Large Organic Molecules Research Articles

Pseudopotential‐fragment spectroscopy for organic molecules and carbon allotropes

AbstractFollowing on from a previous work (Punter et al., IJQC 2019, 119, 23), pseudopotential sets are developed and tested for a variety of sp2 and sp3 carbon fragments. These fragments contain only one or two explicit protons and electrons, and make use of non‐atom‐centered potentials. They are tested with density functional theory calculations in a selection of chemical environments in which several physical characteristics, including orbital and first ionization energies, are found to be well reproduced. They are then employed in the reproduction of molecular absorption spectra for large organic molecules and carbon allotropes, and are found to recreate both absorption and electronic circular dichroism spectra to a high accuracy. They are also found significantly to increase the computational efficiency of time dependent density functional theory (TDDFT) calculations in which they are used.

Isotopic constraints on plant nitrogen acquisition strategies during ecosystem retrogression.

Plant root associations with microbes such as mycorrhizal fungi or N-fixing bacteria enable ecosystems to tap pools of nitrogen (N) that might otherwise be inaccessible, including atmospheric N or N in large soil organic molecules. Such microbially assisted N-foraging strategies may be particularly important in late-successional retrogressive ecosystems where productivity is low and soil nutrients are scarce. Here, we use natural N-stable isotopic composition to constrain pathways of N supplies to different plant functional groups across a well-studied natural soil fertility gradient that includes a highly retrogressive stage. We demonstrate that ectomycorrhizal fungi, ericoid mycorrhizal fungi, and N-fixing bacteria support forest N supplies at all stages of ecosystem succession, from relatively young, N-rich/phosphorus (P)-rich sites, to ancient sites (ca. 500 ky) where both N supplies and P supplies are exceedingly low. Microbially mediated N sources are most important in older ecosystems with very low soil nutrient availability, accounting for 75-96% of foliar N at the oldest, least fertile sites. These isotopically ground findings point to the key role of plant-microbe associations in shaping ecosystem processes and functioning, particularly in retrogressive-phase forest ecosystems.

Insights on Redox Properties of Sumanene Derivatives for High-Performance Organic Cathodes.

Despite the potential of large organic molecules for insoluble cathode materials in lithium-ion batteries, they have attracted less attention owing to the penalty in the molecular weight. Herein, an advanced computational modeling approach is employed to comprehensively explore the electrochemical characteristics and theoretical charge/energy storage capability for a series of sumanene derivatives. It is highlighted from this investigation that the carbonyl moiety is generally beneficial to the improvement of the redox properties for the sumanenes. The sumanene with hexagon rings fully functionalized by six carbonyls particularly exhibits both the remarkably high redox potential (3.53 V vs Li/Li+) and performance parameters (454 mAh/g and 1129 mWh/g), implying its candidacy as high-potential organic cathodes. It is further demonstrated from a universal relationship of redox potential-electronic property-solvation property that a sumanene derivative would experience a two-stage discharging behavior. This indicates that the sumanene derivative would be cathodically inactive due to a sudden increase of solvation energy.

Retention of organics and degradation of micropollutants in municipal wastewater using impregnated ceramics

Pesticides, personal care products, industrial chemicals often pollute surface- and groundwater sources. With trace concentrations and low molecular weights, these micropollutants (MPs) easily penetrate through treatment systems and impose a real health threat on drinking water consumers. The absence of a dedicated MP-retaining treatment technology at water treatment plants results in a constant consumption of MP-contaminated water. Advanced oxidation processes, and in particular the Fenton reaction, can successfully degrade MPs if other, larger, fractions of organics are retained. Here, we suggest a novel combined two-stage retention–degradation approach. Ceramic membranes retain large organics such as bovine serum albumin (BSA). Fenton processes disintegrate nonretained MPs such as methylene blue (MB) and bisphenol A (BPA) that penetrate through the membrane. The efficiency of the suggested approach is high. Single-layered ultrafiltration membrane retains more than 96% BSA and degrades 40–50% of MB and BPA. The degree of degradation depends on both the impregnated metal oxide and the concentration of hydrogen peroxide. Vanadium-based catalysts retain more than 90% MPs but leach into permeate. Ferric oxides were the only stable catalysts that performed better in membranes than when impregnated on α-Al2O3 pellets. A combined retention–degradation can be optimized to result in superior degree of retention. Catalytic ceramic membranes can retain large organic molecules and decompose MPs simultaneously. Three parameters affect the process efficiency: the dynamics of the influent fluid, the catalyst dose and the contact time.Graphic abstract

Visible light-Driven AgBr/AgCl@MIL-101(Fe) Composites For Removal of Organic Contaminant From Wastewater.

