NLOPredict: Visualization and data analysis software for nonlinear optics

Abstract

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/.

Imaging of Protein Crystals with Two-Photon Microscopy

“…Previous studies theoretically analyzed the NLO proprieties of various protein crystals by using NLOPredict plugin (incorporated into molecular graphics software UCSF Chimera (http://plato.cgl.ucsf.edu/chimera/) 39, 40 . Moreover, the properties of SHG in chiral systems also were extensively studied and defined (reviewed in 4, 10 ).…”

Heterotrimeric G protein β 1 γ 2 subunits change orientation upon complex formation with G protein-coupled receptor kinase 2 (GRK2) on a model membrane

“…The GRK2-Gβγ complex contains 31 helical segments (20), and, consequently, analyzing the molecular orientation relies on determining the combined response for all α-helices in the protein (10,13,(29)(30)(31). The net α-helical hyperpolarizability, β protein , can be determined based on the length and relative orientations of all helical segments in the known crystal structure (PDB entry 1omw), so long as the protein conformation remains unchanged (as in the case of GRK2-Gβγ).…”

Imaging the Nonlinear Susceptibility Tensor of Collagen by Nonlinear Optical Stokes Ellipsometry

“…A hyperellipsoid representation of c ð2Þ l and the molecular tensor as b ð2Þ is also shown in Fig. 2, which describes the relative local-frame tensor elements of the structures (37). From the breadth of work on analysis of collagen fiber substructure (20,33,(38)(39)(40)(41), it is apparent that a distribution of tilt angles of collagen …”

“…Consequently, theoretical predictions of b ð2Þ for a single collagen triple helix were combined with experimental methods to determine c ð2Þ l for a fiber, for us to gain insight into helical organization within a fiber. For a collagen triple helix specifically, the nonlinear polarizability tensor, b ð2Þ was calculated using the symmetry additive model (36,37), in which ab initio calculations are used to first predict the nonlinear polarizability of NMA, which serves as a model system for the amide bonds of a protein. The amide contributions were then coherently summed for a single collagen triple helix.…”

“…While it may initially appear overly simplistic to represent the hyperpolarizability of collagen using calculations for just the NMA building block, previous computational and experimental studies support the validity of this approach (37,(49)(50)(51). For all but the aromatic amino acids, the hyperpolarizabilities of polypeptides formed from the common amino acids are dominated by the amide unit connecting amino acid groups, which exhibits a relatively large hyperpolarizability.…”