Overcoming systematic DFT errors for hydrocarbon reaction energies

Despite the widespread use and numerous successful applications of density functional theory, descriptions of hydrocarbon reaction energies remain problematic. Illustrative examples include large underestimation of energies associated with alkane bond separation reactions and poor general description of intramolecular dispersion in hydrocarbons (e.g., B3LYP, MAD=14.1kcalmol−1). More recent, but not readily availably functionals, along with efficient posteriori corrections, not only show considerable improvement in the energy description of hydrocarbons but also help identify the sources of error in traditional DFT. Interactions in branched alkanes and compact hydrocarbons are adequately mimicked by systems compressed below their typical van der Waals distances. At these distances, standard DFT exchange functionals are overly repulsive for non-bonded density overlaps, and significant improvement is offered by the long-range corrected exchange functionals (e.g., LC-BLYP0.33, MAD=5.5kcalmol−1). For those systems, the neglect of long-range dispersion is found to be a critical shortcoming, as well as "overlap dispersion”, for which non-negligible amounts are captured by the correlation functional. Accounting for the missing dispersion interactions is of key importance. Accordingly, most noteworthy improvements over standard functionals are obtained by using non-local van der Waals density functionals (e.g., LC-S-VV09, MAD=3.6kcalmol−1, rPW86-VV09, MAD=5.8kcalmol−1), a dispersion corrected double hybrid (B2PLYP-D, MAD=2.5kcalmol−1), or by the addition of an atom pairwise density-dependent dispersion correction to a standard functional (e.g., PBE-dDXDM, MAD=0.8kcalmol−1). To a lesser extent, the reduction of the delocalization error (e.g., MCY3, MAD=6.3kcalmol−1) or careful parameter fitting (e.g., M06-2X, MAD=5.6kcalmol−1) also lowers the error

Electronic Elements Governing the Binding of Small Molecules to a [Fe]-hydrogenase Mimic

[Fe]-hydrogenase, one of three types of hydrogenases, activates molecular hydrogen. Here, using DFT computations, we examine the electronic elements governing the binding of small ligands to a recently synthesized [Fe]-hydrogenase biomimic. Computed reaction free energies indicate that anionic species, such as CN- and H-, and acceptors, such as CO, bind favourably with the Fe centre. Ligands such as H2O, CH3CN, and H-2, however, do not bind iron. Protonation of an adjacent thiolate ligand on the mimic significantly increases the energies of ligand binding. Additional computational analysis reveals that the degree of electron donation from the ligand to the mimic correlates strongly with overall binding ability. The results give insights into the electronic elements of iron-small-molecule interaction in these model complexes

Natural inspirations for metal–ligand cooperative catalysis

In conventional homogeneous catalysis, supporting ligands act as spectators that do not interact directly with substrates. However, in metal–ligand cooperative catalysis, ligands are involved in facilitating reaction pathways that would be less favourable were they to occur solely at the metal centre. This catalysis paradigm has been known for some time, in part because it is at play in enzyme catalysis. For example, studies of hydrogenative and dehydrogenative enzymes have revealed striking details of metal–ligand cooperative catalysis that involve functional groups proximal to metal active sites. In addition to the more well-known [FeFe]-hydrogenase and [NiFe]-hydrogenase enzymes, [Fe]-hydrogenase, lactate racemase and alcohol dehydrogenase each makes use of cooperative catalysis. This Perspective highlights these enzymatic examples of metal–ligand cooperative catalysis and describes functional bioinspired molecular catalysts that also make use of these motifs. Although progress has been made in developing molecular catalysts, considerable challenges will need to be addressed before we have synthetic catalysts of practical value

Overcoming systematic DFT errors for hydrocarbon reaction energies

Despite the widespread use and numerous successful applications of density functional theory, descriptions of hydrocarbon reaction energies remain problematic. Illustrative examples include large underestimation of energies associated with alkane bond separation reactions and poor general description of intramolecular dispersion in hydrocarbons (e.g., B3LYP, MAD = 14.1 kcal mol-1). More recent, but not readily availably functionals, along with efficient posteriori corrections, not only show considerable improvement in the energy description of hydrocarbons but also help identify the sources of error in traditional DFT. Interactions in branched alkanes and compact hydrocarbons are adequately mimicked by systems compressed below their typical van der Waals distances. At these distances, standard DFT exchange functionals are overly repulsive for non-bonded density overlaps, and significant improvement is offered by the long-range corrected exchange functionals (e.g., LC-BLYP0.33, MAD = 5.5 kcal mol-1). For those systems, the neglect of long-range dispersion is found to be a critical shortcoming, as well as ‘‘overlap dispersion’’, for which non-negligible amounts are captured by the correlation functional. Accounting for the missing dispersion interactions is of key importance. Accordingly, most noteworthy improvements over standard functionals are obtained by using non-local van der Waals density functionals (e.g., LC-S-VV09, MAD = 3.6 kcal mol-1, rPW86-VV09, MAD = 5.8 kcal mol-1), a dispersion corrected double hybrid (B2PLYP-D, MAD = 2.5 kcal mol-1), or by the addition of an atom pairwise densitydependent dispersion correction to a standard functional (e.g., PBE-dDXDM, MAD = 0.8 kcal mol-1). To a lesser extent, the reduction of the delocalization error (e.g., MCY3, MAD = 6.3 kcal mol-1) or careful parameter fitting (e.g., M06-2X, MAD = 5.6 kcal mol-1) also lowers the errors