Microwave-solvothermal synthesized MIL-101(Fe) was successfully loaded by silver halides (AgCl and AgBr) by simple precipitation method. The XRD, FESEM mapping, XPS and DRS measurements reveal the successful fabrication of composite photocatalyst. The results suggested that silver halides altered surface charge, surface area and pore size distribution of MIL-101(Fe). The 20%AgBr@MIL-101(Fe) composite has strong tendency to remove the cationic/anionic dyes (96% of rhodamine B, 100% of malachite green and 92% of methyl orange) from wastewater after 30min of adsorption and 90min under visible light irradiation. The composite photocatalyst revealed the photodegradation stability up to four cycles. The formation of mesopores improves the adsorption ability of the composites for large organic molecules, while loaded silver halides might inhibit the recombination of electron-hole pairs; those were responsible for enhancing the photocatalytic degradation of organic pollutants. ESR suggested , were responsible for dye degradation in visible light by composite photocatalysts. The photocatalytic mechanism of the composite was also explained in this work.

Optimized Alkali-Metal Cationization in Secondary Ion Mass Spectrometry of Polyethylene Glycol Oligomers with up to m/z 10000: Dependence on Cation Species and Concentration.

In secondary ion mass spectrometry (SIMS), the detection of large organic molecules is accomplished using cluster ion bombardment. Ion formation often proceeds via cationization, through the attachment of (alkali) metal ions to the molecule. To study this process, the emission of secondary ions sputtered from polyethylene glycol (PEG) samples with molecular weights (MW) of 1000-10000 was examined. They were mixed with alkali-metal trifluoroacetic acid (X-TFA, where X = Li, Na, K, or Cs) in a wide range of concentrations to investigate the efficiency of cationization for 10 keV Ar2000+ cluster irradiation. Typically, cationized molecular ions [M + X]+ (with repeat units n of up to ∼250, corresponding roughly to m/z 11000) and some characteristic fragment species were observed in the mass spectra. For all alkali cations, the oligomer intensities increase strongly with the molecular composition ratios X-TFA/PEG in the samples, and values of 5-10 seem to be optimal. With increasing molecular weight, the intensity of oligomer ions relative to the total number of ions decreases; as the latter remains rather constant, this implies that more fragment species are formed. The ion yields (detected ions per primary ions) of cationized [M + Na]+ oligomers sputtered from a PEG decrease very strongly with their size n: from 5.2 × 10-6 at n = 21 (MW ∼ 1000) to 4.5 × 10-10 at n ∼ 245 (MW ∼ 11000). By contrast, the total yields Ytot+ show only a small variation for these different specimens, from 1.3 × 10-5 to 3.7 × 10-5.

Predicting equilibrium intramolecular isotope distribution within a large organic molecule by the cutoff calculation

