Multifunctional Organic Compounds Research Articles

Chemical technology principles for selective bioconjugation of proteins and antibodies.

Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.

Ethylene and Jasmonates Signaling Network Mediating Secondary Metabolites under Abiotic Stress

Plants are sessile organisms that face environmental threats throughout their life cycle, but increasing global warming poses an even more existential threat. Despite these unfavorable circumstances, plants try to adapt by developing a variety of strategies coordinated by plant hormones, resulting in a stress-specific phenotype. In this context, ethylene and jasmonates (JAs) present a fascinating case of synergism and antagonism. Here, Ethylene Insensitive 3/Ethylene Insensitive-Like Protein1 (EIN3/EIL1) and Jasmonate-Zim Domain (JAZs)-MYC2 of the ethylene and JAs signaling pathways, respectively, appear to act as nodes connecting multiple networks to regulate stress responses, including secondary metabolites. Secondary metabolites are multifunctional organic compounds that play crucial roles in stress acclimation of plants. Plants that exhibit high plasticity in their secondary metabolism, which allows them to generate near-infinite chemical diversity through structural and chemical modifications, are likely to have a selective and adaptive advantage, especially in the face of climate change challenges. In contrast, domestication of crop plants has resulted in change or even loss in diversity of phytochemicals, making them significantly more vulnerable to environmental stresses over time. For this reason, there is a need to advance our understanding of the underlying mechanisms by which plant hormones and secondary metabolites respond to abiotic stress. This knowledge may help to improve the adaptability and resilience of plants to changing climatic conditions without compromising yield and productivity. Our aim in this review was to provide a detailed overview of abiotic stress responses mediated by ethylene and JAs and their impact on secondary metabolites.

Concurrent dominant pathways of multifunctional products formed from nocturnal isoprene oxidation

Determination of dominant chemical pathways toward the formation of nocturnal secondary organic aerosols (SOA) remains ambiguous by which nitrogen oxides (NOx) always affect oxidation of volatile alkenes. Here, comprehensive chamber simulations on dark isoprene ozonolysis were conducted under different nitrogen dioxides (NO2) mixing ratios to exam multiple functionalized isoprene oxidation products. Aside from that the oxidation processes were concurrently driven by nitrogen radical (NO3) and small hydroxyl radicals (OH), ozone (O3) cycloaddition at isoprene was launched initially regardless of NO2 to rapidly form first-generation oxidation products, i.e., carbonyls and Criegee intermediates (CI) referred to carbonyl oxides. They could further undergo complicated self- and cross-reactions to produce alkylperoxy radicals (RO2). Corresponding to yields of the C5H10O3 tracer, weak OH pathway at night was credited to ozonolysis of isoprene but suppressed by unique NO3 chemistry. Following the ozonolysis of isoprene, NO3 played a crucial supplementary role in nighttime SOA formation. The ensuing production of gas-phase nitrooxy carbonyls (the first-generation nitrates) became dominant in the production of a sizeable pool of organic nitrates (RO2NO2). By contrast, isoprene dihydroxy dinitrates (C5H10N2O8) were outstanding with the elevated NO2, related to typical second-generation nitrates. As such, the yielding number concentrations of dark SOA were promoted to approximately 1.8 × 104 cm−3 but presented a nonlinear relation with excess high-NO2 condition. This study provides valuable insights into importance of multifunctional organic compounds from alkene oxidation to constitute nighttime SOA.

Machine Learning for Predicting Chemical Potentials of Multifunctional Organic Compounds in Atmospherically Relevant Solutions.

We have trained the Extreme Minimum Learning Machine (EMLM) machine learning model to predict chemical potentials of individual conformers of multifunctional organic compounds containing carbon, hydrogen, and oxygen. The model is able to predict chemical potentials of molecules that are in the size range of the training data with a root-mean-square error (RMSE) of 0.5 kcal/mol. There is also a linear correlation between calculated and predicted chemical potentials of molecules that are larger than those included in the training set. Finding the lowest chemical potential conformers is useful in condensed phase thermodynamic property calculations, in order to reduce the number of computationally demanding density functional theory calculations.

