Reversible O-H Bond Activation by Tripodal tris(Nitroxide) Aluminum and Gallium Complexes.

Herein, we report the preparation and characterization of the Group 13 metal complexes of a tripodal tris(nitroxide)-based ligand, designated (TriNOx3-)M (M = Al (1), Ga (2), In (3)). Complexes 1 and 2 both activate the O-H bond of a range of alcohols spanning a ∼10 pKa unit range via an element-ligand cooperative pathway to afford the zwitterionic complexes (HTriNOx2-)M-OR. Structures of these alcohol adduct products are discussed. We demonstrate that the thermodynamic and kinetic aspects of the reactions are both influenced by the identity of the metal, with 1 having higher reaction equilibrium constants and proceeding at a faster rate relative to 2 for any given alcohol. These parameters are also influenced by the pKa of the alcohol, with more acidic alcohols reacting both to more completion and faster than their less acidic counterparts. Possible mechanistic pathways for the O-H activation are discussed.

Ni-Catalyzed Enantioselective Intramolecular Mizoroki-Heck Reaction for the Synthesis of Phenanthridinone Derivatives.

A Ni-catalyzed enantioselective intramolecular Mizoroki-Heck reaction has been developed to transform symmetrical 1,4-cyclohexadienes with attached aryl halides into phenanthridinone analogues containing quaternary stereocenters. Herein, we report important advances in reaction optimization enabling control of unwanted proto-dehalogenation and alkene reduction side products. Moreover, this approach provides direct access to six-membered ring heterocyclic systems bearing all-carbon quaternary stereocenters, which have been much more challenging to form enantioselectively with nickel-catalyzed Heck reactions. A wide range of substrates were demonstrated to work in good to excellent yields. Good enantioselectivity was demonstrated using a new synthesized chiral iQuinox-type bidentate ligand (L27). The sustainability, low price of nickel catalysts, and significantly faster reaction rate (1 h) versus that of a recently reported palladium-catalyzed reaction (20 h) make this process an attractive alternative.

Stereoelectronic Features of a Complex Ketene Dimerization Reaction.

The amidation reaction of a tetrahydroisoquinolin-1-one-4-carboxylic acid is a key step in the multi-kilogram-scale preparation of the antimalarial drug SJ733, now in phase 2 clinical trials. In the course of investigating THIQ carboxamidations, we found that propanephosphonic acid anhydride (T3P) is an effective reagent, although the yield and byproducts vary with the nature and quantity of the base. As a control, the T3P reaction of a 3-(2-thienyl) THIQ was performed in the absence of the amine, and the products were characterized: among them are three dimeric allenes and two dimeric lactones. A nucleophile-promoted ketene dimerization process subject to subtle steric and stereoelectronic effects accounts for their formation. Two novel monomeric products, a decarboxylated isoquinolone and a purple, fused aryl ketone, were also isolated, and mechanisms for their formation from the ketene intermediate are proposed.

Re-Examination of Some Carbocations. Structures, Energies, and Charge Distributions.

Chemists have had a long-standing interest in reactive intermediates such as carbenes, carbon radicals, carbanions, and carbocations. Carbocations are an interesting part of this group because of their tendency to undergo rearrangement, sometimes forming bridged ions, as well as their ability in many cases of spreading out the positive charge over several atoms. We have re-examined some of these cases using high-level compound procedures, W1BD and G4, as well as by considering the charge distributions making use of the Hirshfeld method that has been shown to uniquely correlate with several types of experimental data.

Increase in Strain Energy during Conversion of [4.4.4.5]Fenestrane to [4.4.4.4]Fenestrane: a Method for Estimating the Heats of Formation of Hydrocarbons and Their Derivatives from Ab Initio Energies.