A predicted equilibrium intramolecular isotope distribution (Intra-ID) serves as a reference for measured position-specific (PS) isotope composition variation in an organic molecule. Equilibrium Intra-ID can be estimated from calculated reduced partition function ratios (RPFR or β factor), which are largely absent to date. For relatively small molecules, the PS β factor can be calculated directly. However, estimating the PS β factor considering an entire, large organic molecule is computationally prohibitive. The isotope effect is local in that the vibrational frequencies of an atom are only affected by its proximal bonding environment. Therefore, the cutoff calculation, which simplifies the calculation of an entire molecule to a local area, was previously proposed for large organic molecules. However, the cutoff size was not validated, which has hindered the application of the cutoff calculation. Here, we calculated a series of small organic molecules with 2–18 carbon atoms to test the influence of cutoff size on the 13β value estimation of a target carbon position in a carbon chain or a carbon ring. We calculated nineteen small molecules that have a methyl carbon and a functional group that is at least three bonds away from the target methyl position. The result showed that the equilibrium 13C enrichment of the methyl group relative to CO2 at 25 °C (ln13α(eq)) for the nineteen molecules varied in a small range, with a standard deviation of 0.2‰. Fourteen aromatic hydrocarbons with a benzene and one adjacent functional group were calculated to test the influence of different adjacent functional groups on similar carbon positions in benzene. The results showed that different adjacent functional groups had significant influence only on the predicted ln13α(eq) value of the carbon position directly connected to them (standard deviation = 1.0‰, n = 14), with a negligible influence on the predicted ln13α(eq) value of the remaining carbons in benzene (standard deviation = 0.2‰, n = 14). The PS 13β value of a specific carbon position in CoA calculated by the cutoff calculation differed from that of the entire-molecule calculation by 0.0–0.3‰. We concluded that the cutoff calculation simplified the calculation of a target position from an entire molecule to a cluster of three proximal bonds in a chain and/ or an adjacent ring, providing PS 13β values of sufficient accuracy for large organic molecules.

Indirect probe of quantum gravity using molecular wave-packets

The most obvious obstacle behind a direct test of quantum gravity (QG) is its energy scale (1019 GeV), which remains well outside of any human made machine. The next best possible approach is to provide indirect tests on effective theories of QG which can be performed in a lower energy scale. This paper is aimed in this direction, and shows a promising path to test the existence of the fundamental minimal length scale of Nature by measuring the dispersion of free, large molecular wave-packets. The existence of the minimal length is believed to be the reason for a modified commutation relationship between the position and momentum operators and, in this paper, we show that such a modification of the commutator has a profound effect on the dispersion rate of free wave-packets, and precise measurement on the broadening times of large molecular wave-packets (such as C60, C176 and large organic molecules) provide a promising path for an indirect test of quantum gravity, in a laboratory setting.

Effect of beading parameters on cross-linked chitosan adsorptive properties

Among countless applications, chitosan has the potential to be an effective and cheap adsorbent for pollutant removal in (waste) water. In form of beads, it also exhibits good mechanical and fluid dynamic properties that are suitable for utilization in large-scale adsorption processes (e.g. as column packing). The present study investigates the beading process to prepare chitosan and cross-linked chitosan beads by phase inversion method. Beading parameters (i.e. chitosan amount, acid concentration, non-solvent agent concentration, and temperature) are optimized to obtain an appropriate adsorbent structure to uptake large organic molecules (reactive red 2, a dye, is utilized as model pollutant). Chitosan beads present remarkably enhanced adsorption capacity, mainly thanks to increased specific surface area and porosity. The addition of a cross-linker (diepoxyoctane) further improves pollutant removal. The adsorption process is well-fitted by the Freundlich model, suggesting a multilayer adsorption. The kinetic study also substantiates the complexity of the adsorption mechanism on bead surface, which, however, is satisfactorily predicted by a simple fractal kinetic model. Finally, it is proved that chitosan and cross-linked chitosan beads can be recycled (by washing with NaOH solution) at least 5 times before sensible performance loss.

Predictions of diffusion rates of large organic molecules in secondary organic aerosols using the Stokes–Einstein and fractional Stokes–Einstein relations

Abstract. Information on the rate of diffusion of organic molecules within secondary organic aerosol (SOA) is needed to accurately predict the effects of SOA on climate and air quality. Diffusion can be important for predicting the growth, evaporation, and reaction rates of SOA under certain atmospheric conditions. Often, researchers have predicted diffusion rates of organic molecules within SOA using measurements of viscosity and the Stokes–Einstein relation (D∝1/η, where D is the diffusion coefficient and η is viscosity). However, the accuracy of this relation for predicting diffusion in SOA remains uncertain. Using rectangular area fluorescence recovery after photobleaching (rFRAP), we determined diffusion coefficients of fluorescent organic molecules over 8 orders in magnitude in proxies of SOA including citric acid, sorbitol, and a sucrose–citric acid mixture. These results were combined with literature data to evaluate the Stokes–Einstein relation for predicting the diffusion of organic molecules in SOA. Although almost all the data agree with the Stokes–Einstein relation within a factor of 10, a fractional Stokes–Einstein relation (D∝1/ηξ) with ξ=0.93 is a better model for predicting the diffusion of organic molecules in the SOA proxies studied. In addition, based on the output from a chemical transport model, the Stokes–Einstein relation can overpredict mixing times of organic molecules within SOA by as much as 1 order of magnitude at an altitude of ∼3 km compared to the fractional Stokes–Einstein relation with ξ=0.93. These results also have implications for other areas such as in food sciences and the preservation of biomolecules.