Comparison of saturation vapor pressures of <i>α</i>-pinene + O<sub>3</sub> oxidation products derived from COSMO-RS computations and thermal desorption experiments

Abstract. Accurate information on gas-to-particle partitioning is needed to model secondary organic aerosol formation. However, determining reliable saturation vapor pressures of atmospherically relevant multifunctional organic compounds is extremely difficult. We estimated saturation vapor pressures of α-pinene-ozonolysis-derived secondary organic aerosol constituents using Filter Inlet for Gases and AEROsols (FIGAERO)–chemical ionization mass spectrometer (CIMS) experiments and conductor-like screening model for real solvents (COSMO-RS). We found a good agreement between experimental and computational saturation vapor pressures for molecules with molar masses around 190 g mol−1 and higher, most within a factor of 3 comparing the average of the experimental vapor pressures and the COSMO-RS estimate of the isomer closest to the experiments. Smaller molecules likely have saturation vapor pressures that are too high to be measured using our experimental setup. The molecules with molar masses below 190 g mol−1 that have differences of several orders of magnitude between the computational and experimental saturation vapor pressures observed in our experiments are likely products of thermal decomposition occurring during thermal desorption. For example, dehydration and decarboxylation reactions are able to explain some of the discrepancies between experimental and computational saturation vapor pressures. Based on our estimates, FIGAERO–CIMS can best be used to determine saturation vapor pressures of compounds with low and extremely low volatilities at least down to 10−10 Pa in saturation vapor pressure.

Theoretical study of the formation and nucleation mechanism of highly oxygenated multi-functional organic compounds produced by α-pinene.

In recent years, highly oxygenated organic molecules (HOMs) derived from photochemical reactions of α-pinene, the most abundant monoterpene, have been considered as important precursors of biogenic particles. However, the specific reactions of HOMs remain largely unknown, especially the corresponding formation and nucleation mechanism in the nanoscale. In this study, we implemented quantum chemical calculations and molecular dynamics (MD) simulations to explore the mechanism of the formation of HOM monomers/dimers by ozonolysis and autoxidation of α-pinene. Furthermore, we investigated the mechanisms of HOMs with different oxygen-to‑carbon (O/C) ratios and functional groups participating in neutral and ion-induced nucleation. The results show that the formation of HOMs is hardly affected by water, sulfuric acid and ions. In the ion-induced nucleation, HOM can dominate the initial nucleation steps; however, in the neutral nucleation, HOMs are more likely to participate in the growth stage. In addition, the nucleation ability of HOM has a bearing on the O/C ratio and the types of the functional groups. The current calculations provide valuable insight into the formation mechanism of the pure organic particles at low sulfuric acid concentrations.

Atmospheric fate of two relevant unsaturated ketoethers: kinetics, products and mechanisms for the reaction of hydroxyl radicals with (<i>E</i>)-4-methoxy-3-buten-2-one and (1<i>E</i>)-1-methoxy-2-methyl-1-penten-3-one

Abstract. The kinetics of the gas phase reactions of hydroxyl radicals with two unsaturated ketoethers (UKEs) at (298±3) K and 1 atm of synthetic air have been studied for the first time using the relative-rate technique in an environmental reaction chamber by in situ Fourier-transform infrared spectroscopy (FTIR). The rate coefficients obtained using propene and isobutene as reference compounds were (in units of 10−10 cm3 molecule−1 s−1) as follows: kTMBO (OH + (E)-4-methoxy-3-buten-2-one) = (1.41±0.11) and kMMPO (OH + (1E)-1-methoxy-2-methyl-1-penten-3-one) = (3.34±0.43). In addition, quantification of the main oxidation products in the presence of NOx has been performed, and degradation mechanisms for these reactions were developed. Methyl formate, methyl glyoxal, peroxyacetyl nitrate (PAN) and peroxypropionyl nitrate (PPN) were identified as main reaction products and quantified for both reactions. The results of the present study provide new insights regarding the contribution of these multifunctional volatile organic compounds (VOCs) in the generation of secondary organic aerosols (SOAs) and long-lived nitrogen containing compounds in the atmosphere. Atmospheric lifetimes and implications are discussed in light of the obtained results.

