A perturbation theory approach was developed for predicting the vibrational and electronic second-order nonlinear optical (NLO) polarizabilities of materials and macromolecules comprised of many coupled chromophores, with an emphasis on common protein secondary structural motifs. The polarization-dependent NLO properties of electronic and vibrational transitions in assemblies of amide chromophores comprising the polypeptide backbones of proteins were found to be accurately recovered in quantum chemical calculations by treating the coupling between adjacent oscillators perturbatively. A novel diagrammatic approach was developed to provide an intuitive visual means of interpreting the results of the perturbation theory calculations. Using this approach, the chiral and achiral polarization-dependent electronic SHG, isotropic SFG, and vibrational SFG nonlinear optical activities of protein structures were predicted and interpreted within the context of simple orientational models.

N-Hydroxysuccinimide (NHS) ester terminal groups are commonly used to covalently couple amine-containing biomolecules (e.g., proteins and peptides) to surfaces via amide linkages. This one-step aminolysis is often performed in buffered aqueous solutions near physiological pH (pH 6 to pH 9). Under these conditions, the hydrolysis of the ester group competes with the amidization process, potentially degrading the efficiency of the coupling chemistry. The work herein examines the efficiency of covalent protein immobilization in borate buffer (50 mM, pH 8.50) using the thiolate monolayer formed by the chemisorption of dithiobis (succinimidyl propionate) (DSP) on gold films. The structure and reactivity of these adlayers are assessed via infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS), electrochemical reductive desorption, and contact angle measurements. The hydrolysis of the DSP-based monolayer is proposed to follow a reaction mechanism with an initial nucleation step, in contrast to a simple pseudo first-order reaction rate law for the entire reaction, indicating a strong dependence of the interfacial reaction on the packing and presence of defects in the adlayer. This interpretation is used in the subsequent analysis of IR-ERS kinetic plots which give a heterogeneous aminolysis rate constant, ka, that is over 3 orders of magnitude lower than that of the heterogeneous hydrolysis rate constant, kh. More importantly, a projection of these heterogeneous kinetic rates to protein immobilization suggests that under coupling conditions in which low protein concentrations and buffers of near physiological pH are used, proteins are more likely physically adsorbed rather than covalently linked. This result is paramount for biosensors that use NHS chemistry for protein immobilization due to effects that may arise from noncovalently linked proteins.

The unique symmetry properties of second harmonic generation (SHG) microscopy enabled sensitive and selective imaging of protein microcrystals with negligible contributions from solvated proteins or amorphous protein aggregates. In studies of microcrystallites of green fluorescent protein (GFP) prepared in 500 pL droplets, the SHG intensities rivaled those of fluorescence, but with superb selectivity for crystalline regions. GFP in amorphous aggregates and in solution produced substantial background fluorescence, but no detectable SHG. The ratio of the forward-to-backward detected SHG provides a measure of the particle size, suggesting detection limits down to crystallites 100 nm in diameter under low magnification (10x). In addition to being sensitive and highly selective, second-order nonlinear optical imaging of chiral crystals (SONICC) is directly compatibility with virtually all common protein crystallization platforms.

Uniaxial systems represent the next lowest symmetry below isotropic and are ubiquitous. The objective of the present work is to present a systematic foundation for interpreting polarization-dependent four-wave mixing measurements of oriented and aligned assemblies. Orientational averages connecting the molecular frame to the macroscopic frame in uniaxial assemblies were derived for several common molecular symmetry groups for coherent anti-Stokes Raman spectroscopy (CARS) measurements, coherent anti-Stokes two-photon spectroscopy (CATS) probing electronic transitions, resonant two-photon absorption (2PA), and traditional Raman measurements. First, the complete set of orientational averages connecting the molecular and macroscopic frames was compiled for the most general case of C1 molecular symmetry. Then, the orientational averages of a select few commonly occurring molecular symmetry groups (Cs, C2, C2v, and C3v) were explored in greater detail to illustrate the approach and to facilitate the interpretation of routine experimental measurements. One outcome of this analysis is the prediction of efficient electric dipole-allowed chiral-specific four-wave mixing in uniaxially oriented media.

A data analysis and visualization program was developed to assist in the interpretation of second-order nonlinear optical (NLO) processes, including vibrational sum-frequency generation and electronically resonant second harmonic generation. A novel diagrammatic approach allows concise visual representations of the resonant NLO molecular response. By mapping the predicted NLO response as a function of molecular orientation, molecular modeling results can be combined with experimental measurements for orientational analysis. A method is developed and implemented to predict the nonlinear optical properties of the amide backbones in complete proteins with known structures. NLOPredict is available for most computer operating systems from http://sda.iu.edu/nlopredict/.