Stereoselectivity and expanded substrate scope of an engineered PLP-dependent aldolase.
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Aldehyde-Lyases↗
Biomedical subjects
Kim K Baldridge
Publications and source records attributed to Kim K Baldridge.
Exploring biomolecular machines: energy landscape control of biological reactions.
For almost 15 years, our Pathway model has been the most powerful model in terms of predicting the tunnelling mechanism for electron transfer (ET) in biological systems, particularly proteins. Going beyond the conventional Pathway models, we have generalized our method to understand how protein dynamics modulate not only the Franck-Condon factor, but also the tunnelling matrix element. We have demonstrated that when interference among pathways modulates the electron tunnelling interactions in proteins (particularly destructive interference), dynamical effects are of critical importance. Tunnelling can be controlled by protein conformations that lie far from equilibrium-those that minimize the effect of destructive interference during tunnelling, for example. In the opposite regime, electron tunnelling is mediated by one (or a few) constructively interfering pathway tubes and dynamical effects are modest. This new mechanism for dynamical modulation of the ET rate has been able to explain and/or predict several rates that were later confirmed by experiment. However, thermal fluctuations can also affect these molecular machines in many other ways. For example, we show how global transformations, which control protein functions such as allostery, may involve large-scale motion and possibly partial unfolding during the reaction event.
Azurin↗
d8 rhodium and iridium complexes of corannulene.
[(COE)2M]+ fragments (M = Rh, Ir; COE = cyclooctene) react with corannulene to give eta6-bound complexes [(COE)2Rh(eta6-C20H10)]PF6 and [(COE)2Ir(eta6-C20H10)]PF6. Both compounds were characterized by X-ray diffraction studies, and binding in the solid state is compared with that of their aromatic analogues [(COE)2M(eta6-arene)]PF6 (aryl = benzene and phenanthrene). Solution NMR studies show that the [(COE)2Rh]+ fragment walks over the curved aromatic surface of corannulene, whereas the Ir analogue is not fluxional. Experimental as well as computational studies suggest that inter-ring movement of the Rh complex follows a hub migration mechanism. Initial reactivity studies indicate that the [(COE)2M]+ fragments can undergo chemical transformations, such as transfer dehydrogenation and substitution reactions, while still bound to corannulene.
Journal Article↗
Dodecamethoxy- and hexaoxotricyclobutabenzene: synthesis and characterization.
We report herein the syntheses of dodecamethoxytricyclobutabenzene (TCBB) 1 and hexaoxo-TCBB 2, a class of molecules with structural and theoretical interest. The preparation is based on the 3-fold [2 + 2] cycloadditions of benzyne and ketene silyl acetals (KSAs), where the selectively protected 2-iodophloroglucinol derivative served as a synthetic equivalent of benztriyne I, allowing rapid and regioselective annulation of fully functionalized four-membered rings. Structural study on the former compound showed that the C-C bond lengths in the central benzene ring were essentially the same.
Journal Article↗
Synthesis of fluoranthenes and indenocorannulenes: elucidation of chiral stereoisomers on the basis of static molecular bowls.
Cycloaromatization of a peri diyne with an external alkyne provides a general route to indeno-fused polynuclear aromatics. Fluoranthenes 9 (or 13) are easily accessible in good to excellent yields (75-99%; 18 examples) from the reaction of symmetric (or asymmetric) diynes 4 and alkynes 5 (or norbornadiene) in the presence of Wilkinson's catalyst. This formal [(2+2)+2] cycloaddition can also be applied to generate various indenocorannulenes 28 from 2,3-diethynylcorannulene derivatives 27 and alkynes 5. The indenocorannulenes 28 exist in a static bowl form at room temperature with bowl-to-bowl inversion barriers higher than 24 kcal/mol. This barrier renders the rate of inversion slow enough at room temperature to establish a class of chiral, bowl-shaped stereoiomers containing no tetrahedrally ligated atoms. The crystal structure of 28g provides insight into the bowl-shaped geometry of these compounds. This new synthetic method occurs under neutral conditions and tolerates various functional groups (e.g., alkyl, aryl, alcohols, and esters).
Journal Article↗
Experimental and computational investigation of the uncatalyzed rearrangement and elimination reactions of isochorismate.
