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To explore a proof-of-concept for atomically precise manufacturing (APM) using scanning probe microscopy (SPM), first principle theoretical calculations of atom-by-atom transfer from the apex of an SPM tip to an individual radical on a surface-bound organic molecule have been performed. Atom transfer is achieved by spatially controlled motion of a gold terminated tip to the radical. Two molecular tools for SPM-based APM have been designed and investigated, each comprising an adamantane core, a radical end group, and trithiol linkers to enable strong chemisorption on the Au(111) surface: ethynyl-adamantane-trithiol and adamantyl-trithiol. We demonstrate the details of controlled Au atom abstraction during tip approach toward and retraction from the radical species. Upon approach of the tip, the apical Au atom undergoes a transfer toward the carbon radical at a clearly defined threshold separation. This atomic displacement is accompanied by a net energy gain of the system in the range −0.5 to −1.5 eV, depending on the radical structure. In the case of a triangular pyramidal apex model, two tip configurations are possible after the tip atom displacement: (1) an Au atom is abstracted from the tip and bound to the C radical, not bound to the tip base anymore, and (2) apical tip atoms rearrange to form a continuous neck between the tip and radical. In the second case, subsequent tip retraction leads to the same final configuration as the first, with the abstracted Au atom bound to radical carbon atom of the molecular tool. For the less reactive adamantyl-trithiol radical molecular tool, Au atom transfer is less energetically favored, but this has the advantage of avoiding other apex gold atoms from rearrangement.

The synthesis, physical and spectroscopic properties of a series of metal complexes bridged by the redox-active chloranilate ligand are presented. The effects of Heisenberg spin exchange and a quantitative ligand-field analysis have indicated that the transitions are the consequences of exchange interactions in both the ground- and excited-state manifolds of the compounds.

Two newly synthesized pyrenylcyclam dendrons have displayed unique emissive blue shifts centered at 450 nm upon adding copper triflate, which are attributed to intramolecular excimer emission. Metal complexation and intramolecular photoinduced electron transfer within the dendritic 1:1 cyclam/metal complex have played vital roles in the photophysical properties in metal/dendrimer complexes.

An investigation of the influence of the binding of the calmodulin-binding domain of calmodulin kinase I is conducted on the fast internal dynamics of calcium-saturated calmodulin. The results reveal a fundamental role for residual protein entropy in molecular recognition by calmodulin.

Polymer nanoparticles of 40-400 nm diameter with spiropyran-merocyanine dyes incorporated into their hydrophobic cavities are prepared, and in contrast to their virtually nonfluorescent character in most environments, the merocyanine forms of the encapsulated dyes are highly fluorescent. To evaluate the potential for biological tagging, these optically addressable nanoparticles are delivered into living cells and imaged with liquid nitrogen-cooled CCD.

A combination of synchroton X-ray diffraction and solid-state NMR (SSNMR) shift tensor data is being used to study the structure and characterization of a large number of microcrystalline organic solids. The results obtained from the tests conducted on the widely occurring natural product, ambuic acid powder verifies its phase purity and suggests that the powder diffraction data combined with the NMR measurements is a very powerful tool for studying the challenging organic solids.

Amide-linked spiropyran-anthraquinone (SP-AQ) conjugates were mediated to ZnTPPS(super 4-) photosensitized transmembrane reduction of occluded Co(bpy)(sub 3)(super 3+) within unilamellar phosphatidylcholine vesicles by external EDTA. Examination revealed low quantum yields due to unproductive quenching of ZnTPPS(super 4-) by spiropyran (SP) and merocyanine (MC) groups on the dye and back-electron transfer between semiquinone and ZnTPPS(super 3-).

The syntheses, structures, and physical properties of intramolecular donor/acceptor systems containing naphthalene donors and antiferromagnetically coupled diiron(III) cores as acceptors are described. It is found that photoexcitation of the naphthalene chromophore resulted in intramolecular electronic energy transfer to the Fe(super III)(sub 2) core from both the lowest-lying singlet and triplet excited states of naphthalene.

