Non-aromatic Molecules Research Articles

High-Throughput Predictions of Accurate Enthalpies of Formation for Larger Molecules Utilizing the Bond Difference Correction Method.

The prediction of standard enthalpies of formation (EOFs) for larger molecules involves a trade-off between accuracy and cost, often resulting in non-negligible errors. The connectivity-based hierarchy (CBH) and simple bond additivity correction (BAC) are two promising means for evaluating EOFs, although they cannot achieve strict chemical accuracy. Calculated errors in the CBH are confirmed from accumulated systematic errors associated with bond differences in chemical environments. On the basis of a new set of bond descriptors, our developed bond difference correction (BDC) method effectively solves incremental errors with molecular size and inability applications for aromatic molecules. To balance the accuracy between non-aromatic and aromatic molecules, a more accurate BAC-based method with unpaired electrons and p hybrid orbitals (BAC-EP) is developed. With the incorporation of the two methods above, strict chemical accuracy by the largest deviation is achieved at low costs. These universal, ultrafast, and high-throughput methods greatly contribute to self-consistent thermodynamic parameters in combustion mechanisms.

Chemical reduction of π-expanded functionalized pentacene: cooperation of side group in alkali metal binding.

Chemical reduction of a vertically expanded pentacene, TIPS-peri-pentacenopentacene (TIPS-PPP), with sodium metal in THF readily afforded a doubly-reduced product isolated as [{Na+(THF)3}2(TIPS-PPP2-)]. Single-crystal X-ray diffraction revealed the formation of a π-complex of TIPS-PPP2- with two {Na+(THF)3} moieties. The sodium ion is coordinated to three C-atoms at the most negatively charged edge sites and at the lateral ethynyl group. The delocalisation of the charge on the ethynyl function is accompanied by its notable elongation (Δ = 0.015 Å) coupled with the contraction of the adjacent single C-C bond (Δ = 0.033 Å). Bond length analysis supported by Harmonic Aromaticity Oscillator Model (HOMA) shows that the dianion can be written with four aromatic sextets in agreement with the Clar representation. Although TIPS-PPP2- has 36 π-electrons (4n), it does not show a global magnetic paratropic response. The rings with the most negative charge density have a very low paratropic response, while the other rings have a low diatropic response. Overall, the dianion is a non-aromatic molecule.

Imaging of intracellular protein aggregates through plasmon-assisted clusteroluminescence.

The formation of clusters in non-aromatic molecules can give rise to unconventional luminescence or clusteroluminescence. Typically containing heteroatoms without extended conjugation or aromatic rings, these molecules have drawn much attention owing to the prospects of label-free biological imaging. However, their applications have been limited due to the lack of knowledge of the underlying mechanism. Herein, we have elucidated the mechanism of clusteroluminescence from proteins, which were explicitly aggregated using plasmonic silver nanoparticles. The nanoparticles promoted protein aggregation and induced nitrile formation on the surface, which, along with other lone-pair-containing heteroatoms, contributed to enhanced emission in the visible range. Remarkably, this makes imaging of proteins possible with visible excitations, as co-factor-lacking proteins generally undergo electronic transitions only in the ultraviolet range. Furthermore, the inherent protein-aggregating behaviour of plasmonic nanoparticles was harnessed for imaging of intracellular Huntingtin protein aggregates overexpressed in HeLa cells through clusteroluminescence. Significant plasmon-enhanced and red-shifted fluorescence emission was observed, which helped in the imaging and localization of the intracellular aggregates. Density functional theory calculations and transient absorbance spectroscopy were used to probe the molecular interactions at the protein-nanoparticle interface and the charge transfer states, further elucidating the role of nanoparticles and the emission mechanism. This technique thus opens alternate avenues for label-free fluorescence bioimaging.

Visible light-driven dearomative ring expansion of (aza)arenes to access dihydrofuran-based polycyclic compounds.

