Ashour A. Ahmed

How soil organic matter composition controls hexachlorobenzene–soil-interactions: Adsorption isotherms and quantum chemical modeling

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil<original soil<soil+3 HWE<soil+6 HWE. For the latter three samples this order was also valid for the HCB adsorption. The pyrolyzed soil adsorbed more HCB than the other samples at low initial concentrations, but at higher concentrations the HCB adsorption became weaker than in the samples with HWE addition. This adsorption combined with the differences in the chemical composition between the soil samples suggested that alkylated aromatic, phenol, and lignin monomer compounds contributed most to the HCB adsorption. To obtain a molecular level understanding, a test set has been developed on the basis of elemental analysis which comprises 32 representative soil constituents. The calculated binding energy for HCB with each representative system shows that HCB binds to SOM stronger than to soil minerals. For SOM, HCB binds to alkylated aromatic, phenols, lignin monomers, and hydrophobic aliphatic compounds stronger than to polar aliphatic compounds confirming the above adsorption isotherms. Moreover, quantitative structure-activity relationship (QSAR) of the binding energy with independent physical properties of the test set systems for the first time indicated that the polarizability, the partial charge on the carbon atoms, and the molar volume are the most important properties controlling HCB-SOM interactions.

Controlled experimental soil organic matter modification for study of organic pollutant interactions in soil.

Interactions of organic pollutants with soil organic matter can be studied by adsorption of the pollutants on well-characterized soil samples with constant mineralogy but different organic matter compositions. Therefore, the objectives of the current study are establishing a set of different, well-characterized soil samples by systematic modifications of their organic matter content and molecular composition and prove these modifications by advanced complementary analytical techniques. Modifications were done by off-line pyrolysis and removal/addition of hot-water extracted organic fraction (HWE) from/to the original soil sample. Both pyrolysis-field ionization mass spectrometry (Py-FIMS) and synchrotron-based C- and N- X-ray absorption near-edge structure spectroscopy (XANES) were applied to investigate the composition of the soil organic matter. These complementary analytical methods in addition to elemental analysis agreed in showing the following order of organic matter contents: pyrolyzed soil<soil residue<original soil<soil+3 HWE<soil+6 HWE<HWE. The addition of HWE to the soil sample increases the relative proportions of carbohydrates, N-containing heterocyclic compounds and peptides, and decreases the relative proportions of phenols, lignin monomers and dimers, and lipids. The most abundant organic compound classes in the pyrolyzed sample are aromatics, aliphatic nitriles, aldehydes, five- and six-membered N-containing heterocyclic compounds, and aliphatic carboxylic acids. It can be expected that removal or addition of HWE, that mimic biomass inputs to soil or soil amendments, change the binding capacity for organic pollutants less intensively than heat impact, e.g. from vegetation burning. It will be possible to interpret kinetic data on the pollutants adsorption by these original and modified soil samples on the basis of the bond- and element-specific speciation data through C-XANES and N-XANES and the molecular-level characterization through Py-FIMS. Finally, this combination of analytical techniques can be recommended for similar problems that require characterizing the bulk, non-extracted SOM instead of pre-selected compounds or compound classes.

Glyphosate binding in soil as revealed by sorption experiments and quantum-chemical modeling

The herbicide glyphosate (GLP) is supposed to be rapidly degraded or adsorbed strongly by soil solids but findings in soil years after application and concentrations in waters above legal limits question a harmless disappearance. Therefore, we conducted batch sorption experiments with 23 thoroughly characterized arable surface soils, correlated isotherm coefficients with numerous inorganic and organic soil parameters, and investigated GLP-SOM-complexes by quantum-chemical modeling. The Freundlich sorption model yielded the best fits, and coefficients Kf and nf were correlated positively with the contents of clay/silt. The contents of organic C (Corg) and of the mass-spectrometrically determined SOM-compound classes carbohydrates, phenols/lignin monomers, lignin dimers, lipids, alkylaromatics, non-amide N and amides and sterols all were strongly positively correlated with the Freundlich coefficients. Quantum-chemical modeling showed that both GLP phosphonic and carboxylic functional groups interact similarly with the polar SOM functional groups via H-bond formation but the GLP phosphonic moiety is most important in the GLP-SOM-interaction. Moreover, the interaction mechanism between GLP and every modeled SOM-compound class was explored indicating the importance of the polarity, electron density, and site of attack of the SOM fragments in the GLP-SOM-interaction. Partial binding energies were combined to a total binding energy (EB,tot) of GLP to the SOM, considering the mass spectrometrically quantified compound classes for each individual soil sample. The resulting strongly positive correlation between the EB,tot and the Corg provided compelling new experimental-theoretical evidence for the importance of SOM on the GLP binding and its behavior in the environment. In conclusion, the multitude of binding mechanisms to clay minerals and organic colloids make the occurrence of free GLP rather unlikely but a leaching of GLP complexes via preferential flow path through soil and transfer to waterways rather likely.

Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation

Infrared (IR) excitation of vibrations that participate in the reaction coordinate of an otherwise thermally driven chemical reaction are believed to lead to its acceleration. Attempts at the practical realization of this concept have been hampered so far by competing processes leading to sample heating. Here we demonstrate, using femtosecond IR-pump IR-probe experiments, the acceleration of urethane and polyurethane formation due to vibrational excitation of the reactants for 1:1 mixtures of phenylisocyanate and cyclohexanol, and toluene-2,4-diisocyanate and 2,2,2-trichloroethane-1,1-diol, respectively. We measured reaction rate changes upon selective vibrational excitation with negligible heating of the sample and observed an increase of the reaction rate up to 24%. The observation is rationalized using reactant and transition-state structures obtained from quantum chemical calculations. We subsequently used IR-driven reaction acceleration to write a polyurethane square on sample windows using a femtosecond IR pulse.