Improving Solubility and Activity Estimates of Multifunctional Atmospheric Organics by Selecting Conformers in COSMOtherm.

We estimated aqueous solubilities and activity coefficients of atmospherically relevant highly oxidized multifunctional organic compounds in binary mixtures with water at temperatures between 278.15 and 338.15 K, using the COSMOtherm program. Physicochemical properties of organic aerosol constituents are needed in the modeling of atmospheric aerosol processes. As experimental data are often impossible to obtain, reliable estimates from theoretical approaches are a promising path to fill this gap. We investigated the effect of intramolecular hydrogen bonds on the estimation of these condensed-phase properties, attempting to improve the agreement between experimental and estimated values. Citric, tartaric, malic, and maleic acids, which are often used in atmospheric models as representatives of oxidized compounds, were selected to benchmark our calculations. In addition, we estimated aqueous solubilities and activity coefficients of α-pinene-derived organosulfates and highly oxidized isoprene-derived organic compounds, for which no experimental data are available. Our results indicate that the absolute aqueous solubility and activity coefficient estimates of citric, tartaric, malic, and maleic acids, and likely other multifunctional organics, can be improved significantly by selecting conformers on the basis of their intramolecular hydrogen bonding in COSMOtherm calculations.

THE USE OF TRISTIMULUS COLORIMETRY METHOD APPROACHES IN ACID-BASE EQUILIBRIUM STUDY IN DYES SOLUTIONS (REVIEW)

The present review is concerned with application possibility of tristimulus colorimetry method and argumentation of theoretical basis, and experimental approach of tristimulus colorimetry functions values use as analytical response in studies of acid-base equilibria in solutions of multifunctional organic compounds. A conceptual model is proposed, it is based on the change in tristimulus colorimetry function values in the ionization of functional groups of multifunctional compounds. The definitions of the corresponding terms are described. It has been established that use tristimulus colorimetry functions value as analytical response allows differentiating similar in acid-base characteristics functional groups, to determine the corresponding values of the ionization constants and to build a holistic picture about existing acid-base equilibria in a wide range of acidity of the medium. The values of tristimulus colorimetry functions of the specific and total color difference, the yellowness index, as well as the principles of their calculation within different color spaces by the example of polyfunctional compounds (about 50), namely different classes of dyes (azo-, triphenylmethane, xanthene, anthraquinone and pyrilium derivatives). It is established that all specified functions are suitable for the determination of p Kа , and the use of functions of full color difference makes it possible to simplify the mathematical apparatus for processing experimental data. The advantages of tristimulus colorimetry method before classical instrumental methods (spectrophotometry, potentiometry, conductometry) of studying acid-base equilibria in solutions of polyfunctional compounds are shown.

Single Step Synthesis of Glutamic/tartaric Acid-stabilised Fe3O4 Nanoparticles for Targeted Delivery Systems

This paper aims to improve medical strategies regarding cancer treatment, by developing new targeted cancer therapy nanostructured systems, based on magnetite and natural catabolism products as coating agents (glutamic acid, tartaric acid), with induced cellular internalization. In order to create hydrophilic, biocompatible systems, suitable for targeted cancer therapy, and minimize the negative side effects of current approaches, a one-pot synthesis by co-precipitation technique, starting from Fe2+ and Fe3+ inorganic precursors and multifunctional organic compounds, carefully controlling the reaction parameters (concentration of precursors, pH, temperature etc.) was performed. The obtained Fe3O4 stabilised nanoparticles were subjected to morphological and structural characterization. The formation of inorganic-organic hybrid systems was evaluated using FTIR spectroscopy and complex thermal analysis (TG / DSC) for determining the content of the organic component, while X-ray Diffractometry and Scanning and Transmission Electron Microscopy were used to characterize the crystallinity and particle dimensions and distribution. The magnetic properties at room temperature were also evaluated, recording the magnetic susceptibility relative to the applied magnetic field.