The versatile biosynthetic intermediate isochorismate decomposes in aqueous buffer by two competitive pathways, one leading to isoprephenate by a facile Claisen rearrangement and the other to salicylate via elimination of the enolpyruvyl side chain. Computation suggests that both processes are concerted but asynchronous pericyclic reactions, with considerable C-O cleavage in the transition state but relatively little C-C bond formation (rearrangement) or hydrogen atom transfer to the enolpyruvyl side chain (elimination). Kinetic experiments show that rearrangement is roughly 8-times more favorable than elimination. Moreover, transfer of the C2 hydrogen atom to C9 was verified by monitoring the decomposition of [2-(2)H]isochorismate, which was prepared chemoenzymatically from labeled shikimate, by (2)H NMR spectroscopy and observing the appearance of [3-(2)H]pyruvate. Finally, the isotope effects obtained with the C2 deuterated substrate are in good agreement with calculations assuming pericyclic reaction mechanisms. These results provide a benchmark for mechanistic investigations of isochorismate mutase and isochorismate pyruvate lyase, the enzymes that respectively catalyze the rearrangement and elimination reactions in plants and bacteria.
Chorismate Mutase↗
Modulation of fragmental charge transfer via hydrogen bonds. Direct measurement of electronic contributions.
Hydrogen bonds play an important role in an overwhelming variety of fields from biology to surface and supramolecular chemistry. The term "hydrogen bond" refers to a wide range of interactions with various covalent and polar contributions. In particular, hydrogen bonds have an important role in the folding and packing of peptides and nucleic acids. Recent studies also point to the importance of hydrogen bonding in the context of second-shell interactions, in metal binding and selectivity in metalloproteins, and in controlling the dynamics of membrane proteins. In this study, we demonstrate and quantify the modulation of fragmental charge transfer from hydrogen-bonded ligands to a metal center, by employing our recently introduced molecular potentiometer. The molecular details that affect this type of fragmental charge transfer are presented and a path for transferring chemical information is demonstrated. We found that H-bond interactions in the extended positions of axial ligands provide an effective means of modulating the amount of fragmental charge transfer to a metal center, thereby dramatically influencing the electronic properties of the ligand, the binding affinity, and the binding of additional ligands. The magnitude of fragmental charge-transfer modulation induced by a single ligand-solvent H-bond interaction is comparable to those induced by covalent substitution, although H-bond enthalpy is only on the order of several kilojoules per mole. Importantly, we find a significant change in the ligand electronic properties, even for weak C-H...O=C H-bond formation, where the bond enthalpy is substantially lower than for conventional H-bond interactions. The excess fragmental charge transferred to the metal center, deduced from the spectroscopic measurements, correlates well with the computationally determined values. Our findings underscore the importance of second-shell interactions in the active sites of enzymes, beyond the structural and electrostatic importance that is widely recognized today.
Binding Sites↗
Isochorismate pyruvate lyase: a pericyclic reaction mechanism?
Isochorismate pyruvate lyase (IPL) catalyzes the cleavage of isochorismate to give salicylate and pyruvate, a key step in bacterial siderophore biosynthesis. We investigated the enzyme from Pseudomonas aeruginosa using isochorismate selectively deuterated at C2 as a substrate. Monitoring the reaction by 2H NMR spectroscopy revealed that the label is quantitatively transferred from C2 to C9, producing stoichiometric amounts of [3-2H]pyruvate as product. Moreover, the deuterium kinetic isotope effect of 2.34 +/- 0.08 on kcat indicates that C-H cleavage is significantly rate limiting. Consistent with these data, hybrid density functional theory (HDFT) calculations at the Becke3LYP/DZ+(2d,p) level of theory predict a concerted but highly asynchronous pericyclic transition structure, in which carbon-oxygen bond cleavage is more advanced than hydrogen atom transfer from C2 to C9; the calculated 2H isotope effect of 2.22 at C2 is in excellent accord with the experimental value. Together, these findings indicate that IPL should be added to the small set of proteins that are known to catalyze pericyclic reactions. They also raise the possibility that enzymes, such as chorismate pyruvate lyase, salicylate synthase, 4-amino-4-deoxychorismate lyase, and anthranilate synthase, which accelerate formally similar reaction steps, may also exploit pericyclic mechanisms.
Binding Sites↗
Direct experimental evaluation of charge scheme performance by a molecular charge-meter.