The dearomative expansion of aromatic rings has long been pursued by chemists due to its potential to provide tractable approaches for synthesizing valuable non-aromatic molecules. To circumvent the conventional use of hazardous and unstable diazo compounds, photochemical synthesis has recently emerged as a promising platform. However, protocols that can effectively handle both arenes and azaarenes remain scarce. Herein, we introduce a generic strategy that efficiently converts β-(aza)aryl-β-substituted enones into biologically significant cycloheptatriene derivatives, including their aza-variants. This method allows for the easy modulation of diverse functional groups on the product and demonstrates a wide substrate scope, evidenced by its excellent tolerance to various drug motifs and good compatibility with five-membered azaarenes undergoing ring expansion. Moreover, DFT calculations of plausible mechanisms have motivated the implementation of an important cascade diradical recombination strategy for 1,3-dienones, thus facilitating the synthesis of valuable 2-oxabicyclo[3.1.0]hex-3-ene derivatives.

Probing Molecular-Level Dynamic Interactions of Dissolved Organic Matter with Iron Oxyhydroxide via a Coupled Microfluidic Reactor and an Online High-Resolution Mass Spectrometry System.

The interactions between dissolved organic matter (DOM) and iron (Fe) oxyhydroxide are crucial in regulating the biogeochemical cycling of nutrients and elements, including the preservation of carbon in soils. The mechanisms of DOM molecular assembly on mineral surfaces have been extensively studied at the mesoscale with equilibrium experiments, yet the molecular-level evolution of the DOM-mineral interface under dynamic interaction conditions is not fully understood. Here, we designed a microfluidic reactor coupled with an online solid phase extraction (SPE)-LC-QTOF MS system to continually monitor the changes in DOM composition during flowing contact with Fe oxyhydroxide at circumneutral pH, which simulates soil minerals interacting with constant DOM input. Time-series UV-visible absorption spectra and mass spectrometry data showed that after aromatic DOM moieties were first preferentially sequestered by the pristine Fe oxyhydroxide surface, the adsorption of nonaromatic DOM molecules with greater hydrophobicity, lower acidity, and lower molecular weights (<400) from new DOM solutions was favored. This is accompanied by a transition from mineral surface chemistry-dominated adsorption to organic-organic interaction-dominated adsorption. These findings provide direct molecular-level evidence to the zonal model of DOM assembly on mineral surfaces by taking the dynamics of interfacial interactions into consideration. This study also shows that coupled microfluidics and online high-resolution mass spectrometry (HRMS) system is a promising experimental platform for probing microscale environmental carbon dynamics by integrating in situ reactions, sample pretreatment, and automatic analysis.

Structural origins of two-dimensional elastic bending in a nonaromatic organic molecular crystal.

Mechanically flexible crystals are generally obtained based on weak interactions in the aromatic systems. Here, we reported the remarkable 2D elastic bending behaviors in a nonaromatic organic molecular crystal. The strong hydrogen bonding interactions are also verified to play a crucial role in the reversible bending.

Photochemically Mediated Polymerization of Molecular Furan and Pyridine: Synthesis of Nanothreads at Reduced Pressures.

Nanothreads are emerging one-dimensional sp3-hybridized materials with high predicted tensile strength and a tunable band gap. They can be synthesized by compressing aromatic or nonaromatic small molecules to pressures ranging from 15-30 GPa. Recently, new avenues are being sought that reduce the pressure required to afford nanothreads; the focus has been placed on the polymerization of molecules with reduced aromaticity, favorable stacking, and/or the use of higher reaction temperatures. Herein, we report the photochemically mediated polymerization of pyridine and furan aromatic precursors, which achieves nanothread formation at reduced pressures. In the case of pyridine, it was found that a combination of slow compression/decompression with broadband UV light exposure yielded a crystalline product featuring a six-fold diffraction pattern with similar interplanar spacings to previously synthesized pyridine-derived nanothreads at a reduced pressure. When furan is compressed to 8 GPa and exposed to broadband UV light, a crystalline solid is recovered that similarly demonstrates X-ray diffraction with an interplanar spacing akin to that of the high-pressure synthesized furan-derived nanothreads. Our method realizes a 1.9-fold reduction in the maximum pressure required to afford furan-derived nanothreads and a 1.4-fold reduction in pressure required for pyridine-derived nanothreads. Density functional theory and multiconfigurational wavefunction-based computations were used to understand the photochemical activation of furan and subsequent cascade thermal cycloadditions. The reduction of the onset pressure is caused by an initial [4+4] cycloaddition followed by increasingly facile thermal [4+2]-cycloadditions during polymerization.