Our interest in fenestranes led us to wonder how large the change in strain energy with changes in the ring size might be. This led us to consider if satisfactory estimates of heat of formation could be easily derived from ab initio calculated energies. We started by examining 21 hydrocarbons having well-determined heats of formation via calculations of their enthalpies using W1BD, G4, CBS-APNO, CBS-QB3, and M062X. Making use of the molecular formula and an initial estimate of the energy of a hydrogen atom and of a carbon atom, along with the ab initio enthalpy, we calculated their heats of formation. The carbon energy parameter was adjusted slightly for each model to get the best fit between experiment and our estimate. This approach worked out very well giving an root mean square error of about 0.4 kcal/mol for most methods. This approach was also extended to a larger group of hydrocarbons, and the results were found to be generally useful. The extension to O and N compounds also was examined giving equally good results for the O-containing compounds but somewhat less satisfactory with N-containing compounds. In use, the procedure requires only the molecular formula, the calculated energy, and C, H, O, and N atomic constants given in the tables.

Synthesis of Trialkylamines with Extreme Steric Hindrance and Their Decay by a Hofmann-like Elimination Reaction.

A number of amines with three bulky alkyl groups at the nitrogen, which surpass the steric crowding of triisopropylamine considerably, were prepared by using different synthetic methods. It turned out that treatment of N-chlorodialkylamines with organometallic compounds, for example, Grignard reagents, in the presence of a major excess of tetramethylenediamine offered the most effective access to the target compounds. The limits of this method were also tested. The trialkylamines underwent a dealkylation reaction, depending on the degree of steric stress, even at ambient temperature. Because olefins were formed in this transformation, it showed some similarity with the Hofmann elimination. However, the thermal decay of sterically overcrowded tertiary amines was not promoted by bases. Instead, this reaction was strongly accelerated by protic conditions and even by trace amounts of water. Reaction mechanisms, which were analyzed with the help of quantum chemical calculations, are suggested to explain the experimental results.

Evaluation of 1,1-cyclopropylidene as a thioether isostere in the 4-thio-thienopyrimidine (TTP) series of antimalarials.

The 4-(heteroarylthio)thieno[2,3-d]pyrimidine (TTP) series of antimalarials, represented by 1 and 17, potently inhibit proliferation of the 3D7 strain of P. falciparum (EC50 70-100 nM), but suffer from oxidative metabolism. The 1,1-cyclopropylidene isosteres 6 and 16 were designed to obviate this drawback. They were prepared by a short route that features a combined Peterson methylenation / cyclopropanation transformation of, e. g., ketone 7. Isosteres 6 and 16 possess significantly attenuated antimalarial potency relative to parents 1 and 17. This outcome can be rationalized based on the increased out-of-plane steric demands of the latter two. In support of this hypothesis, the relatively flat ketone 7 retains some of the potency of 1, even though it appears to be a comparatively inferior mimic with respect to electronics and bond lengths and angles. We also demonstrate crystallographically and computationally an apparent increase in the strength of the intramolecular sulfur hole interaction of 1 upon protonation.

Spontaneous transfer of chirality in an atropisomerically enriched two-axis system.

One of the most well-recognized stereogenic elements in a chiral molecule is an sp(3)-hybridized carbon atom that is connected to four different substituents. Axes of chirality can also exist about bonds with hindered barriers of rotation; molecules containing such axes are known as atropisomers. Understanding the dynamics of these systems can be useful, for example, in the design of single-atropisomer drugs or molecular switches and motors. For molecules that exhibit a single axis of chirality, rotation about that axis leads to racemization as the system reaches equilibrium. Here we report a two-axis system for which an enantioselective reaction produces four stereoisomers (two enantiomeric pairs): following a catalytic asymmetric transformation, we observe a kinetically controlled product distribution that is perturbed from the system's equilibrium position. As the system undergoes isomerization, one of the diastereomeric pairs drifts spontaneously to a higher enantiomeric ratio. In a compensatory manner, the enantiomeric ratio of the other diastereomeric pair decreases. These observations are made for a class of unsymmetrical amides that exhibits two asymmetric axes--one axis is defined through a benzamide substructure, and the other axis is associated with differentially N,N-disubstituted amides. The stereodynamics of these substrates provides an opportunity to observe a curious interplay of kinetics and thermodynamics intrinsic to a system of stereoisomers that is constrained to a situation of partial equilibrium.

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation.

