Fast and Accurate Prediction of Refractive Index of Organic Liquids with Graph Machines

The refractive index (RI) of liquids is a key physical property of molecular compounds and materials. In addition to its ubiquitous role in physics, it is also exploited to impart specific optical properties (transparency, opacity, and gloss) to materials and various end-use products. Since few methods exist to accurately estimate this property, we have designed a graph machine model (GMM) capable of predicting the RI of liquid organic compounds containing up to 16 different types of atoms and effective in discriminating between stereoisomers. Using 8267 carefully checked RI values from the literature and the corresponding 2D organic structures, the GMM provides a training root mean square relative error of less than 0.5%, i.e., an RMSE of 0.004 for the estimation of the refractive index of the 8267 compounds. The GMM predictive ability is also compared to that obtained by several fragment-based approaches. Finally, a Docker-based tool is proposed to predict the RI of organic compounds solely from their SMILES code. The GMM developed is easy to apply, as shown by the video tutorials provided on YouTube.

Machine Learning Identification of Organic Compounds Using Visible Light

Identifying chemical compounds is essential in several areas of science and engineering. Laser-based techniques are promising for autonomous compound detection because the optical response of materials encodes enough electronic and vibrational information for remote chemical identification. This has been exploited using the fingerprint region of infrared absorption spectra, which involves a dense set of absorption peaks that are unique to individual molecules, thus facilitating chemical identification. However, optical identification using visible light has not been realized. Using decades of experimental refractive index data in the scientific literature of pure organic compounds and polymers over a broad range of frequencies from the ultraviolet to the far-infrared, we develop a machine learning classifier that can accurately identify organic species based on a single-wavelength dispersive measurement in the visible spectral region, away from absorption resonances. The optical classifier proposed here could be applied to autonomous material identification protocols and applications.

Optical Properties of Secondary Organic Aerosol Produced by Photooxidation of Naphthalene under NOx Condition

Secondary organic aerosols (SOAs) affect incoming solar radiation by interacting with light at ultraviolet and visible wavelength ranges. However, the relationship between the chemical composition and optical properties of SOA is still not well understood. In this study, the complex refractive index (RI) of SOA produced from OH oxidation of naphthalene in the presence of nitrogen oxides (NOx) was retrieved online in the wavelength range of 315-650 nm and the bulk chemical composition of the SOA was characterized by an online high-resolution time-of-flight mass spectrometer. In addition, the molecular-level composition of brown carbon chromophores was determined using high-performance liquid chromatography coupled to a photodiode array detector and a high-resolution mass spectrometer. The real part of the RI of the SOA increases with both the NOx/naphthalene ratio and aging time, likely due to the increased mean polarizability and decreased molecular weight due to fragmentation. Highly absorbing nitroaromatics (e.g., C₆H₅NO₄, C₇H₇NO₄, C₇H₅NO₅, C₈H₅NO₅) produced under higher NOx conditions contribute significantly to the light absorption of the SOA. The imaginary part of the RI linearly increases with the NOx/VOCs ratio due to the formation of nitroaromatic compounds. As a function of aging, the imaginary RI increases with the O/C ratio (slope = 0.024), mainly attributed to the achieved higher NOx/VOCs ratio, which favors the formation of light-absorbing nitroaromatics. The light-absorbing enhancement is not as significant with extensive aging as it is under a lower aging time due to the opening of aromatic rings by reactions.

Optical Properties of Secondary Organic Aerosol Produced by Nitrate Radical Oxidation of Biogenic Volatile Organic Compounds

Nighttime oxidation of biogenic volatile organic compounds (BVOCs) by nitrate radicals (NO₃·) represents one of the most important interactions between anthropogenic and natural emissions, leading to substantial secondary organic aerosol (SOA) formation. The direct climatic effect of such SOA cannot be quantified because its optical properties and atmospheric fate are poorly understood. In this study, we generated SOA from the NO₃· oxidation of a series BVOCs including isoprene, monoterpenes, and sesquiterpenes. The SOA were subjected to comprehensive online and offline chemical composition analysis using high-resolution mass spectrometry and optical properties measurements using a novel broadband (315-650 nm) cavity-enhanced spectrometer, which covers the wavelength range needed to understand the potential contribution of the SOA to direct radiative forcing. The SOA contained a significant fraction of oxygenated organic nitrates (ONs), consisting of monomers and oligomers that are responsible for the detected light absorption in the 315-400 nm range. The SOA created from β-pinene and α-humulene was further photochemically aged in an oxidation flow reactor. The SOA has an atmospheric photochemical bleaching lifetime of >6.2 h, indicating that some of the ONs in the SOA may serve as atmosphere-stable nitrogen oxide sinks or reservoirs and will absorb and scatter incoming solar radiation during the daytime.