Synthesis, Characterization, and Electrochemistry of Copper Dibenzoporphyrin(2.1.2.1) Complexes.

Three copper dibenzoporphyrin(2.1.2.1) complexes having two dipyrromethene units connected through o-phenylen bridges and 4-MePh, Ph, or F5Ph substituents at the meso positions of the dipyrrins were synthesized and characterized according to their spectral, electrochemical, and structural properties. As indicated by the single-crystal X-ray structures, all three derivatives have highly bent molecular structures, with angles between each planar dipyrrin unit ranging from 89° to 85°, indicative of a nonaromatic molecule. The insertion of copper(II) into dibenzoporphyrins(2.1.2.1) induced a change in the macrocyclic cavity shape from rectangular in the case of the free-base precursors to approximately square for the metalated copper derivatives. Solution electron paramagnetic resonance (EPR) spectra at 100 K showed hyperfine coupling of the Cu(II) central metal ion and the N nucleus in the highly bent molecular structures. Electrochemical measurements in CH2Cl2 or N,N-dimethylformamide (DMF) containing 0.1 M tetrabutylammonium perchlorate (TBAP) were consistent with ring-centered electron transfers and, in the case of reduction, were assigned to electron additions involving two equivalent π centers on the bent nonaromatic molecule. The potential separation between the two reversible one-electron reductions ranged from 230 to 400 mV in DMF, indicating a moderate-to-strong interaction between the equivalent redox-active dipyrrin units of the dibenzoporphyrins(2.1.2.1). The experimentally measured highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gaps ranged from 2.14 to 2.04 eV and were smaller than those seen for the planar copper tetraarylporphyrins(1.1.1.1), (Ar)4PCu.

Interfacial charge transfer complex between TiO2 and non-aromatic ligand squaric acid

The attachment of squaric acid, a non-aromatic molecule, to the surface of TiO2 powder induced the optical absorption of the obtained hybrid material in the visible spectral range due to the interfacial charge transfer complex formation. The optical characterization of the hybrid is supported by the density functional theory calculations of the model cluster. The paramagnetic species generated upon excitation with ultraviolet or visible light, in both TiO2 powders, pristine and surface-modified, were identified conducting low-temperature solid-state and indirect electron paramagnetic resonance (EPR) spectroscopy experiments (spin trapping and spin scavenging). The solid-state EPR experiments indicated the promotion of electrons from the organic moiety to the titania conduction band under visible-light excitation of hybrid. Also, the spin scavenging experiments showed that the electrons generated in the hybrid upon the visible-light activation facilitate the reduction of the radical cations present in the dispersion, while these effects are not observed for pristine TiO2.

Molecular dynamics reveals formation path of benzonitrile and other molecules in conditions relevant to the interstellar medium

Polycyclic aromatic hydrocarbons and polycyclic aromatic nitrogen heterocycles are believed to be widespread in different areas of the interstellar medium. However, the astronomical detection of specific aromatic molecules is extremely challenging. As a result, only a few aromatic molecules have been identified, and very little is known about how they are formed in different areas of the interstellar medium. Recently, McGuire et al. [Science 359, 202-205 (2018)] detected the simple aromatic molecule benzonitrile in Taurus Molecular Cloud-1. Although benzonitrile has been observed, the molecular mechanism for its formation is still unknown. In this study, we use quantum chemistry and ab initio molecular dynamics to model ionization processes of van der Waals clusters containing cyanoacetylene and acetylene molecules. We demonstrate computationally that the clusters' ionization leads to molecular formation. For pure cyanoacetylene clusters, we observe bond formation among two and three monomer units, whereas in mixed clusters, bond formation can also occur in up to four units. We show that the large amount of energy available to the system after ionization can lead to barrier crossing and the formation of complex molecules. Our study reveals the rich chemistry that is observed upon ionization of the clusters, with a wide variety of molecules being formed. Benzonitrile is among the observed molecules, and we study the potential energy path for its formation. These results also offer insights that can guide astronomers in their search for aromatic molecules in the interstellar medium.