Membranes with Thin Hydrogel Selective Layers Containing Viral-Templated Palladium Nanoparticles for the Catalytic Reduction of Cr(VI) to Cr(III)

Membranes that simultaneously remove large organic molecules and catalytically treat smaller contaminants can provide a simple, compact, single-step water treatment solution. Incorporating nanopart...

ESCAPE: A novel approach for a fast estimation of dynamic correlation energies: Application to large organic molecules.

Advanced wave function-based quantum chemical ab initio methods, such as CCSD(T), are able to calculate the energies of small- to medium-sized molecules with chemical accuracy. Unfortunately, these methods scale quite unfavorably with the size of the system and are getting too time consuming-and too expensive-for larger molecules. In order to be able to treat larger organic molecules, we propose a novel scheme for a quick and reliable estimate of molecular correlation energies, which we call ESCAPE (EStimation of CorrelAtion energies by Pair Energies). It is based on the pair correlation energies for localized molecular orbitals that have been generated by CCSD[T] and fitted to suitable functional forms. All fit parameters are stored in a large parameter file. Aiming at chemical accuracy (±1 kcal/mol), we have first limited our approach to aliphatic hydrocarbons. The total molecular CCSD[T] correlation energies of a training set of 41 aliphatic hydrocarbons could be reproduced with a mean absolute error (MAE) of 0.56 kcal/mol or 0.11%. A similar accuracy could be obtained for a test set of 11 additional hydrocarbons with up to eight carbon atoms (MAE of 0.65 kcal/mol or 0.09%). In a more critical test, we checked the small energy differences for a set of 13 isomerization reactions. The comparison with experimental data showed that we could reach chemical accuracy as well. Our estimate (MAE of 0.55 kcal/mol) is slightly inferior to the CCSD[T] result (MAE of 0.17 kcal/mol), but superior to SCF, DFT/B3LYP, and DFT/B3LYP + D3. Moreover, in all cases, we obtained the correct sign, that is, the correct equilibrium structure. A similar accuracy could be reached in an application to the three lowest isomers of the C60 molecule. Using the example of a set of eight alcohols, we were able to proof the method's ability for molecules including heteroatoms. Three fast steps are necessary for the application to any aliphatic hydrocarbon or alcohol: (1) An SCF calculation at the selected molecular geometry; it can be fast since a medium size basis set is generally sufficient. (2) The localization of the occupied molecular orbitals and determination of their properties (center of charge and spatial extent). (3) Estimate of the correlation energy using the existing parameter file. © 2019 Wiley Periodicals, Inc.

Structural Evolution of Burmese Amber during Petrifaction Based on a Comparison of the Spectral Characteristics of Amber, Copal, and Rosin

This paper presents a spectroscopic analysis and solubility study of rosin, copal, and Burmese amber samples to reveal the structural changes that occur during amber formation. The infrared spectra indicate that during the long geological process of amber formation, small resin molecules first crosslinked and slowly oxidized, eventually forming a stable organic polymer mixture. An analysis of Raman peak areas demonstrated that among the tested samples, the degree of polymerization is highest in Burmese amber and lowest in rosin. Ultraviolet-visible spectra indicate the presence of unsaturated bonds (e.g., carbonyl groups) or conjugated systems in Burmese amber, copal, and rosin. The evaluation of amber, rosin, and copal solubility in six solvents (ethanol, acetone, 1,4-dioxane, ethylacetate, N,N-dimethylamide, and dichloromethane) demonstrated that solubility decreases in the following order: rosin > copal > Burmese amber. Together, the results suggest that the structure of Burmese amber includes large organic molecules containing six-membered rings along with CH2, CH3, C=O, C=C, C–O, and C–C groups.

