Biomedical subjects

Roie Yerushalmi

Publications and source records attributed to Roie Yerushalmi.

7 recordsLinked to original sources

PubMed2006

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↗

PubMed2006

Submolecular potential profiling across organic monolayers.

Potential profiles across molecular layers are constructed by means of noncontact electrically stimulated photoelectron spectroscopy, probing for the first time the molecule-substrate interface potential and resolving local screening effects across inner phenyl groups.

Journal Article↗

PubMed2005

Uniform approach to bacteriochlorophyll-based monolayers on conducting, semiconducting, and insulating substrates.

A general approach is demonstrated for the formation of monolayers comprised of free-base and metalated Bacteriochlorophyll-based derivatives providing a new vehicle for studying photosynthetic motifs and chromophore thin-film interactions. Accessibility to covalent and self-assembled systems on conducting, semiconducting, and insulating substrates is realized utilizing identical molecular building blocks. The monolayers retain the optical features typical for the new systems in solution. Molecular organization of chromophore interaction motifs can be sequentially designed using preassembled building blocks in solution and expressed in the thin film optical properties. For instance, intramolecular pi-pi stacking is conserved for the dimeric Ni-based chromophores as deduced from the spectroscopic measurements of the monolayers and in solution.

Bacteriochlorophylls↗

PubMed2004

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↗

PubMed2004

Enhancement of molecular properties in thin films by controlled orientation of molecular building blocks.

We demonstrate the design and formation of thin films having divergent physicochemical properties by using two porphyrin building blocks with high chemical and optical resemblance. A predetermined variation in the molecular design is efficiently transferred and enhanced when constituting a two-dimensional film via control of molecular orientation. Variations of the peripheral substituents on the porphyrin ring resulted in control of the molecular orientation at the surface.

Chemical Phenomena↗

PubMed2003

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↗

PubMed2002

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↗