Efficient perovskite solar cells via surface passivation by a multifunctional small organic ionic compound

This work reports an effective surface passivation strategy using the multifunctional organic ionic compound 1-ethylpyridinium chloride in combination with (FAPbI3)0.95(MAPbBr3)0.05.

Interplay between Ionization and Tautomerism in Bioactive β-Enamino Ester-Containing Cyclic Compounds: Study of Annulated 1,2,3,6-Tetrahydroazocine Derivatives.

Depending on the chemical scaffold, a bioactive species could reflect the interplay between ionization and tautomerism, which is often complicated by the possibility of populating different conformational states, in the case of flexible ligands. In this context, theoretical methods can be valuable to discern the role of these factors, as shown here for β-enamino esters of 1,2,3,6-tetrahydroazocino-fused ring systems, some of which had proven to be suitable scaffolds for designing novel acetylcholinesterase inhibitors. The compounds investigated herein form two clusters with distinctive experimental pKa values (i.e., α,β-diesters and β-esters ranging within 6.1-7.3 and 8.2-9.0 pKa intervals, respectively), which implies a drastic difference in the most populated species at physiological conditions. While chemoinformatic tools did not provide a consistent description of the actual pKa values, the theoretical analysis performed for the protonated and neutral species of these compounds revealed a marked change in the tautomeric preference of the tetrahydroazocine moiety upon (de)protonation. Excellent agreement between the calculated and experimental pKa values was found when the tautomeric preference of the protonated and neutral species was considered. Overall, this study highlights the potential use of high-level computational methods to disclose the mutual influence between ionization, tautomerism, and conformational preferences in multifunctional (bio)organic compounds.

Organic Multifunctional Materials: Second Harmonic, Ferroelectric, and Dielectric Properties in N-Benzylideneaniline Analogues

The search for multifunctional organic compounds that display technologically important properties has been pursued in recent years. Here we report the synthesis and structure of a series of single...

Influence of co-catalyst amount/size for selective hydrogenation of 1,3-dinitrobenzene over Au-mTiO2 nanocomposites under visible light

This study demonstrates the co-catalytic effect for selective hydrogenation of a particular group in a multifunctional organic compound. Transmission electron microscopy (TEM) studies revealed that Au loaded nanoparticles were found to be of ∼3.89 nm and ∼8.86 nm with 1 wt% and 3 wt% metal loading respectively by homogeneous deposition precipitation (HDP) method over synthesized mesoporous titanium dioxide (m-TiO2) nanoparticles. The Au particles were deposited in the metallic state which was confirmed from X-ray photoelectron spectroscopy (XPS) with a binding energy of 84.0 eV and 87.7 eV credited to 4f5/2 and 4f7/2 spin states respectively. In this Au-mTiO2 heterojunction, metal particles found to be decisive for 100% selective hydrogenation of 1,3-dinitrobenzene under visible light. Predominantly, m-nitroaniline formed when 1,3-dinitrobenzene was treated with 1 wt% Au-mTiO2 whereas 100% photoreduction of both nitro groups occurred with 3 wt% Au-mTiO2. Hence, 1,3-dinitrobenzene exhibited particle size sensitive photocatalytic hydrogenation under mild conditions without using any reducing agent.

Low-pressure gas chromatography with chemical ionization mass spectrometry for quantification of multifunctional organic compounds in the atmosphere

Abstract. Oxygenated volatile organic compounds (OVOCs) are formed during the oxidation of gas-phase hydrocarbons in the atmosphere. However, analytical challenges have hampered ambient measurements for many of these species, leaving unanswered questions regarding their atmospheric fate. We present the development of an in situ gas chromatography (GC) technique that, when combined with the sensitive and specific detection of chemical ionization mass spectrometry (CIMS), is capable of the isomer-resolved detection of a wide range of OVOCs. The instrument addresses many of the issues typically associated with chromatographic separation of such compounds (e.g., analyte degradation). The performance of the instrumentation is assessed through data obtained in the laboratory and during two field studies. We show that this instrument is able to successfully measure otherwise difficult-to-quantify compounds (e.g., organic hydroperoxides and organic nitrates) and observe the diurnal variations in a number of their isomers.