Yanli Zhao.

"My biggest motivation is the discovery of new therapeutics to save lives. The most significant scientific advance of the last 100 years has been the discovery of polio vaccine …" Find out more about Yanli Zhao in his Author Profile.

Electronic Excitations of Polythiophene within Many-Body Perturbation Theory with and without the Tamm-Dancoff Approximation.

Excited electronic states of small and large π-conjugated organic molecules can be described within ab initio many-body perturbation theory, notably by the GW approximation for the electron self-energy operator combined with the Bethe-Salpeter equation for correlated electron-hole excitations. In this context, the Tamm-Dancoff approximation is routinely employed to reduce the computational effort. It is known that the use of this approximation introduces errors of several 100 meV for small organic molecules but is negligible for extended systems. In this paper, we investigate how exactly the transition between these two regimes happens, by calculating the optical excitation energies of a series of polythiophene molecules of different sizes. We determine which parts of the electron-hole interaction are responsible for the deviation and show that the quantitative effects of the Tamm-Dancoff approximation depend sensitively on the size of the electronic system, in particular on the electronic conjugation length.

VUV Photolysis of CH4–H2O mixture in methane-rich ices: Formation of large complex organic molecules in astronomical environments

The present work aims to highlight the influence of water molecules in the photo-decomposition of methane ice and reveal the photoproducts formed in solid phase upon VUV irradiation of CH4–H2O mixture in methane-rich ices. The analysis of our IR spectra shows that even with very low concentrations of water in methane ices, several oxygenated hydrocarbons are formed as photoproducts derived from the photodecomposition of water and methane at cryogenic temperatures. We show that both alka[e]nes and oxygen bearing organics are efficiently formed at temperatures as low as 3 K. However, while the IR signatures of the alka[e]nes such as C2H6, C2H4 and C2H2 dominate the IR spectra of the irradiated CH4–H2O ices at temperatures lower than 50 K, the heating of the sample to 110 K reveals the formation of large carbon chain complex organic molecules such as ethanol, pronanol, propanal and glycolaldehyde.

Molecular beam/infrared reflection-absorption spectroscopy apparatus for probing heterogeneously catalyzed reactions on functionalized and nanostructured model surfaces.

A new custom-designed ultrahigh vacuum (UHV) apparatus combining molecular beam techniques and in situ surface spectroscopy for reactivity measurements on complex nanostructured model surfaces is described. It has been specifically designed to study the mechanisms, kinetics, and dynamics of heterogeneously catalyzed reactions over well-defined model catalysts consisting of metal nanoparticles supported on thin oxide films epitaxially grown on metal single crystals. The reactivity studies can be performed in a broad pressure range starting from UHV up to the ambient pressure conditions. The UHV system includes (i) a preparation chamber providing the experimental techniques required for the preparation and structural characterization of single-crystal based model catalysts such as oxide supported metal particles or ordered oxide surfaces and (ii) the reaction chamber containing three molecular beams-two effusive and one supersonic, which are crossed at the same point on the sample surface, infrared reflection-absorption spectroscopy for the detection of surface-adsorbed species, and quadrupole mass spectrometry for gas phase analysis. The supersonic beam is generated in a pulsed supersonic expansion and can be modulated via a variable duty-cycle chopper. The effusive beams are produced by newly developed compact differentially pumped sources based on multichannel glass capillary arrays. Both effusive sources can be modulated by a vacuum-motor driven chopper and are capable of providing high flux and high purity beams. The apparatus contains an ambient pressure cell, which is connected to the preparation chamber via an in situ sample transfer system and provides an experimental possibility to study the reactivity of well-defined nanostructured model catalysts in a broad range of pressure conditions-up to ambient pressure-with the gas phase analysis based on gas chromatography. Additionally, a dedicated deposition chamber is connected to the preparation chamber, which is employed for the in situ functionalization of model surfaces with large organic molecules serving as promoters or modifiers of chemical reactions. We present a general overview of the apparatus as well as a description of the individual components and their interplay. The results of the test measurements involving the most important components are presented and discussed.