Bent bond / antiperiplanar hypothesis and antiaromatic, aromatic and nonaromatic molecules

Abstract The stereochemical reactivities of monocyclic unsaturated compounds having 3–5 and 7–8 membered rings and of bicyclic pentalenes and heptalene can be rationalized through the bent bond/antiperiplanar hypothesis (BBAH) orbital model at the molecular level. This new orbital model considers unsaturations as Pauling τ bonds and that electron delocalization with adjacent pyramidal radical structures (derived from resonance structures) must strictly occur in antiperiplanar fashion. The BBAH shows that, contrary to aromatic (4n+2 Huckel) and nonaromatic molecules, antiaromatic molecules (4n Huckel) have adjacent double bonds that cannot conjugate through antiperiplanar electronic delocalization.

Monitoring the Organic Matter Quality Highlights the Ways in Which Organic Matter Is Removed from Wetland Soil

It has long been considered that ferric phases stabilize organic matter (OM) in soils. Temporarily waterlogged soils, in which Fe is submitted to regular reductive solubilization and oxidizing precipitation, have often been used to study these processes. However, few studies have been interested in the evolution of the OM quality under such conditions. We therefore experimentally investigated the impact of a redox cycle on the quality of the dissolved organic matter (DOM) from wetland soil. The DOM quality was monitored using a combination of analyses run on the elements (%C, %N, C/N), isotopes (δ15N, δ13C), optical index (specific UV absorbance at 254 nm), and fluorescence indexes (FI, HIX, BIX). In addition, the cation and anion concentrations were also determined in the soil solutions throughout the experiment. As classically demonstrated, OM is solubilized as terrestrial aromatic molecules in the first stage of the reducing period, and then as nonaromatic molecules until the end of the reduction, in response to the dissimilatory reductive dissolution of Fe-oxyhydroxides in the soil. More interestingly, we demonstrate that the reintroduction of O2 involves significant lysis of reducing bacterial cells involving the production of small labile organic carbon which represents a significant pathway for OM degradation. Moreover, in response to the physical constraints, the newly formed Fe-OM precipitates produce small aggregates rich in aromatic OM that are expected to disseminate in the environment, representing a second significant way to remove OM.

The bright fluorescence of non-aromatic molecules in aqueous solution originates from pH-induced CTE behavior

Non-aromatic fluorescent materials with inherent visible light emission have received widespread attention. In this work, a biomimetic fluorescent molecule CA-AEP with a dipeptide structure is introduced. CA-AEP will emit bright biomimetic fluorescence in aqueous solutions by adjusting the pH, which has never been reported. This unique luminescent characteristic can be rationalized by the clustering-triggered emission (CTE) mechanism. In addition, CA-AEP can be used to monitor the maximum dynamic pH in the alkaline range of aqueous systems. Finally, the cytotoxicity assay to A549 cells showed that CA-AEP was non-toxic. Therefore, this work provides a new type of luminogen, which has potential application prospects in the field of environmental monitoring and cell biology.

Quantifying bond strengths via a Coulombic force model: application to the impact sensitivity of nitrobenzene, nitrogen-rich nitroazole, and non-aromatic nitramine molecules.

The quantification of bond strengths is a useful and general concept in chemistry. In this work, a Coulombic force model based on atomic electric charges computed using the accurate distributed multipole analysis (DMA) partition of the molecular charge density was employed to quantify the weakest N-NO2 and C-NO2 bond strengths of 19 nitrobenzene, 11 nitroazole, and 10 nitramine molecules. These bonds are known as trigger linkages because they are usually related to the initiation of an explosive. The three families of explosives combine different types of molecular properties and structures ranging from essentially aromatic molecules (nitrobenzenes) to others with moderate aromaticity (nitroazoles) and non-aromatic molecules with cyclic and acyclic skeletons (nitramines). We used the results to investigate the impact sensitivity of the corresponding explosives employing the trigger linkage concept. For this purpose, the computed Coulombic bond strength of the trigger linkages was used to build four sensitivity models that lead to an overall good agreement between the predicted values and available experimental sensitivity values even when the model included the three chemical families simultaneously. We discussed the role of the trigger linkages for determining the sensitivity of the explosives and rationalized eventual discrepancies in the models by examining alternative decomposition mechanisms and features of the molecular structures.

