Computational Spectroscopy in Environmental Chemistry

Kubicki, James D.; Mueller, Karl T.

doi:10.1002/9783527633272.ch11

Cited by 5 publications

(8 citation statements)

References 113 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Trivedi and Vasudevan (2007) used a similar approach; however, they also investigated aqueous spectra of Fe 3+ -ciprofloxacin complexes as a function of pH, which was useful for interpreting the spectra of ciprofloxacin bound to goethite. In addition, prediction of FTIR and Raman spectra using molecular modeling can help to further elucidate observed vibrational bands (Kubicki and Mueller, 2010).…”

Section: Organic Molecule Interactions With Mineral Surfacesmentioning

confidence: 99%

Soil Chemical Insights Provided through Vibrational Spectroscopy

Parikh

Goyne

Margenot

et al. 2014

Advances in Agronomy

222

163

View full text Add to dashboard Cite

Section: Organic Molecule Interactions With Mineral Surfacesmentioning

confidence: 99%

Soil Chemical Insights Provided through Vibrational Spectroscopy

Parikh

Goyne

Margenot

et al. 2014

Advances in Agronomy

222

163

View full text Add to dashboard Cite

“…Changes in the electronic orbital energies may be due to various effects, so the interpretation of XANES spectra can be ambiguous. To complement these spectroscopies, molecular simulations are commonly employed [21].…”

Section: Molecular Data-ir/raman Exafs/xanesmentioning

confidence: 99%

Integrating Density Functional Theory Modeling with Experimental Data to Understand and Predict Sorption Reactions: Exchange of Salicylate for Phosphate on Goethite

Kubicki

Ohno

2020

Soil Systems

Self Cite

View full text Add to dashboard Cite

Density functional theory (DFT) calculations are a quantum mechanical approach that can be used to model chemical reactions on an atomistic scale. DFT provides predictions on structures, thermodynamics, spectroscopic parameters and kinetics that can be compared against experimentally determined data. This paper is a primer on the basics of utilizing DFT for applications in mineral-water interfaces. In our case-study, we use DFT to model the surface complexes of phosphate and salicylate adsorbed onto the (101) and (210) surfaces of α-FeOOH (goethite), as an example of combining DFT and experiment. These three components are important in the phosphorus-organic matter interactions in soils, and by comparing the energies of the two surface complexes, the exchange energy of salicylate for phosphate onto goethite can be estimated. The structures of the surface complexes are predicted and the resulting vibrational frequencies calculated based on these structures are compared to previous observations. Upon verification of reasonable surface complex models, the potential energy of exchanging salicylate for phosphate is calculated and shown to be significantly exothermic. This model result is consistent with observations of plant exudates, such as salicylate freeing adsorbed phosphate in soils under P-limited conditions.

show abstract

“…Approaches that incorporate randomized sampling can return slightly different numerical results, but reproducibility of any particular result can be ensured by providing seed values for the pseudo-random number generator. A typical procedure for model development is to select candidate methods that have enjoyed success in similar applications and empirically investigate which techniques provide meaningful performance and interpretability for the current task, after which implementation measures are then pursued (Kuhn and Johnson, 2013). In lieu of selecting a single model, ensemble learning and Bayesian model averaging approaches combine predictions from multiple models (Murphy, 2012).…”

Section: Model Estimationmentioning

confidence: 99%

“…The final model is obtained by refitting the model to all of the available samples in the calibration set and using the number of parameters selected in the CV process. Other strategies and general discussions on the topic of performance metrics and statistical sampling are covered in many textbooks (e.g., Bishop, 2009;Hastie et al, 2009;Kuhn and Johnson, 2013).…”

Section: Model Estimationmentioning

confidence: 99%

“…3. Other strategies for arranging CV include maximizing differences among samples in each fold to reduce chances of overfitting (Kuhn and Johnson, 2013) but have not been explored in this application. Even with specification of model and approach for parameter selection fixed, spectral processing and sample selection can lead to differences in overall model performance.…”

Section: Model Estimationmentioning

confidence: 99%

See 1 more Smart Citation

Atmospheric particulate matter characterization by Fourier transform infrared spectroscopy: a review of statistical calibration strategies for carbonaceous aerosol quantification in US measurement networks

et al. 2019

View full text Add to dashboard Cite

Abstract. Atmospheric particulate matter (PM) is a complex mixture of many different substances and requires a suite of instruments for chemical characterization. Fourier transform infrared (FT-IR) spectroscopy is a technique that can provide quantification of multiple species provided that accurate calibration models can be constructed to interpret the acquired spectra. In this capacity, FT-IR spectroscopy has enjoyed a long history in monitoring gas-phase constituents in the atmosphere and in stack emissions. However, application to PM poses a different set of challenges as the condensed-phase spectrum has broad, overlapping absorption peaks and contributions of scattering to the mid-infrared spectrum. Past approaches have used laboratory standards to build calibration models for prediction of inorganic substances or organic functional groups and predict their concentration in atmospheric PM mixtures by extrapolation. In this work, we review recent studies pursuing an alternate strategy, which is to build statistical calibration models for mid-IR spectra of PM using collocated ambient measurements. Focusing on calibrations with organic carbon (OC) and elemental carbon (EC) reported from thermal–optical reflectance (TOR), this synthesis serves to consolidate our knowledge for extending FT-IR spectroscopy to provide TOR-equivalent OC and EC measurements to new PM samples when TOR measurements are not available. We summarize methods for model specification, calibration sample selection, and model evaluation for these substances at several sites in two US national monitoring networks: seven sites in the Interagency Monitoring of Protected Visual Environments (IMPROVE) network for the year 2011 and 10 sites in the Chemical Speciation Network (CSN) for the year 2013. We then describe application of the model in an operational context for the IMPROVE network for samples collected in 2013 at six of the same sites as in 2011 and 11 additional sites. In addition to extending the evaluation to samples from a different year and different sites, we describe strategies for error anticipation due to precision and biases from the calibration model to assess model applicability for new spectra a priori. We conclude with a discussion regarding past work and future strategies for recalibration. In addition to targeting numerical accuracy, we encourage model interpretation to facilitate understanding of the underlying structural composition related to operationally defined quantities of TOR OC and EC from the vibrational modes in mid-IR deemed most informative for calibration. The paper is structured such that the life cycle of a statistical calibration model for FT-IR spectroscopy can be envisioned for any substance with IR-active vibrational modes, and more generally for instruments requiring ambient calibrations.

show abstract

Computational Spectroscopy in Environmental Chemistry

Cited by 5 publications

References 113 publications

Soil Chemical Insights Provided through Vibrational Spectroscopy

Soil Chemical Insights Provided through Vibrational Spectroscopy

Integrating Density Functional Theory Modeling with Experimental Data to Understand and Predict Sorption Reactions: Exchange of Salicylate for Phosphate on Goethite

Atmospheric particulate matter characterization by Fourier transform infrared spectroscopy: a review of statistical calibration strategies for carbonaceous aerosol quantification in US measurement networks

Contact Info

Product

Resources

About