Influence of Hydronium Ions in Zeolites on Sorption

AbstractIn the presence of sufficient concentrations of water, stable, hydrated hydronium ions are formed in the pores and at the surface of solid acids such as zeolites. For a medium‐pore zeolite, such as zeolite MFI, hydrated hydronium ions consist of eight water molecules and have an effective volume of 0.24 nm3. In their presence, larger organic molecules can only adsorb in the portions of the pore that are not occupied by hydronium ions. As a consequence, the available pore volume decreases proportionally to the concentration of the hydronium ions. The higher charge density (the increasing ionic strength) that accompanies an increasing concentration of hydronium ions leads to an increase in the activity coefficients of the adsorbed substrates, thus, weakening the interactions between the organic part of the molecules and the zeolite and favoring the interactions with polar groups. The quantitative understanding of these interactions makes it possible to link a collective property such as hydrophilicity and hydrophobicity of zeolites to specific interactions on molecular level.

Facile Fabrication of a Multifunctional Metal-Organic Framework-based Sensor Exhibiting Exclusive Solvochromic Behaviors toward Ketone Molecules.

To probe the efficient strategy for preparing a multifunctional sensing material, the facile synthesis strategies and successful examples are urgently required. Through the utilization of a hexadentate ligand derived from cyclotriphosphazene, which displays spiral configurations and multiple connection modes, a novel metal-organic framework (MOF) was constructed via one-step synthesis from low-cost raw materials. The presence of multiple interaction sites decorating the helical channels of the reported MOF gives rise to exclusive solvochromic-sensing behavior for small ketone molecules such as acetone, acetophenone, and 2,5-diketohexane. Additionally, the helical structure of a manganese-carboxylate chain allows for the pore volume not only be available for the adsorption of large organic molecules but also enables the enantiopure selective separation of 1-phenylethanol (ee 35.99 %). Furthermore, the structural analysis of the acetophenone-encapsulated sample allowed the solvochromic mechanism to be elucidated, which should be ascribed to the strong hydrogen-bonding interaction between the guest molecules and specific sites on a host matrix. The experimental results have not only clearly manifested the vital role of starting materials of MOFs, including the connection modes and spatial configuration, but also have provided very valuable insight for the future assembly of novel multifunctional sensing materials.

Triplet Tuning: A Novel Family of Non-Empirical Exchange-Correlation Functionals.

In the framework of density functional theory (DFT), the lowest triplet excited state (T1) can be evaluated using multiple formulations, the most straightforward of which are unrestricted density functional theory (UDFT) and time-dependent density functional theory (TDDFT). Assuming the exact exchange-correlation (XC) functional is applied, UDFT and TDDFT provide identical energies for T1 ( ET), which is also a constraint that we require our XC functionals to obey. However, this condition is not satisfied by most of the popular XC functionals, leading to inaccurate predictions of low-lying, spectroscopically and photochemically important excited states, such as T1 and the lowest singlet excited state (S1). Inspired by the optimal tuning strategy for frontier orbital energies [T. Stein, L. Kronik, and R. Baer, J. Am. Chem. Soc. 2009, 131, 2818], we proposed a novel and nonempirical prescription of constructing an XC functional in which the agreement between UDFT and TDDFT in ET is strictly enforced. Referred to as "triplet tuning", our procedure allows us to formulate the XC functional on a case-by-case basis, using the molecular structure as the exclusive input, without fitting to any experimental data. The first triplet tuned XC functional, TT-ωPBEh, is formulated as a long-range-corrected (LRC) hybrid of Perdew-Burke-Ernzerhof (PBE) and Hartree-Fock (HF) functionals [M. A. Rohrdanz, K. M. Martins, and J. M. Herbert, J. Chem. Phys. 2009, 130, 054112] and tested on four sets of large organic molecules. Compared to existing functionals, TT-ωPBEh manages to provide more accurate predictions for key spectroscopic and photochemical observables, including but not limited to ET, the optical band gap ( ES), the singlet-triplet gap (Δ EST), and the vertical ionization potential ( I⊥), as it adjusts the effective electron-hole interactions to arrive at the correct excitation energies. This promising triplet tuning scheme can be applied to a broad range of systems that were notorious in DFT for being extremely challenging.