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state 1 H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.

Ring Expansion of Alkylidenecarbenes Derived from Lactams, Lactones, and Thiolactones into Strained Heterocyclic Alkynes: A Theoretical Study.

Strained cycloalkynes are of considerable interest to theoreticians and experimentalists, and possess much synthetic value as well. Herein, a series of cyclic alkylidenecarbenes-formally obtained by replacing the carbonyl oxygen of four-, five-, and six-membered lactams, lactones, and thiolactones with a divalent carbon-were modeled at the CCSD(T)/cc-pVTZ//B3LYP/6-311+G** and CCSD(T)/cc-pVTZ//CCSD/6-311+G** levels of theory. The singlet carbenes were found to be more stable than the triplets. The strained heterocyclic alkynes formed by ring expansion of these singlet carbenes were also modeled. Interestingly, the C≡C bonds in the five-membered heterocycles, obtained from the rearrangement of ß-lactam- and ß-lactone-derived alkylidenecarbenes, displayed lengths intermediate between formal double and triple bonds. Furthermore, 2-(1-azacyclobutylidene)carbene was found to be nearly isoenergetic with its ring-expanded isomer, and 1-oxacyclopent-2-yne was notably higher in energy than its precursor carbene. In all other cases, the cycloalkynes were lower in energy than the corresponding carbenes. The transition states for ring-expansion were always lower for the 1,2-carbon shifts than for 1,2-nitrogen or oxygen shifts, but higher than for the 1,2-sulfur shifts. These predictions should be verifiable using carbenes bearing appropriate isotopic labels. Computed vibrational spectra for the carbenes, and their ring-expanded isomers, are presented and could be of value to matrix isolation experiments.

Amide Neighbouring-Group Effects in Peptides: Phenylalanine as Relay Amino Acid in Long-Distance Electron Transfer.

In nature, proteins serve as media for long-distance electron transfer (ET) to carry out redox reactions in distant compartments. This ET occurs either by a single-step superexchange or through a multi-step charge hopping process, which uses side chains of amino acids as stepping stones. In this study we demonstrate that Phe can act as a relay amino acid for long-distance electron hole transfer through peptides. The considerably increased susceptibility of the aromatic ring to oxidation is caused by the lone pairs of neighbouring amide carbonyl groups, which stabilise the Phe radical cation. This neighbouring-amide-group effect helps improve understanding of the mechanism of extracellular electron transfer through conductive protein filaments (pili) of anaerobic bacteria during mineral respiration.

Atomic Charges.

The problem of deriving atomic charges from the results of ab Initio MO calculations has been studied by the use of several reported methods: Mulliken population analysis, the minimal basis set (MBS) procedure, the natural population analysis (NPA), two electrostatic potential fitting methods, M-K and ChelpG, the Hirshfeld population analysis, and CM5 (charge model 5), which is related to the Hirshfeld method. The first set of studies were concerned with hydrogen charges. It was found that the MBS charges were linearly related to the Hirshfeld charges. The Hirshfeld, CM5, and MBS methods, but not the others, provided an excellent correlation for H atomic charge with the H-C-H bond angle, and with calculated gas-phase acidity. The two methods that were linearly related and gave hydrogen charges in agreement with an experimental study of partially deuterated methanes are MBS and Hirshfeld. In order to see which of the two methods is the more satisfactory, the methanol dimer was examined. The calculated H bond energy was 6.2 kcal/mol, which was in good agreement with studies of hydrogen bonds. The Coulombic interaction for the O···H bond was estimated using the MBS and Hirshfeld charges. The latter gave a calculated energy of 3-6 kcal/mol, whereas MBS gave an energy of ∼35 kcal/mol. Clearly, the Hirshfeld method is more satisfactory and should be the method of choice.

How the Arrangement of Alkyl Substituents Affects the Stability of Delocalized Carbocations.