Kinetic modeling studies of SOA formation from <i>α</i>-pinene ozonolysis

Abstract. This paper describes the implementation of a kinetic gas-particle partitioning approach used for the simulation of secondary organic aerosol (SOA) formation within the SPectral Aerosol Cloud Chemistry Interaction Model (SPACCIM). The kinetic partitioning considers the diffusion of organic compounds into aerosol particles and the subsequent chemical reactions in the particle phase. The basic kinetic partitioning approach is modified by the implementation of chemical backward reaction of the solute within the particle phase as well as a composition-dependent particle-phase bulk diffusion coefficient. The adapted gas-phase chemistry mechanism for α-pinene oxidation has been updated due to the recent findings related to the formation of highly oxidized multifunctional organic compounds (HOMs). Experimental results from a LEAK (Leipziger Aerosolkammer) chamber study for α-pinene ozonolysis were compared with the model results describing this reaction system.The performed model studies reveal that the particle-phase bulk diffusion coefficient and the particle-phase reactivity are key parameters for SOA formation. Using the same particle-phase reactivity for both cases, we find that liquid particles with higher particle-phase bulk diffusion coefficients have 310 times more organic material formed in the particle phase compared to higher viscous semi-solid particles with lower particle-phase bulk diffusion coefficients. The model results demonstrate that, even with a moderate particle-phase reactivity, about 61 % of the modeled organic mass consists of reaction products that are formed in the liquid particles. This finding emphasizes the potential role of SOA processing. Moreover, the initial organic aerosol mass concentration and the particle radius are of minor importance for the process of SOA formation in liquid particles. A sensitivity study shows that a 22-fold increase in particle size merely leads to a SOA increase of less than 10 %.Due to two additional implementations, allowing backward reactions in the particle phase and considering a composition-dependent particle-phase bulk diffusion coefficient, the potential overprediction of the SOA mass with the basic kinetic approach is reduced by about 40 %. HOMs are an important compound group in the early stage of SOA formation because they contribute up to 65 % of the total SOA mass at this stage. HOMs also induce further SOA formation by providing an absorptive medium for SVOCs (semi-volatile organic compounds). This process contributes about 27 % of the total organic mass. The model results are very similar to the LEAK chamber results. Overall, the sensitivity studies demonstrate that the particle reactivity and the particle-phase bulk diffusion require a better characterization in order to improve the current model implementations and to validate the assumptions made from the chamber simulations. The successful implementation and testing of the current kinetic gas-particle partitioning approach in a box model framework will allow further applications in a 3-D model for regional-scale process investigations.

Highly Oxygenated Multifunctional Compounds in α-Pinene Secondary Organic Aerosol

Highly oxygenated multifunctional organic compounds (HOMs) originating from biogenic emissions constitute a widespread source of organic aerosols in the pristine atmosphere. However, the molecular forms in which HOMs are present in the condensed phase upon gas-particle partitioning remain unclear. In this study, we show that highly oxygenated molecules that contain multiple peroxide functionalities are readily cationized by the attachment of Na+ during electrospray ionization operated in the positive ion mode. With this method, we present the first identification of HOMs characterized as C8-10H12-18O4-9 monomers and C16-20H24-36O8-14 dimers in α-pinene derived secondary organic aerosol (SOA). Simultaneous detection of these molecules in the gas phase provides direct evidence for their gas-to-particle conversion. Molecular properties of particulate HOMs generated from ozonolysis and OH oxidation of unsubstituted (C10H16) and deuterated (C10H13D3) α-pinene are investigated using coupled ion mobility spectrometry with mass spectrometry. The systematic shift in the mass of monomers in the deuterated system is consistent with the decomposition of isomeric vinylhydroperoxides to release vinoxy radical isotopologues, the precursors to a sequence of autoxidation reactions that ultimately yield HOMs in the gas phase. The remarkable difference observed in the dimer abundance under O3- versus OH-dominant environments underlines the competition between intramolecular hydrogen migration of peroxy radicals and their bimolecular termination reactions. Our results provide new and direct molecular-level information for a key component needed for achieving carbon mass closure of α-pinene SOA.

Real-time detection of highly oxidized organosulfates and BSOA marker compounds during the F-BEACh 2014 field study

Abstract. The chemical composition of ambient organic aerosols was analyzed using complementary mass spectrometric techniques during a field study in central Europe in July 2014 (Fichtelgebirge – Biogenic Emission and Aerosol Chemistry, F-BEACh 2014). Among several common biogenic secondary organic aerosol (BSOA) marker compounds, 93 acidic oxygenated hydrocarbons were detected with elevated abundances and were thus attributed to be characteristic for the organic aerosol mass at the site. Monoterpene measurements exhibited median mixing ratios of 1.6 and 0.8 ppbV for in and above canopy levels respectively. Nonetheless, concentrations for early-generation oxidation products were rather low, e.g., pinic acid (c = 4.7 (±2.5) ng m−3). In contrast, high concentrations were found for later-generation photooxidation products such as 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA, c = 13.8 (±9.0) ng m−3) and 3-carboxyheptanedioic acid (c = 10.2 (±6.6) ng m−3), suggesting that aged aerosol masses were present during the campaign period. In agreement, HYSPLIT trajectory calculations indicate that most of the arriving air masses traveled long distances (> 1500 km) over land with high solar radiation. In addition, around 47 % of the detected compounds from filter sample analysis contained sulfur, confirming a rather high anthropogenic impact on biogenic emissions and their oxidation processes. Among the sulfur-containing compounds, several organosulfates, nitrooxy organosulfates, and highly oxidized organosulfates (HOOS) were tentatively identified by high-resolution mass spectrometry. Correlations among HOOS, sulfate, and highly oxidized multifunctional organic compounds (HOMs) support the hypothesis of previous studies that HOOS are formed by reactions of gas-phase HOMs with particulate sulfate. Moreover, periods with high relative humidity indicate that aqueous-phase chemistry might play a major role in HOOS production. However, for dryer periods, coinciding signals for HOOS and gas-phase peroxyradicals (RO2•) were observed, suggesting RO2• to be involved in HOOS formation.

Endo-Cyclization of unsaturated RO2 radicals from the gas-phase ozonolysis of cyclohexadienes.

Unsaturated RO2 radicals from the ozonolysis of cyclodienes can readily undergo an endo-cyclization step under atmospheric conditions forming a new ring-containing RO2 radical after further O2 addition. This path represents an extension of the atmospheric autoxidation scheme forming highly oxidized multifunctional organic compounds (HOMs). HOMs play an important role for Earth's organic aerosol burden.

Hydroxyl radical-induced formation of highly oxidized organic compounds.

Explaining the formation of secondary organic aerosol is an intriguing question in atmospheric sciences because of its importance for Earth's radiation budget and the associated effects on health and ecosystems. A breakthrough was recently achieved in the understanding of secondary organic aerosol formation from ozone reactions of biogenic emissions by the rapid formation of highly oxidized multifunctional organic compounds via autoxidation. However, the important daytime hydroxyl radical reactions have been considered to be less important in this process. Here we report measurements on the reaction of hydroxyl radicals with α- and β-pinene applying improved mass spectrometric methods. Our laboratory results prove that the formation of highly oxidized products from hydroxyl radical reactions proceeds with considerably higher yields than previously reported. Field measurements support these findings. Our results allow for a better description of the diurnal behaviour of the highly oxidized product formation and subsequent secondary organic aerosol formation in the atmosphere.