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Item Dual-technique assay for the analysis of organophosphorus compounds for environmental and chemical defense applications(Elsevier, 2022) Dowling, Sarah N.; Manicke, Nicholas E.; Chemistry and Chemical Biology, School of ScienceForensic and environmental sciences often rely on chromatographic separations coupled to mass spectrometry to detect contaminants in complex matrices. However, these methods require lengthy analysis times and sample preparation that is not suitable for analysis in the field. In this work, two analytical methods were combined that are known for their potential for portable analysis. The ambient ionization technique, paper spray mass spectrometry (paper spray-MS) was coupled to paper-based surface enhanced Raman spectroscopy (pSERS) to detect toxic organophosphorus molecules from the same substrate, with a total analysis time of less than five minutes. The coupling of these techniques presents a potential for portable Raman screening followed by MS confirmation in a field-forward laboratory. A cartridge insert was designed and 3D printed to facilitate the sample collection and analysis for PS-MS and pSERS. Three chemical warfare agent simulants: dimethyl methylphosphonate (DMMP), diethyl phosphoramidate (DEPA), and diisopropyl methylphosphonate (DIMP) were included in the method due to having similar chemistries to G- and V-series chemical warfare agents (CWAs). Organophosphorus pesticides, malathion and dichlorvos, with similar mechanisms of action to the CWAs, were also included in the method. Because CWAs quickly degrade in the environment, the CWA hydrolysis products, ethyl methylphosphonic acid (EMPA), isopropyl methylphosphonic acid (IMPA), pinacolyl methylphosphonic acid (PinMPA), methylphosphonic acid (MPA), 2-Diethylaminoethanethiol (EDA), and 2-Diisopropylaminoethanethiol (IDA) were also studied. A mixture of the analytes was used to create calibration curves using the dual-polarity, PS-MS method with sub-ng to low ng limits of detection. A dilution series, spanning 3 orders of magnitude, was made using pSERS, also with low ng limits of detection. These experiments show the potential and feasibility for PS-MS coupled to pSERS to be used to rapidly, screen and confirm the presence of organophosphorus molecules, in complex matrices, with portable instrumentation.Item Influence of the Ligand-Field on EPR Parameters of cis- and trans-Isomers in MoV Systems Relevant to Molybdenum Enzymes: Experimental and Density Functional Theory Study(Elsevier, 2023) Nemykin, Victor N.; Sabin, Jared R.; Kail, Brian W.; Upadhyay, Anup; Hendrich, Michael P.; Basu, Partha; Chemistry and Chemical Biology, School of ScienceThe electron paramagnetic resonance (EPR) investigation of mononuclear cis- and trans-(L1O)MoOCl2 complexes [L1OH = bis(3,5-dimethylpyrazolyl)-3-tert-butyl-2-hydroxy-5-methylphenyl)methane] reveals a significant difference in their spin Hamiltonian parameters which reflect different equatorial and axial ligand fields created by the heteroscorpionate donor atoms. Density functional theory (DFT) was used to calculate the values of principal components and relative orientations of the g and A tensors, and the molecular framework in four pairs of isomeric mononuclear oxo‑molybdenum(V) complexes (cis- and trans-(L1O)MoOCl2, cis,cis- and cis,trans-(L-N2S2)MoOCl [L-N2S2H2 = N,N'-dimethyl-N,N'-bis(mercaptophenyl)ethylenediamine], cis,cis- and cis,trans-(L-N2S2)MoO(SCN), and cis- and trans-[(dt)2MoO(OMe)]2- [dtH2 = 2,3-dimercapto-2-butene]). Scalar relativistic DFT calculations were conducted using three different exchange-correlation functionals. It was found that the use of hybrid exchange-correlation functional with 25% of the Hartree-Fock exchange leads to the best quantitative agreement between theory and experiment. A simplified ligand-field approach was used to analyze the influence of the ligand fields in all cis- and trans-isomers on energies and contributions of molybdenum d-orbital manifold to g and A tensors and relative orientations. Specifically, contributions that originated from the spin-orbit coupling of the dxz, dyz, and dx2-y2 orbitals into the ground state have been discussed. The new findings are discussed in the context of the experimental data of mononuclear molybdoenzyme, DMSO reductase.Item Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation(AIP, 2023) Snyder, Ryan; Kim, Bryant; Pan, Xiaoliang; Shao, Yihan; Pu, Jingzhi; Chemistry and