EVAPORATION: a new vapour pressure estimation methodfor organic molecules  including non-additivity and intramolecular interactions

Abstract. We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict (subcooled) liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

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EVAPORATION: a new vapor pressure estimation method for organic molecules including non-additivity and intramolecular interactions

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-11-13229-2011 ◽

2011 ◽

Vol 11 (4) ◽

pp. 13229-13278

Author(s):

S. Compernolle ◽

K. Ceulemans ◽

J.-F. Müller

Keyword(s):

Molecular Structure ◽

Vapor Pressure ◽

Functional Groups ◽

Vapour Pressure ◽

Simple Formula ◽

Organic Molecules ◽

Intramolecular Interaction ◽

Estimation Method ◽

Organic Aerosol ◽

Intramolecular Interactions

Abstract. We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict vapour pressure p0 of organic molecules needing only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: carbonyls, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

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Estimating fusion properties for functionalised acids

Atmospheric Chemistry and Physics ◽

10.5194/acp-11-8385-2011 ◽

2011 ◽

Vol 11 (16) ◽

pp. 8385-8394 ◽

Cited By ~ 6

Author(s):

S. Compernolle ◽

K. Ceulemans ◽

J.-F. Müller

Keyword(s):

Vapour Pressure ◽

Estimation Error ◽

Estimation Method ◽

Organic Aerosol ◽

Estimation Methods ◽

Fusion Temperature ◽

Subcooled Liquid ◽

Fusion Data ◽

Simple Estimation ◽

Data Estimation

Abstract. Multicomponent organic aerosol (OA) is likely to be liquid, or partially liquid. Hence, to describe the partitioning of these components, their liquid vapour pressure is desired. Functionalised acids (e.g. diacids) can be a significant part of OA. But often measurements are available only for solid state vapour pressure, which can differ by orders of magnitude from their liquid counterparts. To convert such a sublimation pressure to a subcooled liquid vapour pressure, fusion properties (two out of these three quantities: fusion enthalpy, fusion entropy, fusion temperature) are required. Unfortunately, experimental knowledge of fusion properties is sometimes missing in part or completely, hence an estimation method is required. Several fusion data estimation methods are tested here against experimental data of functionalised acids, and a simple estimation method is developed, specifically for this family of compounds, with a significantly smaller estimation error than the literature methods.

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Novel methods for predicting gas–particle partitioning during the formation of secondary organic aerosol

Atmospheric Chemistry and Physics ◽

10.5194/acp-14-13189-2014 ◽

2014 ◽

Vol 14 (23) ◽

pp. 13189-13204 ◽

Cited By ~ 17

Author(s):

F. Wania ◽

Y. D. Lei ◽

C. Wang ◽

J. P. D. Abbatt ◽

K.-U. Goss

Keyword(s):

Functional Groups ◽

Vapour Pressure ◽

Secondary Organic Aerosol ◽

Prediction Method ◽

Organic Aerosol ◽

Estimation Methods ◽

Minor Effect ◽

Normal Alkanes ◽

Sorption Data ◽

Order Of Magnitude

Abstract. Several methods have been presented in the literature to predict an organic chemical's equilibrium partitioning between the water insoluble organic matter (WIOM) component of aerosol and the gas phase, Ki,WIOM, as a function of temperature. They include (i) polyparameter linear free energy relationships calibrated with empirical aerosol sorption data, as well as (ii) the solvation models implemented in SPARC and (iii) the quantum-chemical software COSMOtherm, which predict solvation equilibria from molecular structure alone. We demonstrate that these methods can be used to predict Ki,WIOM for large numbers of individual molecules implicated in secondary organic aerosol (SOA) formation, including those with multiple functional groups. Although very different in their theoretical foundations, these methods give remarkably consistent results for the products of the reaction of normal alkanes with OH, i.e. their partition coefficients Ki,WIOM generally agree within one order of magnitude over a range of more than ten orders of magnitude. This level of agreement is much better than that achieved by different vapour pressure estimation methods that are more commonly used in the SOA community. Also, in contrast to the agreement between vapour pressure estimates, the agreement between the Ki,WIOM estimates does not deteriorate with increasing number of functional groups. Furthermore, these partitioning coefficients Ki,WIOM predicted SOA mass yields in agreement with those measured in chamber experiments of the oxidation of normal alkanes. If a Ki,WIOM prediction method was based on one or more surrogate molecules representing the solvation properties of the mixed OM phase of SOA, the choice of those molecule(s) was found to have a relatively minor effect on the predicted Ki,WIOM, as long as the molecule(s) are not very polar. This suggests that a single surrogate molecule, such as 1-octanol or a hypothetical SOA structure proposed by Kalberer et al. (2004), may often be sufficient to represent the WIOM component of the SOA phase, greatly simplifying the prediction. The presented methods could substitute for vapour-pressure-based methods in studies such as the explicit modelling of SOA formation from single precursor molecules in chamber experiments.

