NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity.

Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the ß-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for ß-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.

Protonation states of the tryptophan synthase internal aldimine active site from solid-state NMR spectroscopy: direct observation of the protonated Schiff base linkage to pyridoxal-5'-phosphate.

The acid-base chemistry that drives catalysis in pyridoxal-5'-phosphate (PLP)-dependent enzymes has been the subject of intense interest and investigation since the initial identification of PLP's role as a coenzyme in this extensive class of enzymes. It was first proposed over 50 years ago that the initial step in the catalytic cycle is facilitated by a protonated Schiff base form of the holoenzyme in which the linking lysine ε-imine nitrogen, which covalently binds the coenzyme, is protonated. Here we provide the first (15)N NMR chemical shift measurements of such a Schiff base linkage in the resting holoenzyme form, the internal aldimine state of tryptophan synthase. Double-resonance experiments confirm the assignment of the Schiff base nitrogen, and additional (13)C, (15)N, and (31)P chemical shift measurements of sites on the PLP coenzyme allow a detailed model of coenzyme protonation states to be established.

Homology modeling of cannabinoid receptors: discovery of cannabinoid analogues for therapeutic use.

Cannabinoids represent a promising class of compounds for developing novel therapeutic agents. Since the isolation and identification of the major psychoactive component Δ(9)-THC in Cannabis sativa in the 1960s, numerous analogues of the classical plant cannabinoids have been synthesized and tested for their biological activity. These compounds primarily target the cannabinoid receptors 1 (CB1) and Cannabinoid receptors 2 (CB2). This chapter focuses on CB1. Despite the lack of crystal structures for CB1, protein-based homology modeling approaches and molecular docking methods can be used in the design and discovery of cannabinoid analogues. Efficient synthetic approaches for therapeutically interesting cannabinoid analogues have been developed to further facilitate the drug discovery process.

Thermal isomerization of cannabinoid analogues.

Thermal isomerization of CBC(an) to THC(an) [nonaromatic analogues of plant cannabinoids cannabichromene (CBC) and Delta(1)-tetrahydrocannabinol (THC), respectively] is predicted in silico and demonstrated experimentally. Density functional theory calculations support a similar isomerization mechanism for the corresponding plant cannabinoids. Docking studies suggest that THC(an), although nonaromatic, has a CB(1) receptor binding affinity similar to that of natural THC.

Molecular springs, muscles, rheostats, and precessing gyroscopes: from review to preview.

The concepts of molecular springs and gyroscopes have existed for some time, and there have been numerous reports published about these fascinating topics. Here we describe our interest in this topic, reviewing our initial progress. This is not a complete story, rather an offering of synthetic strategies, interesting molecular structures, observations, and possibilities. In many cases, the "properties" component of the structure-property relationship for a given compound is the result of a computational prediction. Given the present state of theoretical chemistry, a computer's predictive power can far exceed that which can be presently accomplished by existing experimental analytical means. The theoretical results reported here allude to intriguing possibilities. Hopefully, this intrigue will help catalyze the development of definitive, albeit rather esoteric, single-molecule analytical experiments. The intentionally speculative nature of this review is intended to stimulate new challenges for and perspectives from those in related fields of interest; hopefully presenting a preview of what is to come.

Visualization method to predict the nucleophilic asymmetric induction of prochiral electrophiles.

[reaction: see text] This work focuses on the development of a simple technique to accurately predict and visualize the diastereoselectivity of ketone, aldehyde, and allyl chloride reductions by mapping electrostatic potential onto the frontier molecular orbital involved in the reduction. A distinct difference of electrostatic potential on the faces of the carbonyl can be used to predict the face of nucleophilic attack with a high level of accuracy.

1,4-Addition of benzene to a dihydrocyclopent[a]indene diradical: synthesis and DFT study.

Photochemical cyclization of compound 1, a homoenediyne (-CCC=CCH2CC-) bearing two ethynylanthracene chromophores, yields two isomeric dihydrocyclopent[a]indene ring systems, spiro-fused to the 9-position of a 9,10-dihydroanthracene moiety. Evidence of a photochemically initiated diradical cyclization pathway is proposed on the basis of (i) hydrogen abstraction from reaction with 1,4-cyclohexadiene (1,4-CHD) and (ii) the observation of 1,4-addition of benzene (solvent). The reaction was further analyzed by a complete density functional theory (DFT) study, using an unrestricted approach (UBLYP) with a 6-31G* basis set for the open-shell triplet states of the reactants, products, and diradical intermediates to model the photochemical nature of observed transformation. A mechanism detailing the observed cyclization/addition reaction is proposed.