The remarkable advances accomplished in the past two decades in theoretical and computational capabilities have made the in silico study of complex chemical systems feasible. However, this progress is in strong contrast to the lag in experimental capabilities relating to the measurement of fundamental chemical quantities within convoluted environments such as solvents or protein milieu. As a result, many works rely extensively on predictions provided by ab initio methodologies without having independent experimental support. Such a proliferation of theory and computational approaches without being substantiated by appropriate experimental data is undesirable. The feasibility of using nickel-bacteriochlorophyll as a molecular potentiometer was recently demonstrated for the systematic evaluation of fragmental charge density transfer for metal complexes in solution, thus providing an experimental assay with high accuracy and sensitivity (better than +/-0.005 e(-); Yerushalmi, R.; Baldridge, K. K.; Scherz, A. J. Am. Chem. Soc. 2003, 125, 12706-12707). Here the experimentally determined fragmental charge density transfer values measured by the molecular potentiometer for metal complexes in solvent are used to provide, for the first time, an independent and critical experimental evaluation of theoretical approaches commonly used in determining atomic charges and fragmental charge density transfer among interacting molecular systems. Importantly, these findings indicate that the natural population analysis (NPA) charge analysis is highly robust and well-suited for determining charge transfer processes involving donor-acceptor coordination interactions. The majority of computational charge schemes fail to provide an accurate chemical picture for the whole range of systems considered here. In cases where the role of electronic correlation varies significantly among chemically related structures, as with mono- and biligated complexes, the widely used electrostatic potential fit-based methods for evaluating atomic charges may prove to be problematic for predictive studies. In such cases, alternative methods that do not rely on the net dipole moment or other higher multipoles of the system for determining charges should be employed.
Bacteriochlorophylls↗
Ring selectivity and migratory aptitude of Cp*Ru+ complexation to acecorannulene.
Synthesis and spectral characterization of acecorannulene CpRu+ complexes, in combination with ab initio quantum chemical computations, leads to the hypothesis that eta6-metal binding prefers the exo face in the region of least curvature.
Journal Article↗
An experimental look into subelectron charge flow.
The prediction and measurement of charge distribution among interacting chemical entities in complex environments is a major challenge for modern chemistry. It encompasses information concerning fundamental quantities such as the electronic chemical potential and hardness of molecular fragments as well as their interactions with the surroundings. Although a wealth of theoretical work has been accumulated from the days of Pauling to the present, a specific molecular model system that allows quantitative and direct measurement of these properties has not yet been reported. Because atomic charges are not quantum mechanical observables, they cannot be derived from first principles, but rather they rely on the availability of high-precision experimental data and the interpretation of related experimental observables. Here, we demonstrate, for the first time, that a fragmental charge flow between a chelated metal center and reversibly bound molecules can be accurately monitored experimentally.
Electrons↗
Ring-strain effects on the oxidation potential of enediynes and enediyne complexes.
The metal-enediyne complexes [(eta 5-C5H5)Fe[eta 5-1,2-C5H3C identical to C(CH2)nC identical to]] (4, n = 4; 5, n = 5) and [(eta 5-C5H5)-Fe[eta 5-1,2-C5H3(C identical to C Me)2]] (6) were prepared from 1,2-diethynylferrocene (3). Complexes 4 and 5 were characterized in the solid state by X-ray crystallographic analysis. The structures of 4 and 6 were determined by computation using ab initio methods. A correlation was observed between ring-strain and increased ease of electrochemical oxidation along the series 6 (+0.164 V) to 5(+0.152 V) to 4 (+0.123 V). A similar trend in ionization potentials was identified in both the gas phase and in solution by computational methods.
Crystallography, X-Ray↗
Synthesis and properties of sym-pentasubstituted derivatives of corannulene.
Alkyl, aryl, and alkynyl as well as heteroatom derivatives of sym-pentasubstituted corannulenes have been synthesized from sym-pentachlorocorannulene. These units form potential building blocks for future work on superstructures based on corannulene. Absorption/emission properties follow expected trends from the parent 1. sym-Pentasubstitution gives rise to variations in the chemical dynamics of bowl inversion. van der Waals attraction is cited to explain an anomalously high barrier to bowl inversion in 10.
Journal Article↗
Through-space interactions between face-to-face, center-to-edge oriented arenes: importance of polar-pi effects.
Two series of conformationally restricted polycyclic compounds (1-3 and 4-7) have been synthesized as model systems for studying the through-space interactions between face-to-face, center-to-edge (parallel-offset) oriented arenes. These compounds feature different X substituents on one of the interacting rings. By monitoring the variation of the delta Gz for the rotation around the aryl-aryl bond in 1-7 as a function of X by 2D [1H,1H] EXSY NMR spectroscopy, it was found that the barriers increase on passing from electron-donating to electron-withdrawing substituted derivatives. Quantum mechanical calculations [MP2/DVZ (2d,p)//B3LYP/DVZ(2d,p)] gave barrier values and variations in agreement with the experimental data. The results are consistent with a repulsive arene-arene interaction dominated by electrostatic effects.
Journal Article↗
Flexibility and molecular recognition in the immune system.