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On the detection of oxidized and highly oxidized organic molecules by CHARON PTR-MS via ammonium adduct ionization

10.5194/egusphere-egu2020-4471 ◽

2020 ◽

Author(s):

Markus Müller ◽

Felix Piel ◽

Armin Wisthaler

Keyword(s):

Mass Spectrometry ◽

Functional Groups ◽

Organic Molecules ◽

Organic Aerosol ◽

Proton Transfer Reaction ◽

Protonated Form ◽

Ionization Mass ◽

Single Digit ◽

Target Analytes ◽

Ammonium Adduct

Oxidized and highly oxidized organic molecules are important target analytes in atmospheric air samples. In recent years, several chemical ionization mass spectrometry (CIMS) methods have been developed for detecting these target analytes in real time and at ultra-trace levels. One of these CIMS techniques is proton-transfer-reaction mass spectrometry (PTR-MS), which, in combination with the so-called CHARON inlet, measures oxidized and highly oxidized organic molecules in the atmosphere in the gaseous and particulate state. PTR-MS typically uses hydronium ions (H3O+) as reagent ions for detecting organic analytes in their protonated form, [A+H+]. H3O+ ions react with all oxidized organics at unit efficiency, meaning that PTR-MS universally detects these target analytes, with little dependency of the signal response on their oxidation state. A drawback of PTR-MS operation in the H3O+ mode is that oxidized functional groups are often ejected upon protonation.Herein, we present the results obtained when a CHARON PTR-MS analyzer was operated with ammonium (NH4+) ions as CI reagent ions. We studied the instrumental response to a set of oxidized and highly oxidized compounds including hydroxy, carboxy and peroxy functional groups. We found that fragmentation was greatly suppressed, with ammonium adducts, [A+NH4]+, being the main analyte ions formed. The ionization efficiency ranged from 10 to 80% of the collisional limit, meaning that the NH4+ mode is less quantitative than the H3O+ mode. The performance and advantages of ammonium adduct ionization are demonstrated on two application examples: i) secondary organic aerosol generated in the laboratory from the ozonolysis of limonene, with a particular focus on the detection of peroxides and dimers, and (ii) ambient organic aerosol in Innsbruck, Austria, which was characterized at the molecular level at single digit ng m-&#179; mass concentrations.

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Novel methods for predicting gas-particle partitioning during the formation of secondary organic aerosol

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-14-21341-2014 ◽

2014 ◽

Vol 14 (15) ◽

pp. 21341-21385 ◽

Cited By ~ 2

Author(s):

F. Wania ◽

Y. D. Lei ◽

C. Wang ◽

J. P. D. Abbatt ◽

K.-U. Goss

Keyword(s):