The molecular electronic structure revealed by the magnetically induced Lorentz force density.

The energy change occurring by perturbing a closed-shell molecule, either fixed in space or randomly tumbling, by a uniform external magnetic field has been expressed in terms of the magnetically induced Lorentz force density, which, at difference with previously introduced energy-based quantities, is independent of the point-of-view. The divergence of the isotropically averaged magnetically induced Lorentz force density allows for a local definition of diamagnetic and paramagnetic responses and enables us to distinguish aromatic, antiaromatic, and non-aromatic molecules, as shown by calculations on benzene, cyclooctatetraene, and borazine. The isotropically averaged magnetically induced Lorentz force density turns out very similar to the gradient of the electron density. This similarity is justified in terms of the current knowledge on the current density. A way is opened for an insightful and simplified topological characterization of molecular electronic structure via the magnetic response.

Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence

Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.

Synthesis of thiophene-fused heptalenes by cycloaddition of azulenothiophenes with dimethyl acetylenedicarboxylate

Heptalene has a fused structure of two cycloheptatrienes which is one of the non-aromatic bicyclic molecules with a 12π-electronic structure. We report herein the synthesis of thiophene-fused heptalene derivatives from the corresponding azulenothiophenes via cycloaddition reaction with dimethyl acetylenedicarboxylate. Their structure was clarified by single-crystal X-ray structural analysis. The electronic properties of the thiophene-fused heptalenes obtained by this study were characterized by UV/Vis and fluorescence spectroscopy measurements. The electrochemical features of these derivatives were also examined by voltammetry and spectroelectrochemical experiments.

Bent Bond/Antiperiplanar Hypothesis and the Chemical Reactivity of Annulenes.

The properties and stereochemical reactivity of cyclobutadiene, benzene, cyclooctatetraene, and the [10]- to [14]annulenes can be uniformly rationalized through the bent bond/antiperiplanar hypothesis (BBAH). This new orbital model considers electronic delocalization between pyramidal diradical resonance structures and associated bent bonds, as it applies to aromatic, nonaromatic, and antiaromatic molecules.

Ab initio studies of the effect of the fluorination on deprotonation reaction of the benzene sulfonic acid.

We carried out quantum chemical calculations to analyze the effects of fluorination on the activation energy (Ea) of sulfonic group deprotonation by water molecules. The model molecule was 2,3,4,5,6-pentafluorobenzenesulfonic acid (5FBSA), which was obtained by substituting all aromatic hydrogen atoms of benzenesulfonic acid (BSA) for fluorine atoms. The target hydration level was three. Our analysis indicated that the Ea of deprotonation in 5FBSA was lower than that of BSA, suggesting that the cation of 5FBSA was stabilized. Previous studies have reported that fluorinated molecules have a lower Ea to deprotonation and a stabilized deprotonated state even at a hydration level of three. This effect is attributed to the strong electron withdrawing ability of fluorine. However, compared with non-aromatic molecules, the Ea of deprotonation of aromatic molecules is slightly higher, and the overall energy change (ΔE) is lower, even if the molecule is fluorinated.

The Generated Databases (GDBs) as a Source of 3D-shaped Building Blocks for Use in Medicinal Chemistry and Drug Discovery.

Drug discovery is in constant need of new molecules to develop drugs addressing unmet medical needs. To assess the chemical space available for drug design, our group investigates the generated databases (GDBs) listing all possible organic molecules up to a defined size, the largest of which is GDB-17 featuring 166.4 billion molecules up to 17 non-hydrogen atoms. While known drugs and bioactive compounds are mostly aromatic and planar, the GDBs contain a plethora of non-aromatic 3D-shaped molecules, which are very useful for drug discovery since they generally have more desirable absorption, distribution, metabolism, excretion and toxicity (ADMET) properties. Here we review GDB enumeration methods and the selection and synthesis of GDB molecules as modulators of ion channels. We summarize the constitution of GDB subsets focusing on fragments (FDB17), medicinal chemistry (GDBMedChem) and ChEMBL-like molecules (GDBChEMBL), and the ring system database GDB4c as a rich source of novel 3D-shaped chiral molecules containing quaternary centers, such as the recently reported trinorbornane.