Chemical Biology, School of ScienceFree energy simulations that employ combined quantum mechanical and molecular mechanical (QM/MM) potentials at ab initio QM (AI) levels are computationally highly demanding. Here, we present a machine-learning-facilitated approach for obtaining AI/MM-quality free energy profiles at the cost of efficient semiempirical QM/MM (SE/MM) methods. Specifically, we use Gaussian process regression (GPR) to learn the potential energy corrections needed for an SE/MM level to match an AI/MM target along the minimum free energy path (MFEP). Force modification using gradients of the GPR potential allows us to improve configurational sampling and update the MFEP. To adaptively train our model, we further employ the sparse variational GP (SVGP) and streaming sparse GPR (SSGPR) methods, which efficiently incorporate previous sample information without significantly increasing the training data size. We applied the QM-(SS)GPR/MM method to the solution-phase SN2 Menshutkin reaction, NH3+CH3Cl→CH3NH3++Cl-, using AM1/MM and B3LYP/6-31+G(d,p)/MM as the base and target levels, respectively. For 4000 configurations sampled along the MFEP, the iteratively optimized AM1-SSGPR-4/MM model reduces the energy error in AM1/MM from 18.2 to 4.4 kcal/mol. Although not explicitly fitting forces, our method also reduces the key internal force errors from 25.5 to 11.1 kcal/mol/Å and from 30.2 to 10.3 kcal/mol/Å for the N-C and C-Cl bonds, respectively. Compared to the uncorrected simulations, the AM1-SSGPR-4/MM method lowers the predicted free energy barrier from 28.7 to 11.7 kcal/mol and decreases the reaction free energy from -12.4 to -41.9 kcal/mol, bringing these results into closer agreement with their AI/MM and experimental benchmarks.Item Pressure sensitive adhesives and paper spray-mass spectrometry for the collection and analysis of fentanyl-related compounds from shipping materials(Wiley, 2023-09) Prunty, Sarah; Carmany, Daniel; Dhummakupt, Elizabeth S.; Manicke, Nicholas E.; Chemistry and Chemical Biology, School of ScienceThe rise of fentanyl and fentanyl analogs in the drug supply pose serious threats to public health. Much of these compounds enter the United States through shipping routes. Here we provide a method for fentanyl screening and analysis that utilizes pressure-sensitive adhesive (PSA) lined paper to recover drug residues from parcel-related surfaces. The paper used is commercially available repositionable notes (also called post-it or sticky notes). From this paper, mass spectra were obtained by paper spray-mass spectrometry (PS-MS), where PSA paper served as both a sampling and analysis substrate. Seven fentanyl-related compounds were analyzed: fentanyl, 4-anilino-N-phenethylpiperidine (4-ANPP), N,1-diphenethyl-N-phenylpiperidin-4-amine (phenethyl-4-ANPP), valerylfentanyl, 4-fluoroisobutyrylfentanyl (4-FIBF), carfentanil, and p-fluorofentanyl. These compounds were recovered by PSA paper and identified by PS-MS from packaging tape and plastic at 50 ng and from cardboard and shipping labels at 100 ng. The impact of cutting agents on PS-MS analysis of fentanyl analogs was explored. No trends of analyte suppression were found at high concentrations of the cutting agents caffeine, diphenhydramine, and lidocaine when recovered from surfaces. A cartridge that required no precise cutting of PSA paper prior to sampling or analysis was evaluated for use in PS-MS for fentanyl screening. Recovery and detection of fentanyl from plastic sheeting was demonstrated with this cut-free cartridge. The cut-free cartridge showed somewhat less consistency and lower analyte signal than the standard cartridge, but performance was suitable for potential screening applications. In combining PSA surface sampling with PS-MS for drug screening, both sampling and detection of fentanyl-related compounds is simple, rapid, and low-cost.Item Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations(RSC, 2023) Yao, Songyuan; Van, Richard; Pan, Xiaoliang; Park, Ji Hwan; Mao, Yuezhi; Pu, Jingzhi; Mei, Ye; Shao, Yihan; Chemistry and Chemical Biology, School of ScienceInspired by the recent work from Noé and coworkers on the development of machine learning based implicit solvent model for the simulation of solvated peptides [Chen et al., J. Chem. Phys., 2021, 155, 084101], here we report another investigation of the possibility of using machine learning (ML) techniques to “derive” an implicit solvent model directly from explicit solvent molecular dynamics (MD) simulations. For alanine dipeptide, a machine learning potential (MLP) based on the DeepPot-SE representation of the molecule was trained to capture its interactions with its average solvent environment configuration (ASEC). The predicted forces on the solute deviated only by an RMSD of 0.4 kcal mol−1 Å−1 from the reference values, and the MLP-based free energy surface differed from that obtained from explicit solvent MD simulations by an RMSD of less than 0.9 kcal mol−1. Our MLP training protocol could also accurately reproduce combined quantum mechanical molecular mechanical (QM/MM) forces on the quantum mechanical (QM) solute in ASEC environment, thus enabling the development of accurate ML-based implicit solvent models for ab initio-QM MD simulations. Such ML-based implicit solvent models for QM calculations are cost-effective in both the training stage, where the use of ASEC reduces the number of data points to be labelled, and the inference stage, where the MLP can be evaluated at a relatively small additional cost on top of the QM calculation of the solute.Item Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation(Elsevier, 2023-05) Hege, Mellisa; Li, Lei; Pu, Jingzhi; Chemistry and Chemical Biology, School of ScienceIn bacterial endospores, a cross-linked thymine dimer, 5-thyminyl-5,6-dihydrothymine, commonly referred to as the spore photoproduct (SP), is found as the dominant DNA photo lesion under UV radiation. During spore germination, SP is faithfully repaired by the spore photoproduct lyase (SPL) for normal DNA replication to resume. Despite this general mechanism, the exact way in which SP modifies the duplex DNA structure so that the damaged site can be recognized by SPL to initiate the repair process is still unclear. A previous X-ray crystallographic study, which used a reverse transcriptase as a DNA host template, captured a protein-bound duplex oligonucleotide containing two SP lesions; the study showed shortened hydrogen bonds between the AT base pairs involved in the lesions and widened minor grooves near the damaged sites. However, it remains to be determined whether the results accurately reflect the conformation of SP-containing DNA (SP-DNA) in its fully hydrated pre-repair form. To uncover the intrinsic changes in DNA conformation caused by SP lesions, we performed molecular dynamics (MD) simulations of SP-DNA duplexes in aqueous solution, using the nucleic acid portion of the previously determined crystal structure as a template. After MD relaxation, our simulated SP-DNAs showed weakened hydrogen bonds at the damaged sites compared to those in the undamaged DNA. Our analyses of the MD trajectories revealed a range of local and global structural distortions of DNA induced by SP. Specifically, the SP region displays a greater tendency to adopt an A-like-DNA conformation, and curvature analysis revealed an increase in the global bending compared to the canonical B-DNA. Although these SP-induced DNA conformational changes are relatively minor, they may provide a sufficient structural basis for SP to be recognized by SPL during the lesion repair process.Item Photoactivities of thiophene monomer/polymer transition in gel–based photoelectrochemical assembly: A theoretical/experimental approach(Elsevier, 2023-04) Kasem, Kasem K.; Pu, Jingzhi; Cox, Logan; Chemistry and Chemical Biology, School of SciencePhotoactivities of bithiophene and/or terthiophene monomers and their mixtures were studied before and after being subjected to in situ oxidative electropolymerization in gel electrolyte (GE). Measured band gaps and density functional theory calculations supported the presence of oligomers in conjunction with the expected polymers. More oligomers formed during polymerization of the mixed monomers than with pure monomers. The generated photocurrent from the polymer/oligomer was always greater than that of the monomer. These results support the assumption that increasing π-bond conjugation leads to better e/h formation, and charge separation. The study also shows that the increase of the TerTh percentage in the monomer’s mix increased the generated photocurrent by the existing polymer/oligomer mix in a linear monotonic relationship.Item Influence of Choline Chloride/Urea and Glycerol Plasticizers on the Mechanical Properties of Thermoplastic Starch Plastics(MDPI, 2024-03-09) Staker, Jacob; Schott, Sydney; Singh, Riya; Collier, Kourtney; Druschel, Gregory; Siegel, Amanda P.; Tovar, Andres; Chemistry and Chemical