Functional Groups ◽

Vapour Pressure ◽

Secondary Organic Aerosol ◽

Organic Aerosol ◽

Basis Sets ◽

Estimation Methods ◽

Minor Effect ◽

Normal Alkanes ◽

Sorption Data ◽

Better Than

Abstract. Several methods have been presented in the literature to predict an organic chemical's equilibrium partitioning between the water insoluble organic matter (WIOM) component of aerosol and the gas phase, Ki, WIOM as a function of temperature. They include (i) polyparameter linear free energy relationships calibrated with empirical aerosol sorption data, as well as (ii) the solvation models implemented in SPARC and (iii) the quantum-chemical software Cosmotherm, which predict solvation equilibria from molecular structure alone. We demonstrate that these methods can be used to predict Ki, WIOM for large numbers of individual molecules implicated in secondary organic aerosol (SOA) formation, including those with multiple functional groups. Although very different in their theoretical foundations, these methods give remarkably consistent results for the products of the reaction of normal alkanes with OH, i.e. their partition coefficients Ki, WIOM generally agree within one order of magnitude over a range of more than ten orders of magnitude. This level of agreement is much better than that achieved by different vapour pressure estimation methods that are more commonly used in the SOA community. Also, in contrast to the agreement between vapour pressure estimates, that between the Ki, WIOM estimates does not deteriorate with increasing number of functional groups. Furthermore, these partitioning coefficients Ki, WIOM are found to predict the SOA mass yield in chamber experiments of the oxidation of normal alkanes as good or better than a vapour pressure based method. If a Ki, WIOM prediction method was based on one or more surrogate molecules representing the solvation properties of the mixed OM phase of SOA, the choice of those molecule(s) was found to have a relatively minor effect on the predicted Ki, WIOM, as long as the molecule(s) are not very polar. This suggests that a single surrogate molecule, such as 1-octanol or a hypothetical SOA structure proposed by Kalberer et al. (2004), may often be sufficient to represent the WIOM component of the SOA phase, greatly simplifying the prediction. The presented methods could substitute for vapour pressure based methods in studies such as the explicit modeling of SOA formation from single precursor molecules in chamber experiments or the assignment of SOA-forming molecules to volatility basis sets.

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On the relation between isotope effects on vapour pressure and molecular structure

Journal de Chimie Physique ◽

10.1051/jcp/1963600052 ◽

1963 ◽

Vol 60 ◽

pp. 52-55

Author(s):

István Kiss ◽

Lajos Matus ◽

István Opauszky

Keyword(s):

Molecular Structure ◽

Vapour Pressure ◽

Isotope Effects

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Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

10.26434/chemrxiv.6015611.v1 ◽

2018 ◽

Author(s):

Maximiliano Riquelme ◽

Alejandro Lara ◽

David L. Mobley ◽

Toon Vestraelen ◽

Adelio R Matamala ◽

...

Keyword(s):

Force Field ◽

Functional Groups ◽

Electrostatic Interactions ◽

Organic Molecules ◽

Force Fields ◽

Chemical Elements ◽

Atomic Charges ◽

Free Energies ◽

Molecular Systems ◽

Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol-1 for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

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Structure of 4,4-Bisphenylsulfonyl-N,N-dimethylbutylamine: Interplay of Intramolecular C–H···N, C–H···O=S, and ?···? Interactions

Australian Journal of Chemistry ◽

10.1071/ch09303 ◽

2009 ◽

Vol 62 (9) ◽

pp. 1062 ◽

Cited By ~ 17

Author(s):

Jiong Ran ◽

Ming Wah Wong

Keyword(s):

Molecular Structure ◽

Hydrogen Bond ◽

Significant Interaction ◽

Chemical Shifts ◽

Intramolecular Interactions ◽

Methyl Derivative ◽

Polar Medium ◽

Conformational Properties ◽

Density Analysis ◽

Experimental Findings

Conformations of 4,4-bisphenylsulfonyl-N,N-dimethylbutylamine (BSDBA) were examined by ab initio calculations. Intramolecular C–H···N, C–H···O, and π···π interactions are found to play an important role in governing the conformational properties. This finding is supported by charge density analysis based on the theory of atoms in molecules. The calculated molecular structure and 1H chemical shifts of the methyl derivative (BSTBA) are in excellent agreement with experimental findings. The intramolecular C–H···N hydrogen bond in BSDBA is estimated to have a significant interaction energy of 25 kJ mol–1. The sulfonyl oxygens in BSDBA interact readily with neighbouring methylene, methyl and phenyl hydrogens via C–H···O=S hydrogen bonds. In agreement with experiment, solvent effect calculations indicate that these weaker intramolecular interactions prevail in an aprotic polar medium.

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