A computational study of hexachlorobenzene-soil organic matter-interactions

The fate of hexachlorobenzene (HCB) in soil represents a critical environmental problem. Once HCB has reached the soil it will interact with soil constituents, especially soil organic matter (SOM). The understanding of this interaction is important for choosing effective remediation procedures. Here we report a study of binding of HCB to a test set of molecules, which was developed to mimic representative functional groups of SOM. The binding energy of complexes formed by HCB and the test set molecules were investigated at different levels of theory. Effects of different types of dispersion correction to DFT, basis sets and DFT-functionals have been studied. Moreover, the general ability of dispersion-corrected DFT to represent this interaction has been benchmarked against methods such as MP2 and CCSD. As a result the B3LYP-D3 dispersion correction combined with the 6-311++G(2d,2p) basis set was found to be a compromise between accuracy and efficiency and it is recommended for studying this type of non-covalent interaction. Moreover, the performance of the GROMOS force field in the description of this interaction has been tested.

Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction

Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM.

Molecular level investigation of the role of peptide interactions in the glyphosate analytics

The detection of the herbicide glyphosate (GLP) in environmental samples is most often conducted after derivatizing the target molecule with the chromophore 9-fluorenylmethyloxycarbonyl chloride (FMOC-Cl). However, this method is sensitive to all primary and secondary amines, which can occur in the sample matrix as well. In order to quantify the interference of primary and secondary amines on GLP detection, we have used well-defined peptides such as pentaglycine (PG) and albumin as well as mixtures of peptides such as peptone. These peptides have been added to the derivatization solution of GLP at different constant concentration levels and UV extinction coefficients have been determined. Data analysis supported by quantum chemical modeling of the GLP-peptide, FMOC-GLP, and FMOC-peptide complexation reactions facilitated the identification of two interfering impacts of peptide on GLP derivatization: (i) increase of the signal due to reaction with FMOC-Cl leading to an overestimation of GLP concentration and (ii) decrease of GLP recovery due to complex formation and therefore inhibition of GLP derivatization, which leads to an underestimation. Specifically, our results indicated that the GLP-peptide- and peptide-FMOC-interactions are mainly affected by type of interfering peptides as well as concentration of each peptide and GLP in the environmental samples.

Regioselective synthesis and ab initio calculations of fused heterocycles thermally and under microwave irradiation.

Pyrazolo[1,5-a]pyrimidine, triazolo[1,5-a]pyrimidine, and pyrimido[1,2-a]benzimidazole, pyrido[1,2-a]benzimidazole ring systems incorporating phenylsulfonyl moiety were synthesized via the reaction of 3-(N,N-dimethylamino)-1-(thiophen-2-yl)-2-(phenylsulfonyl)prop-2-en-1-one derivatives with the appropriate aminoazoles as 1,3-binucleophiles and 1H-benzimidazol-2-ylacetonitrile using conventional methods as well as microwave irradiation. The regioselectivity of the cyclocondensation reactions was confirmed both experimentally by alternative synthesis of reaction products and theoretically using ab initio quantum chemical calculations namely the Density Functional Theory (DFT). The theoretical work was carried out using the Becke, three parameter, Lee-Yang-Parr hybrid functional (B3LYP) combined with the 6-311++G(d,p) basis set. It was found that the final cyclocondensation reaction product depends mainly on the initial addition to the activated double bond by the nitrogen atom of the 1,3-binucleophiles that has the higher electron density.

Exploring the nature of the clopidogrel–bromocresol green interaction via spectrophotometric measurements and quantum chemical calculations

Clopidogrel is an oral, thienopyridine class antiplatelet agent used to inhibit blood clots in coronary arteries, peripheral vascular and cerebrovascular diseases. A spectrophotometric method was developed for clopidogrel bisulfate (CLOP·H2SO4) determination using bromocresol green (BCG) as an ion-pairing agent. To explore the binding nature of CLOP·H2SO4 with BCG at a molecular level, quantum chemical calculations have been performed. DFT based full geometry optimization has been carried out for BCG and clopidogrel in basic (CLOP) and protonated (CLOP+) forms as well as for BCG ion-pairs with CLOP and CLOP·H2SO4. The DFT calculations referred to the stability of the BCG–CLOP+ ion-pair and its spontaneous formation reaction from BCG and CLOP·H2SO4 compared to the BCG–CLOP-ion-pair. Furthermore, the UV-visible spectra and their corresponding excited states and electronic transitions for BCG, BCG–CLOP+ ion-pair, and BCG–CLOP ion-pair have been investigated. These spectra provided a molecular level understanding of the nature of the different intra-molecular and intermolecular electronic transitions in the BCG ion-pairs with CLOP+. Moreover, the quantitative analysis based on extracting a yellow-formed ion-pair into chloroform from aqueous medium was carried out. The ion-pair exhibits an absorption maximum at 413 nm. The optimum conditions of the reactions were studied experimentally and optimized. The calibration graph shows that CLOP·H2SO4 can be determined up to 100.0 μg mL−1 with detection limit (LOD) of 0.57 μg mL−1 and quantification limit (LOQ) of 1.86 μg mL−1. The low relative standard deviation values, 0.16–1.16, indicate good precision. The results were compared to other published data and were treated statistically using F and t-tests.

Conformation and electronic structure of Carbidopa. A QM/MD study

Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311++G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework.