Computational Study of Catalytic Urethane Formation

Polyurethanes (PUs) are widely used in different applications, and thus various synthetic procedures including one or more catalysts are applied to prepare them. For PU foams, the most important catalysts are nitrogen-containing compounds. Therefore, in this work, the catalytic effect of eight different nitrogen-containing catalysts on urethane formation will be examined. The reactions of phenyl isocyanate (PhNCO) and methanol without and in the presence of catalysts have been studied and discussed using the G3MP2BHandHLYP composite method. The solvent effects have also been considered by applying the SMD implicit solvent model. A general urethane formation mechanism has been proposed without and in the presence of the studied catalysts. The proton affinities (PA) were also examined. The barrier height of the reaction significantly decreased (∆E0 > 100 kJ/mol) in the presence of the studied catalysts, which proves the important effect they have on urethane formation. The achieved results can be applied in catalyst design and development in the near future.

Fragmentation inside PTR-based mass spectrometers limits the detection of ROOR and ROOH peroxides

Proton-transfer-reaction (PTR) is a commonly applied ionization technique for mass spectrometers, where hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later generation PTR-instruments have been designed for better throughput of less volatile species, allowing detection of more functionalized molecules as well. For example, the recently developed Vocus PTR time-of-flight mass spectrometer (PTR-TOF) has been shown to agree well with an iodide adduct based chemical ionization mass spectrometer (CIMS) for products with 3-5 O-atoms from oxidation of monoterpenes (C10H16). However, while several different types of CIMS instruments (including those using iodide) detect abundant signals also at “dimeric” species, believed to be primarily ROOR peroxides, no such signals have been observed in the Vocus PTR, even though these compounds fulfil the condition of having higher proton affinity than water. More traditional PTR instruments have been limited to volatile molecules as the inlets have not been designed for transmission of easily condensable species. Some newer instruments, like the Vocus PTR, have overcome this limitation, but are still not able to detect the full range of functionalized products, suggesting that other limitations need to be considered. One such limitation, well-documented in PTR literature, is the tendency of protonation to lead to fragmentation of some analytes. In this work, we evaluate the potential for PTR to detect dimers and the most oxygenated compounds, as these have been shown to be crucial for forming atmospheric aerosol particles. We studied the detection of dimers using a Vocus PTR-TOF in laboratory experiments as well as through quantum chemical calculations. Only noisy signals of potential dimers were observed during experiments on the ozonolysis of the monoterpene α-pinene, while a few small signals of dimeric compounds were detected during the ozonolysis of cyclohexene. During the latter experiments, we also tested varying the pressures and electric fields in the ionization region of the Vocus PTR-TOF, finding that only small improvements were possible in the relative dimer contributions. Calculations for model ROOR and ROOH systems showed that most of these peroxides should fragment partially following protonation. With inclusion of additional energy from the ion-molecule collisions driven by the electric fields in the ionization source, computational results suggest substantial or nearly complete fragmentation of dimers. Our study thus suggests that while the improved versions of PTR-based mass spectrometers are very powerful tools for measuring hydrocarbons and their moderately oxidized products, other types of CIMS are likely more suitable for the detection of ROOR and ROOH species.

Directional Proton Conductance in Bacteriorhodopsin Is Driven by 2 Concentration Gradient, Not Affinity Gradient

It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Directional proton conductance in bacteriorhodopsin is driven by concentration gradient, not affinity gradient

It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Directional proton conductance in bacteriorhodopsin is driven by concentration gradient, not affinity gradient

It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Directional proton conductance in bacteriorhodopsin is driven by concentration gradient, not affinity gradient

It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Push–Pull Effect on the Gas-Phase Basicity of Nitriles: Transmission of the Resonance Effects by Methylenecyclopropene and Cyclopropenimine π-Systems Substituted by Two Identically Strong Electron Donors

The gas-phase basicity of nitriles can be enhanced by a push–pull effect. The role of the intercalated scaffold between the pushing group (electron-donor) and the pulling (electron-acceptor) nitrile group is crucial in the basicity enhancement, simultaneously having a transmission function and an intrinsic contribution to the basicity. In this study, we examine the methylenecyclopropene and the N-analog, cyclopropenimine, as the smallest cyclic π systems that can be considered for resonance propagation in a push–pull system, as well as their derivatives possessing two strong pushing groups (X) attached symmetrically to the cyclopropene scaffold. For basicity and push–pull effect investigations, we apply theoretical methods (DFT and G2). The effects of geometrical and rotational isomerism on the basicity are explored. We establish that the protonation of the cyano group is always favored. The push–pull effect of strong electron donor X substituents is very similar and the two π-systems appear to be good relays for this effect. The effects of groups in the two cyclopropene series are found to be proportional to the effects in the directly substituted nitrile series X–C≡N. In parallel to the basicity, changes in electron delocalization caused by protonation are also assessed on the basis of aromaticity indices. The calculated proton affinities of the nitrile series reported in this study enrich the gas-phase basicity scale of nitriles to around 1000 kJ mol−1.

RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions

We present RegioSQM20, a new version of RegioSQM (Chem Sci 9:660, 2018), which predicts the regioselectivities of electrophilic aromatic substitution (EAS) reactions from the calculation of proton affinities. The following improvements have been made: The open source semiempirical tight binding program is used instead of the closed source program. Any low energy tautomeric forms of the input molecule are identified and regioselectivity predictions are made for each form. Finally, RegioSQM20 offers a qualitative prediction of the reactivity of each tautomer (low, medium, or high) based on the reaction center with the highest proton affinity. The inclusion of tautomers increases the success rate from 90.7 to 92.7%. RegioSQM20 is compared to two machine learning based models: one developed by Struble et al. (React Chem Eng 5:896, 2020) specifically for regioselectivity predictions of EAS reactions (WLN) and a more generally applicable reactivity predictor (IBM RXN) developed by Schwaller et al. (ACS Cent Sci 5:1572, 2019). RegioSQM20 and WLN offers roughly the same success rates for the entire data sets (without considering tautomers), while WLN is many orders of magnitude faster. The accuracy of the more general IBM RXN approach is somewhat lower: 76.3–85.0%, depending on the data set. The code is freely available under the MIT open source license and will be made available as a webservice (regiosqm.org) in the near future.

On the Spatial Design of Co-Fed Amines for Selective Dehydration of Methyl Lactate to Acrylates

Co-feeding an inert and site-selective chemical titrant provides desirable selectivity tuning when titrant adsorption is favored over side reaction pathways on a solid acid catalyst. Here, a selectivity enhancement from 61 to 84 C % was demonstrated for methyl lactate dehydration to methyl acrylate and acrylic acid over NaY zeolite catalyst using amines as the co-fed titrants to suppress side reactions on in situ generated Brønsted acid sites (BAS). The effectiveness of BAS titration was evaluated by considering both the basicity and steric properties of the titrant molecule with the goal to maximize the selectivity enhancement. The presence of electron-donating alkyl functional groups enhances amine basicity but also introduces additional steric constraints to the molecule with respect to the pore dimensions of the NaY zeolite. While higher basicity of titrant amines favors stronger adsorption on BAS, steric limitations hinder site binding through contributions from internal diffusion limitations and local steric repulsion between titrant and the zeolite wall around the BAS. Titrant bases with proton affinities above ~1040 kJ/mol and sizes below 85% of the NaY supercage window or pore diameter are predicted to afford dehydration selectivities above 90 C % to acrylate products.