Photon echo spectroscopy has been used to measure the response of three antibody-binding sites to perturbation from electronic excitation of a bound antigen, fluorescein. The three antibodies show motions that range in time scale from tens of femtoseconds to nanoseconds. Relative to the others, one antibody, 4-4-20, possesses a rigid binding site that likely results from a short and inflexible heavy chain complementarity-determining region 3 (HCDR3) loop and a critical Tyr that acts as a "molecular splint," rigidifying the antigen across its most flexible internal degree of freedom. The remaining two antibodies, 34F10 and 40G4, despite being generated against the same antigen, possess binding sites that are considerably more flexible. The more flexible combining sites likely result from longer HCDR3 loops and a deletion in the light chain complementarity-determining region 1 (LCDR1) that removes the critical Tyr residue. The binding site flexibilities may result in varying mechanisms of antigen recognition including lock-and-key, induced-fit, and conformational selection.
Amino Acid Sequence↗
Mutual control of axial and equatorial ligands: model studies with [Ni]-bacteriochlorophyll-a.
Modification of the metal's electronic environment by ligand association and dissociation in metalloenzymes is considered cardinal to their catalytic activity. We have recently presented a novel system that utilizes the bacteriochlorophyll (BChl) macrocycle as a ligand and reporter. This system allows for charge mobilization in the equatorial plane and experimental estimate of changes in the electronic charge density around the metal with no modification of the metal's chemical environment. The unique spectroscopy, electrochemistry and coordination chemistry of [Ni]-bacteriochlorophyll ([Ni]-BChl) enable us to follow directly fine details and steps involved in the function of the metal redox center. This approach is utilized here whereby electro-chemical reduction of [Ni]-BChl to the monoanion [Ni]-BChl(-) results in reversible dissociation of biologically relevant axial ligands. Similar ligand dissociation was previously detected upon photoexcitation of [Ni]-BChl (Musewald, C.; Hartwich, G.; Lossau, H.; Gilch, P.; Pollinger-Dammer, F.; Scheer, H.; Michel-Beyerle, M. E. J. Phys. Chem. B 1999, 103, 7055-7060 and Noy, D.; Yerushalmi, R.; Brumfeld, V.; Ashur, I.; Baldridge, K. K.; Scheer, H.; Scherz, A. J. Am. Chem. Soc. 2000, 122, 3937-3944). The electrochemical measurements and quantum mechanical (QM) calculations performed here for the neutral, singly reduced, monoligated, and singly reduced, monoligated [Ni]-BChl suggest the following: (a) Electroreduction, although resulting in a pi anion [Ni]-BChl(-) radical, causes electron density migration to the [Ni]-BChl core. (b) Reduction of nonligated [Ni]-BChl does not change the macrocycle conformation, whereas axial ligation results in a dramatic expansion of the metal core and a flattening of the highly ruffled macrocycle conformation. (c) In both the monoanion and singly excited [Ni]-BChl ([Ni]-BChl*), the frontier singly occupied molecular orbital (SOMO) has a small but nonnegligible metal character. Finally, (d) computationally, we found that a reduction of [Ni]-BChl*imidazole results in a weaker metal-axial ligand bond. Yet, it remains weakly bound in the gas phase. The experimentally observed ligand dissociation is accounted for computationally when solvation is considered. On the basis of the experimental observations and QM calculations, we propose a mechanism whereby alterations in the equatorial pi system and modulation of sigma bonding between the axial ligands and the metal core are mutually correlated. Such a mechanism highlights the dynamic role of axial ligands in regulating the activity of metal centers such as factor F430 (F430), a nickel-based coenzyme that is essential in methanogenic archea.
Bacteriochlorophyll A↗
Directing power of cyclobutenoid annelations on the double bonds of planar cyclooctatetraenes.
Ab initio and hybrid density functional quantum mechanical computations are applied to the structure and energetics of a series of two-atom-bridge annelated cyclooctatetraenes. The contribution of each annelation to the exo/endo relative energy is estimated. Key directing factors for a given type of annelation, such as strain, electronegativity, or cyclic electron count, can be sorted out by comparison of various bridge compositions. Overall, electron count and the essential components of the Clar/Robinson rule work well to predict the exo/endo preferences. Specifically, three 4-e(-) Hückel systems (CH-CH, NH-BH and NH-C(O)) display dominant exo forms whereas the three 4n + 2 Hückel counterparts (C(O)-C(O), BH-BH, and planar NH-NH) display a common preference for endo. These endo systems act like four independent four-membered "aromatic" rings linked by "single" bonds. An analysis based on the effective hybridization of carbon atoms in the annulene (Bent's rule) provides a rationale for subtle trends in their specific annulene geometry.
Alkenes↗