The radical addition of H3PO2 to N-/C-protected vinyl glycine led to the corresponding H-phosphinic acid in excellent yield. The non-nucleophilic H-phosphinic acid was converted to a nucleophilic P(super III) species, RP(OTMS)2, which was used in two approaches to the target phosphinic acid containing pseudopeptide.

The reactions of achiral dispiro-1,2,4-trioxolane and dispiro-1,2,4-trioxanes with ferrous bromide and 4-oxo-TEMPO are presented. The results suggest a small preference for attack of Fe(II) on the nonketal peroxide oxygen atom of artemisinin.

The binding affinity of six sulfonamide inhibitors to two isozymes is analyzed by both thermofluor and isothermal titration calorimetry (ITC). This combined investigation by thermofluor, ITC and DSC provides a detailed picture of the linkage between ligand binding and protein stability.

A simple method is presented for patterning of protein antigens at a gold surface for use in surface plasmon resonance (SPR) imaging experiments. Microfluidic devices fabricated from poly(dimethylsiloxane) were used to flow various fluids over a gold substrate in spatially defined channels. This technique was used to pattern the surface chemistry of the gold as well as to adsorb antigens from solution to the modified substrates. The resulting antigen arrays were probed with complementary antibodies in order to demonstrate the effectiveness of the patterning for antibody capture experiments. SPR imaging was used to aid in the optimization of array fabrication and to observe the interactions of unlabeled antibodies with these microarrays. This work presents a means of fabricating microarrays with controlled surface density of antigens. SPR imaging provides both quantitative and qualitative evaluation of antibody binding in a label free format.

Repetitive mass spectrometric measurement of the istopic distribution of O2 formed in reactions catalyzed by (sub 18)O-labeled catalyst established the existence of two reaction pathways characterized by products containing either one atom each from a ruthenyl O and solvent H2O or both O atoms from solvent molecules.

Rate coefficients have been measured for the H + HC3N (cyanoacetylene) reaction at T=200, 250, and 298 K and at P=0.5, 1.0, and 2.0 Torr He using a discharge-flow mass spectrometry apparatus. The reaction was monitored under pseudo-first-order conditions with the H atom concentration in large excess over the HC(sub 3)N concentration.

The synthesis of poly (hydridocarbyne), one of a class of carbon-based random network polymers and a structural isomer of polyacetlyene is reported. The network backbone of this polymer is primarily composed of tetrahedrally hybridized carbon atoms, each bearing one hydride substituent and linked through three carbon-carbon single bonds into three-dimensional random network of fused rings.

Carbon NMR chemical shit tensors are measured for two forms of solid 10-deacetyl baccatin lll to find out more about the origins of solid-state NMR shift differences in polymorphs. Tensor differences that were observed seem to be basically because of conformational variations in ring substituents and the cyclohexenyl ring.

Numerous carbohydrate-processing enzymes facilitate catalysis via stabilization of positive charges near the C1, C4, C5 or C6 positions, but reactions catalyzed by these enzymes are diverse. An easy method that allows easy access to different varieties of 5-fluoro group glycosides as well as glycosyl phosphates is developed with the aim to solve the difficulties faced in introducing the 5-fluoro substituent after radical halogenation.

The ground- and excited-state electronic structures of the solar cell sensitizer bis(4,4'-dicarboxylato-2,2'-bipyridine)bis(isothiocyanato)ruthenium(II) are examined. Density functional theory calculations are used for this purpose.

The synthesis and spectroscopic properties of elongated ruthenium dihydrogen complexes are detailed. The ruthenium dihydrogen complexes are prepared by reaction of the corresponding neutral chloride complexes with hydrogen in the presence of NaB(ArF)4. Treatment with D2 or T2 gas leads to incorporation of deuterium or tritium in the dihydrogen ligand.

A solid-state NMR technique is described for establishing sterochemistry using the natural product terrein as a model compound. This method involves comparison of experimental (super 13) C tensor principal values with ab initio computed values for all possible computer-generated stereoisomers.