Alkynylation of Thiols with Ethynylbenziodoxolone (EBX) Reagents: alpha- or beta- pi-Addition?

The alkynylation of thiols with EthynylBenziodoXolone (EBX) reagents is a fast and chemoselective method for the synthesis of thioalkynes. Combined experimental and computational studies are reported, which led to the identification of a new mechanism for this reaction, proceeding via an initial sulfur iodine interaction followed by beta-addition, alpha-elimination, and a 1,2-shift. Depending on the substituent on the alkyne, this mechanism can be favored over the previously disclosed concerted alpha-addition rti pathway

Bimetallic Oxidative Addition in Nickel-Catalyzed Alkyl-Aryl Kumada Coupling Reactions

The mechanism of alkylaryl Kumada coupling catalyzed by the nickel pincer complex Nickamine was studied. Experiments using radical-probe substrates and DFT calculations established a bimetallic oxidative addition mechanism. Kinetic measurements showed that transmetalation rather than oxidative addition was the turnover-determining step. The transmetalation involved a bimetallic pathway

A Monometallic Iron(I) Organoferrate

Tetra-n-butylammonium (TBA) (eta(6)-biphenyl)diphenyfferrate was formed unexpectedly in the reaction of (TBA)(2)[Fe4S4Cl4] with an excess of phenyllithium. This complex belongs to a novel type of organoferrate

Room temperature decarboxylative cyanation of carboxylic acids using photoredox catalysis and cyanobenziodoxolones: a divergent mechanism compared to alkynylation

The one-step conversion of aliphatic carboxylic acids to the corresponding nitriles has been accomplished via the merger of visible light mediated photoredox and cyanobenziodoxolones (CBX) reagents. The reaction proceeded in high yields with natural and non-natural alpha-amino and alpha-oxy acids, affording a broad scope of nitriles with excellent tolerance of the substituents in the alpha position. The direct cyanation of dipeptides and drug precursors was also achieved. The mechanism of the decarboxylative cyanation was investigated both computationally and experimentally and compared with the previously developed alkynylation reaction. Alkynylation was found to favor direct radical addition, whereas further oxidation by CBX to a carbocation and cyanide addition appeared more favorable for cyanation. A concerted mechanism is proposed for the reaction of radicals with EBX reagents, in contrast to the usually assumed addition elimination process

Bimetallic Oxidative Addition Involving Radical Intermediates in Nickel-Catalyzed Alkyl-Alkyl Kumada Coupling Reactions

Many nickel-based catalysts have been reported for cross-coupling reactions of nonactivated alkyl halides. The mechanistic understanding of these reactions is still primitive. Here we report a mechanistic study of alkyl-alkyl Kumada coupling catalyzed by a preformed nickel(II) pincer complex ([(N2N)Ni-Cl]). The coupling proceeds through a radical process, involving two nickel centers for the oxidative addition of alkyl halide. The catalysis is second-order in Grignard reagent, first-order in catalyst, and zero-order in alkyl halide. A transient species, [(N2N)Ni-alkyl(2)] (alkyl(2)-MgCl), is identified as the key intermediate responsible for the activation of alkyl halide, the formation of which is the turnover-determining step of the catalysis

General and Practical Formation of Thiocyanates from Thiols

A new method for the cyanation of thiols and disulfides using cyanobenziodoxol(on)e hypervalent iodine reagents is described. Both aliphatic and aromatic thiocyanates can be accessed in good yields in a few minutes at room temperature starting from a broad range of thiols with high chemioselectivity. The complete conversion of disulfides to thiocyanates was also possible. Preliminary computational studies indicated a low energy concerted transition state for the cyanation of the thiolate anion or radical. The developed thiocyanate synthesis has broad potential for various applications in synthetic chemistry, chemical biology and materials science