Effect of chemical structure on optical properties of secondary organic aerosols derived from C12 alkanes

With the development of the economy, anthropogenic emissions in the atmospheric environment increases, and air pollution has caused wide public concern. Vehicle exhaust is an important emission source in the atmosphere, and alkanes are the representative components in it. In this study, the optical properties of secondary organic aerosol (SOA) derived from several C₁₂ alkanes (2-methylundecane, hexylcyclohexane, and cyclododecane) in the absence of NO_X were determined. Absorption (imaginary part of the refractive index (RI), k) at 532 nm was negligible for all the derived SOA, and the scattering (real part of RI, n) of the SOA at 532 nm followed the order of cyclododecane SOA < hexylcyclohexane SOA < 2-methylundecane SOA, at both room- (25 °C) and low- (5 °C) temperature. The chemical compositions of the SOA formed were analyzed with an electrospray ionization time-of-flight mass spectrometer (ESI-TOF-MS). The mass spectra showed that the oligomers were generated in the reactions. It was shown that the different reaction pathways (due to various alkane structures) leaded to the difference in SOA chemical composition, which changed the RI values. The low-temperature condition promoted the progress of the oligomerization reaction so that the final RI values also changed. This work suggested that when estimating the radiative forcing of SOA using regional or global models, the structure of the precursors and reaction conditions should be taken into account.

Formation of Secondary Brown Carbon in Biomass Burning Aerosol Proxies through NO3 Radical Reactions

Atmospheric brown carbon (BrC) is an important contributor to the radiative forcing of climate by organic aerosols. Because of the molecular diversity of BrC compounds and their dynamic transformations, it is challenging to predictively understand BrC optical properties. OH radical and O₃ reactions, together with photolysis, lead to diminished light absorption and lower warming effects of biomass burning BrC. The effects of night-time aging on the optical properties of BrC aerosols are less known. To address this knowledge gap, night-time NO₃ radical chemistry with tar aerosols from wood pyrolysis was investigated in a flow reactor. This study shows that the optical properties of BrC change because of transformations driven by reactions with the NO₃ radical that form new absorbing species and lead to significant absorption enhancement over the ultraviolet-visible (UV-vis) range. The overnight aging increases the mass absorption coefficients of the BrC by a factor of 1.3-3.2 between 380 nm and 650 nm. Nitrated organic compounds, particularly nitroaromatics, were identified as the main products that contribute to the enhanced light absorption in the secondary BrC. Night-time aging of BrC aerosols represents an important source of secondary BrC and can have a pronounced effect on atmospheric chemistry and air pollution.

The wavelength-dependent optical properties of weakly absorbing aqueous aerosol particles

A model for calculating the wavelength-dependent refractive index of multicomponent mixtures is presented and applied to aqueous systems in the atmosphere and oceans.

Benchmarking DFT approaches for the calculation of polarizability inputs for refractive index predictions in organic polymers

In a previous study, we introduced a new computational protocol to accurately predict the index of refraction (RI) of organic polymers using a combination of first-principles and data modeling. This protocol is based on the Lorentz-Lorenz equation and involves the calculation of static polarizabilities and number densities of oligomer sequences, which are extrapolated to the polymer limit. We chose to compute the polarizabilities within the density functional theory (DFT) framework using the PBE0/def2-TZVP-D3 model chemistry. While this ad hoc choice proved remarkably successful, it is also relatively expensive from a computational perspective. It represents the bottleneck step in the overall RI modeling protocol, thus limiting its utility for virtual high-throughput screening studies, in which efficiency is essential. For polymers that exhibit late-onset extensivity, the employed linear extrapolation scheme can require demanding calculations on long-oligomer sequences, thus becoming another bottleneck. In the work presented here, we benchmark DFT model chemistries to identify approaches that optimize the balance between accuracy and efficiency for this application domain. We compare results for conjugated and non-conjugated polymers, augment our original extrapolation approach with a non-linear option, analyze how the polarizability errors propagate into the RI predictions, and offer guidance for method selection.

