard the reaction. Drawing on these results, we analyzed the relationship between alkyne bond angles, which we determined using X-ray crystallography, and reactivity, quantified by experimental second-order rate constants, for a range of cyclooctynes. Our results suggest a correlation between decreased alkyne bond angle and increased cyclooctyne reactivity. Finally, we obtained structural and computational data that revealed the relationship between the conformation of BARAC's central lactam and compound reactivity. Collectively, these results indicate that the distortion/interaction model combined with bond angle analysis will enable predictions of cyclooctyne reactivity and the rational design of new reagents for copper-free click chemistry.

/pdf/reactivity-of-biarylazacyclooctynones-in-copper-free-click-77t23xx6tt.pdf

Reactivity of biarylazacyclooctynones in copper-free click chemistry

The distortion/interaction model has been used to explain and predict reactivity in a variety of reactions where more common explanations, such as steric and electronic factors, do not suffice. This model has also provided new fundamental insight into regioselectivity trends in reactions of unsymmetrical arynes, which in turn has fueled advances in aryne methodology and natural product synthesis. This article describes a systematic experimental and computational study of one particularly important class of arynes, 3-halobenzynes. 3-Halobenzynes are useful synthetic building blocks whose regioselectivities have been explained by several different models over the past few decades. Our efforts show that aryne distortion, rather than steric factors or charge distribution, are responsible for the regioselectivities observed in 3-haloaryne trapping experiments. We also demonstrate the synthetic utility of 3-halobenzynes for the efficient synthesis of functionalized heterocycles, using a tandem aryne-trapping/cross-coupling sequence involving 3-chlorobenzyne.

/pdf/the-role-of-aryne-distortions-steric-effects-and-charges-in-34ai1b11ym.pdf

The role of aryne distortions, steric effects, and charges in regioselectivities of aryne reactions.

The azide-dibenzocyclooctyne and trans-cyclooctene-tetrazine cycloadditions are both bioorthogonal and mutually orthogonal: trans-cyclooctene derivatives greatly prefer to react with tetrazines rather than azides, while dibenzocyclooctyne derivatives react with azides but not with tetrazines under physiological conditions. DFT calculations used to identify the origins of this extraordinary selectivity are reported, and design principles to guide discovery of new orthogonal cycloadditions are proposed. Two new bioorthogonal reagents, methylcyclopropene and 3,3,6,6-tetramethylthiacycloheptyne, are predicted to be mutually orthogonal in azide and tetrazine cycloadditions.

Control and design of mutual orthogonality in bioorthogonal cycloadditions.

We report an experimental and computational study of 3-silylarynes. The addition of nucleophiles yield ortho-substituted products as a result of aryne distortion, but meta-substituted products form predominately when the nucleophile is large. Computations correctly predict the preferred site of attack observed in both nucleophilic addition and cycloaddition experiments. Nucleophilic additions to 3-tert-butylbenzyne, which is not significantly distorted, give meta-substituted products.

Steric Effects Compete with Aryne Distortion to Control Regioselectivities of Nucleophilic Additions to 3-Silylarynes

The regioselectivity and stereoselectivity aspects of the Diels-Alder/radical hydrodenitration reaction sequence leading to trans-fused ring systems have been investigated with density functional calculations. A continuum of transition structures representing Diels-Alder and hetero-Diels-Alder cycloadditions as well as a sigmatropic rearrangement have been located, and they all lie very close in energy on the potential energy surface. All three pathways are found to be important in the formation of the Diels-Alder adduct. Reported regioselectivities are reproduced by the calculations. The stereoselectivity of radical hydrodenitration of the cis-Diels-Alder adduct is found to be related to the relative conformational stabilities of bicyclic radical intermediates. Overall, the computations provide understanding of the regioselectivities and stereoselectivities of the trans-Diels-Alder paradigm.

/pdf/origins-of-stereoselectivity-in-the-trans-diels-alder-2rdj6pbrb9.pdf

Joel L. Mackey

Papers

Reactivity of biarylazacyclooctynones in copper-free click chemistry

The role of aryne distortions, steric effects, and charges in regioselectivities of aryne reactions.

Control and design of mutual orthogonality in bioorthogonal cycloadditions.

Steric Effects Compete with Aryne Distortion to Control Regioselectivities of Nucleophilic Additions to 3-Silylarynes

Origins of Stereoselectivity in the trans-Diels-Alder Paradigm