Sinisa Vukovic

How Amidoximate Binds the Uranyl Cation

This study identifies how the amidoximate anion, AO, interacts with the uranyl cation, UO(2)(2+). Density functional theory calculations have been used to evaluate possible binding motifs in a series of [UO(2)(AO)(x)(OH(2))(y)](2-x) (x = 1-3) complexes. These motifs include monodentate binding to either the oxygen or the nitrogen atom of the oxime group, bidentate chelation involving the oxime oxygen atom and the amide nitrogen atom, and η(2) binding with the N-O bond. The theoretical results establish the η(2) motif to be the most stable form. This prediction is confirmed by single-crystal X-ray diffraction of UO(2)(2+) complexes with acetamidoxime and benzamidoxime anions.

De novo structure-based design of bis-amidoxime uranophiles.

This paper presents a computational approach to the deliberate design of host architectures that recognize and bind specific guests. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential structures. The efficacy of this computer-aided design methodology is illustrated with a search for bis-amidoxime chelates that are structurally organized for complexation with the uranyl cation.

Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

The ability to predict the equilibrium constants for the formation of 1:1 uranyl/ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We use density functional theory (B3LYP) and the integral equation formalism polarizable continuum model (IEF-PCM) to compute aqueous stability constants for UO2(2+) complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root-mean-square deviation from experiment <1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono- and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelating capability to uranyl.

N-pyrrolylketene: a nonconjugated heteroarylketene.

N-Pyrrolylketene (5) is calculated to be destabilized and nonconjugated, with a preferred geometry with the pyrrolyl ring orthogonal to the ketenyl group. Ketene 5 is generated from N-pyrrolylacetic acid (7) with use of Mukaiyamas reagent, and reacts with imines forming β-lactams 10, with a product ratio correlation of log(cis/trans) with σ(+). Photolysis of N-diazoacetylpyrrole (14) in MeOH gives methyl N-pyrrolylacetate (15) from 5 and also ester 17, evidently by trapping of 2-(1-pyrrolylketene) (21), formed by a new vinylogous Wolff rearrangement.

Edge versus interior in the chemical bonding and magnetism of zigzag edged triangular graphene molecules

Ab initio density functional theory calculations show that the CC bond lengths fall into three distinct groups: core, apex, and edge, irrespective of whether the molecular center is a single atom or a C(6)-ring. The core, with a geometry that approximates infinite graphene, extends to the penultimate triangular row of carbon atoms, except in the vicinity of an apex. Impressed on the core bonds starting at the center is a small increasing length oscillation. The perimeter CC bonds joined at the apex are the shortest in the molecule. The edge carbon atoms are separated from interior atoms by the longest bonds in the molecule. The spin density localized primarily on edge (not apex) carbons with attached hydrogen (A-sublattice) is likely the highest attainable in any graphene molecule. The CC bonds in the high spin section of the edges are uniform in length and longer than perimeter CC bonds in the zigzag edged linear acenes, hexangulenes, annulenes, and benzene. This is attributed to the large number of edge localized nonbonding molecular orbitals (NBMOs) that sequestered pi-charge making it unavailable for bonding.

Spiro-Aziridine and Bislactam Formation from Bisketene−Imine Cycloadditions

1,2-Bisketenes 6 react with imines PhCHNAr, (E)-2, forming spiro-aziridines 7. DFT computations indicate that this occurs by nucleophilic attack of the imine on the carbonyl carbon of the more reactive arylketene moiety, followed by cyclization, and not by prior cyclization of the 1,2-bisketene forming a carbene lactone intermediate. Computations also indicate that the previously studied bisketene 10 from benzocyclobutadiene 9 is 4.0 kcal/mol less stable than carbene lactone 12 that would result from cyclization but that the failure to observe 12 results from a lower barrier for 10 to instead revert to 9. 1,2-, 1,3-, and 1,4-Bisketenylbenzenes 16, 19, and 22 react with imines forming bis(β-lactams), with a preference for formation of mixtures of trans, trans chiral (±) and achiral diastereomeric products.

Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

Pyridylketenes: Structure reactivity effects in nucleophilic and radical addition

2-, 3-, and 4-Pyridylketenes have been generated in CH3CN by photochemical Wolff rearrangements and identified by their ketenyl absorption in the infrared at 2127, 2125, and 2128 cm–1, respectively. Reaction of these pyridylketenes with n-BuNH2 results in the formation of intermediate amide enols from the 3- and 4-pyridylketenes, which are then converted to the corresponding pyridylacetamides. However , 2-pyridylketene forms a long-lived 1,2-dihydropyridine intermediate stabilized by an intramolecular hydrogen bond, and this is converted to the 2-pyridylacetamide with a rate constant 107 less than those for the conversion of the amide enols from the 3- and 4-pyridylketenes to amides. Hydration of the pyridylketenes results in the formation of an acid enol intermediate in the case of the 3-isomer, while the 2- and 4-isomers form longer-lived dihydropyridines. The pyridylketenes react with the stable free radical tetramethylpiperidinyloxyl (TEMPO,TO) forming 1,2-diaddition products ArCH(OT)CO2T.

Ketene reactions with tertiary amines.

Tertiary amines react rapidly and reversibly with arylketenes in acetonitrile forming observable zwitterions, and these undergo amine catalyzed dealkylation forming N,N-disubstituted amides. Reactions of N-methyldialkylamines show a strong preference for methyl group loss by displacement, as predicted by computational studies. Loss of ethyl groups in reactions with triethylamine also occur by displacement, but preferential loss of isopropyl groups in the phenylketene reaction with diisopropylethylamine evidently involves elimination. Quinuclidine rapidly forms long-lived zwitterions with arylketenes, providing a model for catalysis by cinchona and related alkaloids in stereoselective additions to ketenes.

Structural Effects on Interconversion of Oxygen-Substituted Bisketenes and Cyclobutenediones

Cyclobutenediones 5 disubstituted with HO (a), MeO (b), EtO (c), i-PrO (d), t-BuO (e), PhO (f), 4-MeOC6H4O (g), 4-O2NC6H4O (h), and 3,4-bridging OCH2CH2O (i) substituents upon laser flash photolysis gave the corresponding bisketenes 6a-i, as detected by their distinctive doublet IR absorptions between 2075 and 2106 and 2116 and 2140 cm-1. The reactivities in ring closure back to the cyclobutenediones were greatest for the group 6b-e, with the highest rate constant of 2.95 x 10(7) s-1 at 25 degrees C for 6e (RO = t-BuO) in isooctane, were less for 6a (RO = OH, k = 2.57 x 10(6) s-1 in CH3CN), while 6f-i were the least reactive, with the lowest rate constant of 3.8 x 10(4) s-1 in CH3CN for 6h (RO = 4-O2NC6H4O). The significantly reduced rate constants for 6f-i are attributed to diminution of the electron-donating ability of oxygen to the cyclobutenediones 5f-h by the ArO substituents compared to alkoxy groups and to angle strain in the bridged product cyclobutenedione 5i. The reactivities of the ArO-substituted bisketenes 6f-h in CH3CN varied by a factor of 50 and gave an excellent correlation of the observed rate constants log k with the sigma p constants of the aryl substituents. Computational studies at the B3LYP/6-31G(d) level of ring-closure barriers are consistent with the measured reactivities. Photolysis of squaric acid (5a) in solution provides a convenient preparation of deltic acid (7).