Helical sexithiophenes: an experimental and theoretical study implicating the alternating 2,2':3,3' regioisomer as a reliable helical motif.

Perchlorinated sexithiophene regioisomer, 2,2' '' ''-diX-5,5',5' ',5' '',5' '' ',5' '' ''-hexachloro-[3,3';2',2' ';3' ',3' '';2' '',2' '' ';3' '' ',3' '' '']sexithiophene (compound 1), demonstrates a reliable helical conformation in the solid state, regardless of a broad range of substituents, X. The synthesis and composition of compound 1a (X = H) synthetically accommodates substituent diversity at the 2- and 2' '' ''-sites. X-ray crystal structures (X = H, Cl, Br) and theoretical geometry optimizations (X = H, Cl, Br, I, Me, Et, t-Bu, and Ph) both confirm that the helical state, a conformation likely dictated by internal torsional strain, is predominant and unaffected by substituent X. It is predicted (ACID/B3LYP/6-31G(d) calculations and UV-visible spectra) that the helical structure exists as a fully conjugated system.

Synthesis and photochromic properties of molecules containing [e]-annelated dihydropyrenes. Two and three way pi-switches based on the dimethyldihydropyrene-metacyclophanediene valence isomerization.

The syntheses of several new simple negative, a simple positive, and multiple negative photochromes containing the dihydropyrene-cyclophanediene photochromic system are described. The photo-openings of the negative photochromes, the [e]-annelated benzo (7), naphtho (9), anthro (11), furano (19), and triphenyleno (15) derivatives of the parent 2,7-di-tert-butyl-trans-10b,10c-dimethyl-dihydropyrene (5), as well as its 4,5-dibromo derivative (13), are described to give the corresponding cyclophanedienes, as well as their photoclosures and thermal closures back to the dihydropyrenes. These are compared to the results obtained for the positive photochrome dibenzo[e,l]dihydropyrene (21) and to the bis(dihydropyreno)chrysene (44) and the (dihydropyrenobenzo)(benzo)metacyclophanediene (47) photochromes, which have more than one photochromic switch present and thus have more than a simple "on-off" state. Thermodynamic data are obtained for the thermal closing reactions. The anthrodihydropyrene (12) has the fastest thermal closing (tau(1/2) = 20 min), while the furanodihydropyrene (19') has the slowest (tau(1/2) = 63 h) at 46 degrees C. An electrochemical readout of the state of the switch is demonstrated for the benzodihydropyrene (7).

Classic annulenes, nonclassical applications.

This Account details the application of [n]annulenes as functional building blocks for electromechanical actuators, double-helical ladder polymers, and protecting groups for supramolecular interactions. Specifically, redox-induced conformational changes occurring in [8]annulenes are utilized as the transducing element in polymeric electromechanical actuators. Conversely, rigid [8]annulenes are utilized as double-helical fragments for the synthesis of double-helical octaaryl macromolecules. Last, Dewar benzenes are prepared from [4 + 2] cycloadditions (where the 4pi component is a [4]annulene). The potential of using Dewar benzenes as protecting groups for [6]annulne-[6]annulene supramolecular interactions is exemplified by demonstration of photolithographic crystallization (amorphous [4]annulene --> crystalline [6]annulene) on a surface, followed by subsequent X-ray analysis of the resulting [6]annulene crystals.

Tetra[2,3-thienylene]: a building block for single-molecule electromechanical actuators.

Tetra(2,3-thienylene) is a thiophene-fused [8]annulene capable of undergoing redox-induced dimensional changes. The feasibility of efficiently translating this intrinsic function into a single polymeric electromechanical actuator is investigated by both experiment and density functional theory (B3LYP 6-31G[d,p]). A study of tetra(2,3-thienylene) and its homodimer reveal that redox-induced conformational change is conserved upon dimerization, a result that implicates similar behavior in the corresponding polymer. Theoretical predictions yield a maximum redox-induced dimensional change of 5.92% per repeat unit for the homodimer. Cyclic voltammetry reveals complete reversibility for the corresponding redox cycle. The latter two facts establish tetra(2,3-thienylene) as a suitable building block for single-molecule electromechanical actuators.