Matthew P. Jacobson

Baseline subtraction using robust local regression estimation

Abstract A technique entitled robust baseline estimation is introduced, which uses techniques of robust local regression to estimate baselines in spectra that consist of sharp features superimposed upon a continuous, slowly varying baseline. The technique is applied to synthetic spectra, to evaluate its capabilities, and to laser-induced fluorescence spectra of OH (produced from the reaction of ozone with hydrogen atoms). The latter example is a particularly challenging case for baseline estimation because the experimental noise varies as a function of frequency.

Pure bending dynamics in the acetylene X̃ 1Σg+ state up to 15 000 cm−1 of internal energy

We investigate the large-amplitude bending dynamics of acetylene, in its ground electronic state, using an effective Hamiltonian model that reproduces all relevant experimental data, up to 15u2009000 cm−1 in internal energy, with 1.4 cm−1 accuracy (1σ). The experimental data which make this analysis possible are derived from the dispersed fluorescence (DF) data set that we recently reported [J. P. O’Brien et al., J. Chem. Phys. 108, 7100 (1998)] for the acetylene Au20091Au→Xu20091Σg+ system, which includes DF spectra recorded from five different vibrational levels of the Au20091Au state. A numerical pattern recognition technique has permitted the assignment of polyad quantum numbers to observed transitions in these spectra, with up to 15u2009000 cm−1 in internal energy. Here we analyze a special subset of the identified polyads, those which involve excitation exclusively in the trans and cis bending modes: the pure bending polyads. The bending dynamics that is encoded in these polyads is analyzed using both frequency and ti...

State-by-state assignment of the bending spectrum of acetylene at 15 000 cm−1: A case study of quantum-classical correspondence

Techniques of quantum, semiclassical, and nonlinear classical mechanics are employed to investigate the bending dynamics of acetylene, as represented by a recently reported effective Hamiltonian [J. Chem. Phys. 109, 121 (1998)], with particular emphasis on the dynamics near 15u200a000 cm−1 of internal energy. At this energy, the classical mechanics associated with the bending system is profoundly different from that at low energy, where normal mode motions (trans and cis bend) dominate. Specifically, at 15u200a000 cm−1, classical chaos coexists with stable classical motions that are unrelated to the normal mode motions; these high-energy stable bending motions include those that we call “local bend” (one hydrogen bending) and “counter-rotation” (the two hydrogens undergoing circular motion at opposite ends of the molecule), as well as more complicated motions which can be considered hybrids of the local bend and counter-rotation motions. The vast majority of the bending quantum eigenstates near 15u200a000 cm−1 have n...

Structural and Kinetic Studies of a Cisplatin-modified DNA Icosamer Binding to HMG1 Domain B

The high mobility group (HMG) domain is a DNA-binding motif found in the non-histone chromosomal proteins, HMG1 and HMG2, and some transcription factors. Experimental evidence has demonstrated that HMG-domain proteins can play a role in sensitizing cells to the anticancer drug cisplatin. Fluorescence resonance energy transfer (FRET) experiments were performed in the present study to investigate structural changes that accompany complex formation between the HMG domain B of HMG1 and a cisplatin-modified, 20-base pair double-stranded DNA probe containing fluorescein and rhodamine tethered at its two ends. The binding affinity of HMG1 domain B for the cisplatin-modified DNA probe was investigated in fluorescence titration experiments, and a value of 60 ± 30 nm was determined for the dissociation constant. Single photon counting methods were employed to measure the fluorescence lifetime of the fluorescein donor in the presence and absence of HMG1 domain B. These FRET experiments revealed a distance change that was used to estimate a bend angle of 80–95° for the cisplatin-modified DNA upon protein binding. Stopped-flow fluorescence spectroscopic experiments afforded kinetic parameters for HMG1 domain B binding to the cisplatin-modified DNA probe, with k on = 1.1 ± 0.1 × 109 m −1 s−1 andk off = 30 ± 4 s−1.

Local mode behavior in the acetylene bending system

above these energies, the eigenstates are better described in terms of local mode quantum numbers. The local mode behavior in the bend degrees of freedom of acetylene that is described here is in many ways analogous to the local mode behavior that has been observed in the stretching degrees of freedom of many ABA molecules. However, the local mode behavior in the acetylene bend degrees of freedom, because it involves two two-dimensional rather than two one-dimensional vibrational modes, encompasses a richer range of motions. Specifically, in the ‘‘local’’ limit, the bending eigenfunctions are describable in terms of a continuum of motions ranging from local bend ~one hydrogen bending! to counter-rotation ~the two hydrogens executing rotations in opposite directions! .© 1999 American Institute of Physics.@S0021-9606~99!00702-3#

Numerical pattern recognition analysis of acetylene dispersed fluorescence spectra

Polyad quantum numbers have been assigned to 134 vibrational levels of the X1Σg+ state of acetylene with internal energies from 3,000 to 15,000 cm−1. These polyad assignments have been made possible by two advances: (1) the recording of new, rigorously calibrated acetylene A1Au→X1Σg+ dispersed fluorescence spectra, and (2) the development of a numerical pattern recognition technique which identifies groups of transitions in the spectra that terminate on eigenstates with the same polyad quantum numbers. This pattern recognition technique is based on the Extended Cross-Correlation, which has been reported previously in this Journal [J. Chem. Phys. 107, 8349, 8357 (1997)], and requires neither a priori knowledge of the number of polyads in the spectra nor the pattern of spectral lines that is associated with each polyad. No evidence for the breakdown of the polyad quantum numbers is found, at the 7 cm−1 resolution of our spectra, at internal energies up to at least 15,000 cm−1. The ability to assign polyad...

Anomalously slow intramolecular vibrational redistribution in the acetylene X̃ 1Σg+ state above 10 000 cm−1 of internal energy

We have identified, in dispersed fluorescence spectra of acetylene Au20091Au→Xu20091Σg+ emission, a series of bright states between 10u2009000 and 15u2009000 cm−1u2002of internal energy which display anomalously slow intramolecular vibrational redistribution. That is, these bright states display virtually no fractionation at internal energies at which the majority of other observed bright states are fractionated over several hundred cm−1u2002in a complicated fashion. The anomalous bright states are distinguished from the other nearly isoenergetic bright states only by the way in which the vibrational excitation is distributed among the CC stretch and transu2002bend modes; specifically, the anomalous bright states have relatively low excitation in the transu2002bend mode (v4⩽8), with the remainder of the vibrational excitation in the CC stretch mode (v2⩽6). A refinement of the acetylene global effective Hamiltonian permits detailed insight into the mechanism of the anomalously slow intramolecular vibrational redistribution, and reveals ...

The infrared-ultraviolet dispersed fluorescence spectrum of acetylene: New classes of bright states

Single rotational levels of ungerade vibrational levels, 2ν3′+ν6′ and 3ν3′+ν6′ (both with bu symmetry), in the Au200a1Au electronically excited state of acetylene were excited by an IR-UV double resonance scheme via the ν3″ fundamental level in the Xu200a1Σg+ state, and the rotationally resolved dispersed fluorescence (DF) spectra were recorded at 3.2–4.5 cm−1 resolution. The term values of the new ungerade levels were determined within an accuracy of 0.56 cm−1(1σ) through careful calibration achieved by frequency standard atomic Fe and Hg lines. A total of 111 new ungerade vibrational levels with Σu+, Σu−, and Δu symmetry below 10u200a000 cm−1 was identified in the high-resolution IR-UV-DF spectra, which provide access to new classes of Xu200a1Σg+ bright states: (i) (0,v2″,0,v4″1,1−1)Σu+, (0,v2″,0,v4″1,11)Δu, and (0,v2″,0,v4″3,1−1)Δu, which are the Franck–Condon (FC) bright levels from the nν3′+ν6′ (n=2,3) levels in the Au200a1Au state; (ii) (0,v2″,0,v4″−1,11)Σu− levels which appear through the a-axis Corioris interaction...

Extended cross correlation: A technique for spectroscopic pattern recognition

Recent improvements in spectrum excitation, recording, and processing capabilities have led to enormous enhancement in the quality and quantity of spectroscopic data sets. We describe here a pattern recognition technique, extended cross correlation (XCC), that is well suited to take advantage of large, high quality data sets. In particular, spectra are used to decode each other without any knowledge of or assumptions about the patterns that are sought. This paper describes the motivation for and construction of the XCC, and illustrates one of its simplest applications: To identify, in spectra of mixtures of chemical species, which peaks correspond to which chemical species. This application of the XCC is illustrated with both synthetic data and experimental data on mixtures of ammonia isotopic species.

Identifying patterns in multicomponent signals by extended cross correlation

The analysis of current problems in physical chemistry often requires the identification of patterns that encode the composition, structure, and dynamics of a system. Overlapped patterns, unexpected patterns, and patterns whose forms are initially unknown are especially difficult to identify and to extract. We have developed two new techniques for pattern recognition and extraction designed for these situations. These techniques, extended cross correlation (XCC) and extended auto correlation (XAC), identify and extract multiple patterns from experimental data even when the number of derived patterns exceeds the number of experiments. The XCC, which is the focus of this paper, allows the rapid identification and extraction of patterns that are repeated in multiple experimental records. The related XAC technique permits the identification of complex patterns that are parameterized in a multidimensional way, even when the patterns are obscured by the presence of interfering data. The XCC and XAC provide stra...