G-4 calculations are used to explore which carbon atoms of methylated butadienes, methylated cyclopentadienes, and methylated benzenes are most readily protonated to yield delocalized allyl and pentadienyl cations. While it is not surprising that alkylation of the positions bearing formal positive charge stabilizes these cations, several other effects are less obvious. First, alkylation of positions in the delocalized cation that do not bear formal charge is beneficial, to an extent about a quarter to a third as great as at charged positions. Second, alkylation of the position receiving the proton disfavors protonation. Finally, at least in the acyclic systems, the more symmetrical substitution pattern that is 2° at both ends is moderately preferred to the less symmetrical pattern that is 3° at one end and 1° at the other. Taking all three of these factors into account, as well as substitution at the formally charged centers, models the stability of all 94 delocalized cations quite well.

Butadiene and Heterodienes Revisited.

Surprising features in a recently published high-level calculation of the rotational profile of butadiene led us to compare butadiene with a set of 17 heterodienes. The rotational profiles for this large group of compounds varied widely, thereby possessing a high information content. These data were subjected to a Fourier analysis yielding 1- through 6-fold terms: the one-fold terms represent the change in steric energy on going from 180° to 0°, while the changes in the 2-fold terms correspond to the expected change in π-delocalization energy with structure; the 3-fold terms were significant and found to be linearly correlated to the average of the atomic charges of the atoms at the central single bond of the cis-forms, but their origins are still not clear; we propose a novel 1,4 π-interactions that may account for this phenomenon. The 4-fold terms were at times comparable in magnitude to the 3-fold terms but overall appeared to mainly modify the 3-fold terms slightly without introducing any qualitatively new features. The 5- and 6-fold terms were negligible.

Methoxymethane C-O Bond Strengths: Do Their Changes Result from Hyperconjugation or Polar Effects?

The methoxymethanes have been studied and compared with the fluoromethanes. The energies and atomic charges were calculated using MP2/aug-cc-pVTZ, and the group separation energies and bond dissociation enthalpies were calculated using CBS-QB3. The group separation energies are endothermic and the BDE increases with additional substitution as a result of the increase in charge at the central carbon. The greater charge leads to a stronger bond to the new substituent as well as to the original substituents. With the methoxymethanes, there is a linear relationship between the BDE and the atomic charge at C. The energies of the several methoxymethane conformers were calculated, and their energies usually increase with increasing values of the electronic spatial extent in accord with a proposal by Gillespie. The role of hyperconjugation in these cases is not settled.

Rotamer-Restricted Fluorogenicity of the Bis-Arsenical ReAsH.

Fluorogenic dyes such as FlAsH and ReAsH are used widely to localize, monitor, and characterize proteins and their assemblies in live cells. These bis-arsenical dyes can become fluorescent when bound to a protein containing four proximal Cys thiols-a tetracysteine (Cys4) motif. Yet the mechanism by which bis-arsenicals become fluorescent upon binding a Cys4 motif is unknown, and this nescience limits more widespread application of this tool. Here we probe the origins of ReAsH fluorogenicity using both computation and experiment. Our results support a model in which ReAsH fluorescence depends on the relative orientation of the aryl chromophore and the appended arsenic chelate: the fluorescence is rotamer-restricted. Our results do not support a model in which fluorogenicity arises from the relief of ring strain. The calculations identify those As-aryl rotamers that support fluorescence and those that do not and correlate well with prior experiments. The rotamer-restricted model we propose is supported further by biophysical studies: the excited-state fluorescence lifetime of a complex between ReAsH and a protein bearing a high-affinity Cys4 motif is longer than that of ReAsH-EDT2, and the fluorescence intensity of ReAsH-EDT2 increases in solvents of increasing viscosity. By providing a higher resolution view of the structural basis for fluorogenicity, these results provide a clear strategy for the design of more selective bis-arsenicals and better-optimized protein targets, with a concomitant improvement in the ability to characterize previously invisible protein conformational changes and assemblies in live cells.

How alkyl halide structure affects E2 and SN2 reaction barriers: E2 reactions are as sensitive as SN2 reactions.