Biology, School of ScienceBio-based plastics made of food-safe compostable materials, such as thermoplastic starch (TPS), can be designed into films that have potential to replace many non-biodegradable single-use plastic (SUP) items. TPS film characteristics, such as elongation at break and tensile strength, are largely affected by the choice of the plasticizers used in formulation. Our work identifies the mechanical properties and the chemical structural differences between TPS films made with two different plasticizer mixtures that have not yet been compared alongside one another: deep eutectic solvent choline chloride/urea (1:2) (CC:U) and glycerol with an acetic acid catalyst (AA:G). Potato-based TPS samples were formed by mixing each plasticizer with a consistent amount of potato starch and distilled water with heat. After gelation formation, the viscous TPS mixture was centrifuged to degas and extruded. Films were dried at controlled room temperature. Characterization included the tensile testing of coupons according to ASTM (American Society of Testing and Materials) standard D638, attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, X-ray diffraction (XRD), melting point (MP), and scanning electron microscopy (SEM). The AA:G films displayed significantly higher tensile strength (M = 2.04 ± 1.24 MPa) than the CC:U films (M = 0.18 ± 0.08 MPa); however, the CC:U films had higher elongation at break (M = 47.2 ± 3.6%) than the AA:G films (M = 31.1 ± 12.6%). This can be explained by the difference in functional groups, composition, and the degree of crystallinity evidenced by the FTIR, XRD, MP, and SEM results. Our findings suggest that potato-based TPS films with an AA:G plasticizer mixture hold promise for SUP applications that require more strength, while CC:U films may be more suited for wraps and bags that require flexibility. These innovations can aid to mitigate the environmental impact of harmful plastic waste.Item Photoredox-Catalyzed Divergent Radical Cascade Annulations of 1,6-Enynes via Pyridine N-Oxide-Promoted Vinyl Radical Generation(American Chemical Society, 2023) Wang, Ban; Singh, Jujhar; Deng, Yongming; Chemistry and Chemical Biology, School of ScienceThe divergent organophotoredox-catalyzed radical cascade annulation reactions of 1,6-enynes were developed. A series of cyclopropane-fused hetero- and carbo-bicyclic, tricyclic, and spiro-tetracyclic compounds were facilely synthesized from a broad scope of 1,6-enynes and 2,6-lutidine N-oxide under mild and metal-free conditions with blue light-emitting diode light irradiation. The cascade annulation reaction occurs with the intermediacy of a β-oxyvinyl radical, which is produced from photocatalytically generated pyridine N-oxy radical addition to the carbon-carbon triple bond.Item Facilitating Ab Initio QM/MM Free Energy Simulations by Gaussian Process Regression with Derivative Observations(Royal Society of Chemistry, 2022-10-27) Snyder, Ryan; Kim, Bryant; Pan, Xiaoliang; Shao, Yihan; Pu, Jingzhi; Chemistry and Chemical Biology, School of ScienceIn combined quantum mechanical and molecular mechanical (QM/MM) free energy simulations, how to synthesize the accuracy of ab initio (AI) methods with the speed of semiempirical (SE) methods for a cost-effective QM treatment remains a long-standing challenge. In this work, we present a machine-learning-facilitated method for obtaining AI/MM-quality free energy profiles through efficient SE/MM simulations. In particular, we use Gaussian process regression (GPR) to learn the energy and force corrections needed for SE/MM to match with AI/MM results during molecular dynamics simulations. Force matching is enabled in our model by including energy derivatives into the observational targets through the extended-kernel formalism. We demonstrate the effectiveness of this method on the solution-phase SN2 Menshutkin reaction using AM1/MM and B3LYP/6-31+G(d,p)/MM as the base and target levels, respectively. Trained on only 80 configurations sampled along the minimum free energy path (MFEP), the resulting GPR model reduces the average energy error in AM1/MM from 18.2 to 5.8 kcal mol-1 for the 4000-sample testing set with the average force error on the QM atoms decreased from 14.6 to 3.7 kcal mol-1 Å-1. Free energy sampling with the GPR corrections applied (AM1-GPR/MM) produces a free energy barrier of 14.4 kcal mol-1 and a reaction free energy of -34.1 kcal mol-1, in closer agreement with the AI/MM benchmarks and experimental results.