Improved model for the refractive index: application to potential components of ambient aerosol

Understanding the impact of atmospheric aerosols on the global radiative balance requires knowing the refractive index (RI) of their components. Currently available methods to estimate this property from molecular structure are mostly empirical and exhibit significant errors (>10%). This work reports a more physically sound model leading to predictions within ±5% from experiment. The root mean square relative error is <1% for general organic compounds, and <2% for oxygen-rich compounds of special interest in aerosol chemistry. In this approach, the RI is obtained from the Lorentz-Lorenz equation. The molar volume and polarizability required as input are obtained from the addition of a so-called geometrical fragment (GF) associated with every non-hydrogen atom in the molecule. The value of this GF method to the study of ambient aerosol is demonstrated through extensive validation and application to compounds that may be present in aerosol droplets. In so doing, insight is provided into the origin of significant errors previously noted using earlier methods. Moreover, it is demonstrated that reference values of the refractive index reported in widely used compilations should be considered with caution. Finally, a Python script is provided as supplementary information for easy use of the present model to estimate molar volume and refractive index for any molecule.

Evolution of the Complex Refractive Index of Secondary Organic Aerosols during Atmospheric Aging

The wavelength-dependence of the complex refractive indices (RI) in the visible spectral range of secondary organic aerosols (SOA) are rarely studied, and the evolution of the RI with atmospheric aging is largely unknown. In this study, we applied a novel white light-broadband cavity enhanced spectroscopy to measure the changes in the RI (400-650 nm) of β-pinene and p-xylene SOA produced and aged in an oxidation flow reactor, simulating daytime aging under NO _x-free conditions. It was found that these SOA are not absorbing in the visible range, and that the real part of the RI, n, shows a slight spectral dependence in the visible range. With increased OH exposure, n first increased and then decreased, possibly due to an increase in aerosol density and chemical mean polarizability for SOA produced at low OH exposures, and a decrease in chemical mean polarizability for SOA produced at high OH exposures, respectively. A simple radiative forcing calculation suggests that atmospheric aging can introduce more than 40% uncertainty due to the changes in the RI for aged SOA.

Emulsified and Liquid-Liquid Phase-Separated States of α-Pinene Secondary Organic Aerosol Determined Using Aerosol Optical Tweezers

We demonstrate the first capture and analysis of secondary organic aerosol (SOA) on a droplet suspended in an aerosol optical tweezers (AOT). We examine three initial chemical systems of aqueous NaCl, aqueous glycerol, and squalane at ∼75% relative humidity. For each system we added α-pinene SOA-generated directly in the AOT chamber-to the trapped droplet. The resulting morphology was always observed to be a core of the original droplet phase surrounded by a shell of the added SOA. We also observed a stable emulsion of SOA particles when added to an aqueous NaCl core phase, in addition to the shell of SOA. The persistence of the emulsified SOA particles suspended in the aqueous core suggests that this metastable state may persist for a significant fraction of the aerosol lifecycle for mixed SOA/aqueous particle systems. We conclude that the α-pinene SOA shell creates no major diffusion limitations for water, glycerol, and squalane core phases under humid conditions. These experimental results support the current prompt-partitioning framework used to describe organic aerosol in most atmospheric chemical transport models and highlight the prominence of core-shell morphologies for SOA on a range of core chemical phases.

Group Contribution Approach To Predict the Refractive Index of Pure Organic Components in Ambient Organic Aerosol

We introduce and assess a group contribution scheme by which the refractive index (RI) (λ = 589 nm) of nonabsorbing components common to secondary organic aerosols can be predicted from the molecular formula and chemical functionality. The group contribution method is based on representative values of ratios of the molecular polarizability and molar volume of different functional groups derived from data for a training set of 234 compounds. The training set consists of 106 nonaromatic compounds common to atmospheric aerosols, 64 aromatic compounds, and 64 compounds containing halogens; a separate group contribution model is provided for each of these three classes of compound. The resulting predictive model reproduces the RIs of compounds in the training set with mean errors of ±0.58, ±0.36, and ±0.30% for the nonaromatic, aromatic, and halogen-containing compounds, respectively. We then evaluate predictions from the group contribution model for compounds with no previously reported RI, comparing values with predictions from previous treatments and with measurements from single aerosol particle experiments. We illustrate how such comparisons can be used to further refine the predictive model. We suggest that the accuracy of this model is already sufficient to better constrain the optical properties of organic aerosol of known composition.

Enhanced Light Scattering of Secondary Organic Aerosols by Multiphase Reactions

Secondary organic aerosol (SOA) plays a pivotal role in visibility and radiative forcing, both of which are intrinsically linked to the refractive index (RI). While previous studies have focused on the RI of SOA from traditional formation processes, the effect of multiphase reactions on the RI has not been considered. Here, we investigate the effects of multiphase processes on the RI and light-extinction of m-xylene-derived SOA, a common type of anthropogenic SOA. We find that multiphase reactions in the presence of liquid water lead to the formation of oligomers from intermediate products such as glyoxal and methylglyoxal, resulting in a large enhancement in the RI and light-scattering of this SOA. These reactions will result in increases in light-scattering efficiency and direct radiative forcing of approximately 20%-90%. These findings improve our understanding of SOA optical properties and have significant implications for evaluating the impacts of SOA on the rapid formation of regional haze, global radiative balance, and climate change.

Optical properties of secondary organic aerosols derived from long-chain alkanes under various NOx and seed conditions

Long-chain alkanes are a type of important intermediate-volatile organic compounds (IVOCs) in the atmosphere, which contribute to a large proportion of secondary organic aerosol (SOA). However, the optical properties of SOA derived from long-chain alkanes remain poorly understood. Here, we investigate the refractive index (RI) of SOA derived from photo-oxidation of dodecane (C12), pentadecane (C15) and heptadecane (C17) under low-NO_x and high-NO_x conditions with the absence or presence of inorganic aerosol seeds. The RIs of these SOAs are found to be in the range of 1.33 to 1.57 at the wavelength of 532nm. The results from mass spectroscopy indicate that both reaction mechanisms influenced by NO_x level and gas-particle partitioning influenced by seeds have important impact on the chemical compositions of SOAs, which further influence the optical properties like RI. Finally, by comparing the RI values to other literature and model results, we suggest that various RIs of SOAs derived from long-chain alkanes should be applied in atmospheric and climate models.

Comparison of Methods for Predicting the Compositional Dependence of the Density and Refractive Index of Organic-Aqueous Aerosols

Representing the physicochemical properties of aerosol particles of complex composition is of crucial importance for understanding and predicting aerosol thermodynamic, kinetic, and optical properties and processes and for interpreting and comparing analysis methods. Here, we consider the representations of the density and refractive index of aqueous-organic aerosol with a particular focus on the dependence of these properties on relative humidity and water content, including an examination of the properties of solution aerosol droplets existing at supersaturated solute concentrations. Using bulk phase measurements of density and refractive index for typical organic aerosol components, we provide robust approaches for the estimation of these properties for aerosol at any intermediate composition between pure water and pure solute. Approximately 70 compounds are considered, including mono-, di- and tricarboxylic acids, alcohols, diols, nitriles, sulfoxides, amides, ethers, sugars, amino acids, aminium sulfates, and polyols. We conclude that the molar refraction mixing rule should be used to predict the refractive index of the solution using a density treatment that assumes ideal mixing or, preferably, a polynomial dependence on the square root of the mass fraction of solute, depending on the solubility limit of the organic component. Although the uncertainties in the density and refractive index predictions depend on the range of subsaturated compositional data available for each compound, typical errors for estimating the solution density and refractive index are less than ±0.1% and ±0.05%, respectively. Owing to the direct connection between molar refraction and the molecular polarizability, along with the availability of group contribution models for predicting molecular polarizability for organic species, our rigorous testing of the molar refraction mixing rule provides a route to predicting refractive indices for aqueous solutions containing organic molecules of arbitrary structure.

Optical properties of secondary organic aerosols generated by photooxidation of aromatic hydrocarbons

The refractive index (RI) is the fundamental characteristic that affects the optical properties of aerosols, which could be some of the most important factors influencing direct radiative forcing. The secondary organic aerosols (SOAs) generated by the photooxidation of benzene, toluene, ethylbenzene and m-xylene (BTEX) under low-NOx and high-NOx conditions are explored in this study. The particles generated in our experiments are considered to be spherical, based on atomic force microscopy (AFM) images, and nonabsorbent at a wavelength of 532 nm, as determined by ultraviolet-visible light (UV-Vis) spectroscopy. The retrieved RIs at 532 nm for the SOAs range from 1.38-1.59, depending on several factors, such as different precursors and NOx levels. The RIs of the SOAs are altered differently as the NOx concentration increases as follows: the RIs of the SOAs derived from benzene and toluene increase, whereas those of the SOAs derived from ethylbenzene and m-xylene decrease. Finally, by comparing the experimental data with the model values, we demonstrate that the models likely overestimate the RI values of the SOA particles to a certain extent, which in turn overestimates the global direct radiative forcing of the organic particles.

Remote sensing of atmospheric optical depth using a smartphone sun photometer

In recent years, smart phones have been explored for making a variety of mobile measurements. Smart phones feature many advanced sensors such as cameras, GPS capability, and accelerometers within a handheld device that is portable, inexpensive, and consistently located with an end user. In this work, a smartphone was used as a sun photometer for the remote sensing of atmospheric optical depth. The top-of-the-atmosphere (TOA) irradiance was estimated through the construction of Langley plots on days when the sky was cloudless and clear. Changes in optical depth were monitored on a different day when clouds intermittently blocked the sun. The device demonstrated a measurement precision of 1.2% relative standard deviation for replicate photograph measurements (38 trials, 134 datum). However, when the accuracy of the method was assessed through using optical filters of known transmittance, a more substantial uncertainty was apparent in the data. Roughly 95% of replicate smart phone measured transmittances are expected to lie within ±11.6% of the true transmittance value. This uncertainty in transmission corresponds to an optical depth of approx. ±0.12–0.13 suggesting the smartphone sun photometer would be useful only in polluted areas that experience significant optical depths. The device can be used as a tool in the classroom to present how aerosols and gases effect atmospheric transmission. If improvements in measurement precision can be achieved, future work may allow monitoring networks to be developed in which citizen scientists submit acquired data from a variety of locations.

Complex refractive indices in the near-ultraviolet spectral region of biogenic secondary organic aerosol aged with ammonia

Distribution of the number of N atoms and the change in the complex refractive index of unreacted and NH₃-aged limonene SOA.

Complex refractive indices of thin films of secondary organic materials by spectroscopic ellipsometry from 220 to 1200 nm

The complex refractive indices of three different types of secondary organic material (SOM) were obtained for 220 to 1200 nm using a variable angle spectroscopic ellipsometer. Aerosol particles were produced in a flow tube reactor by ozonolysis of volatile organic compounds, including the monoterpenes α-pinene and limonene and the aromatic catechol (benzene-1,2-diol). Optically reflective thin films of SOM were grown by electrostatic precipitation of the aerosol particles onto silicon substrates. The ellipsometry analysis showed that both the real and imaginary components of the refractive indices decreased with increasing wavelength. The real part n(λ) could be parametrized by the three-term form of Cauchy's equation, as follows: n(λ) = B + C/λ(2) + D/λ(4) where λ is the wavelength and B, C, and D are fitting parameters. The real refractive indices of the three SOMs ranged from 1.53 to 1.58, 1.49-1.52, and 1.48-1.50 at 310, 550, and 1000 nm, respectively. The catechol-derived SOM absorbed light in the ultraviolet (UV) range. By comparison, the UV absorption of the monoterpene-derived SOMs was negligible. On the basis of the measured refractive indices, optical properties were modeled for a typical atmospheric particle population. The results suggest that the wavelength dependence of the refractive indices can vary the Angstrom exponent by up to 0.1 across the range 310 to 550 nm. The modeled single-scattering albedo can likewise vary from 0.97 to 0.85 at 310 nm (UV-B). Variability in the optical properties of different types of SOMs can imply important differences in the relative effects of atmospheric particles on tropospheric photochemistry, as well as possible inaccuracies in some satellite-retrieved properties such as optical depth and mode diameter.