High-level electronic structure calculations, including a continuum treatment of solvent, are employed to elucidate and quantify the effects of alkyl halide structure on the barriers of SN2 and E2 reactions. In cases where such comparisons are available, the results of these calculations show close agreement with solution experimental data. Structural factors investigated include α- and ß-methylation, adjacency to unsaturated functionality (allyl, benzyl, propargyl, α to carbonyl), ring size, and α-halogenation and cyanation. While the influence of these factors on SN2 reactivity is mostly well-known, the present study attempts to provide a broad comparison of both SN2 and E2 reactivity across many cases using a single methodology, so as to quantify relative reactivity trends. Despite the fact that most organic chemistry textbooks say far more about how structure affects SN2 reactions than about how it affects E2 reactions, the latter are just as sensitive to structural variation as are the former. This sensitivity of E2 reactions to structure is often underappreciated.

N-methylimidazole promotes the reaction of homophthalic anhydride with imines.

The addition of N-methylimidazole (NMI) to the reaction of homophthalic anhydride with imines such as pyridine-3-carboxaldehyde-N-trifluoroethylimine (9) reduces the amount of elimination byproduct and improves the yield of the formal cycloadduct, tetrahydroisoquinolonic carboxylate 10. Carboxanilides of such compounds are of interest as potential antimalarial agents. A mechanism that rationalizes the role of NMI is proposed, and a gram-scale procedure for the synthesis and resolution of 10 is also described.

Optimized end-stacking provides specificity of N-methyl mesoporphyrin IX for human telomeric G-quadruplex DNA.

N-methyl mesoporphyrin IX (NMM) is exceptionally selective for G-quadruplexes (GQ) relative to duplex DNA and, as such, has found a wide range of applications in biology and chemistry. In addition, NMM is selective for parallel versus antiparallel GQ folds, as was recently demonstrated in our laboratory. Here, we present the X-ray crystal structure of a complex between NMM and human telomeric DNA dAGGG(TTAGGG)(3), Tel22, determined in two space groups, P2(1)2(1)2 and P6, at 1.65 and 2.15 Å resolution, respectively. The former is the highest resolution structure of the human telomeric GQ DNA reported to date. The biological unit contains a Tel22 dimer of 5'-5' stacked parallel-stranded quadruplexes capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. NMM is capable of adjusting its macrocycle geometry to closely match that of the terminal G-tetrad required for efficient π-π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. On the basis of the biochemical data, binding of NMM to Tel22 does not rely on relatively nonspecific electrostatic interactions, which characterize most canonical GQ ligands, but rather it is hydrophobic in nature. The structural features observed in the NMM-Tel22 complex described here will serve as guidelines for developing new quadruplex ligands that have excellent affinity and precisely defined selectivity.

Quantum-chemical simulation of 1H NMR spectra. 2. Comparison of DFT-based procedures for computing proton-proton coupling constants in organic molecules.

The performance of 250 different computational protocols (combinations of density functionals, basis sets and methods) was assessed on a set of 165 well-established experimental (1)H-(1)H nuclear coupling constants (J(H-H)) from 65 molecules spanning a wide range of "chemical space". Thereby we found that, if one uses core-augmented basis sets and allows for linear scaling of the raw results, calculations of only the Fermi contact term yield more accurate predictions than calculations where all four terms that contribute to J(H-H) are evaluated. It turns out that B3LYP/6-31G(d,p)u+1s is the best (and, in addition, one of the most economical) of all tested methods, yielding predictions of J(H-H) with a root-mean-square deviation from experiment of less than 0.5 Hz for our test set. Another method that does similarly well, without the need for additional 1s basis functions, is B3LYP/cc-pVTZ, which is, however, ca. 8 times more "expensive" in terms of CPU time. A selection of the better methods was tested on a probe set comprising 61 J(H-H) values from 37 molecules. In this set we also included five molecules where conformational averaging is required. The rms deviations were better than or equal to those with the training set, which indicates that the method we recommend is generally applicable for organic molecules. We give instructions on how to carry out calculations of (1)H chemical shifts and J(H-H) most economically and provide scripts to extract the relevant information from the outputs of calculations with the Gaussian program in clearly arranged form, e.g., to feed them into programs for simulating entire (1)H NMR spectra.