Theoretical study on NO3-initiated oxidation of acenaphthene in the atmosphere

2008 ◽  
Vol 86 (2) ◽  
pp. 129-137 ◽  
Author(s):  
Xiaohui Qu ◽  
Qingzhu Zhang ◽  
Wenxing Wang
Keyword(s):  
Product Information ◽  
Environmental Concern ◽  
Single Point ◽  
Basis Set ◽  
Orbital Theory ◽  
Night Time ◽  
Point Energy ◽  
Secondary Reactions ◽  
Favorable Reaction ◽  
High Level

Acenaphthene is widespread and toxic, and thus of substantial environmental concern. The reaction with NO3 radicals is an important atmospheric loss process of acenaphthene at night time. In this work, the mechanism for the NO3-initiated atmospheric oxidation reaction of acenaphthene has been studied using high level molecular orbital theory. Geometries of all the related species have been optimized at the MPWB1K level with the 6–31G(d,p) basis set. The single-point energy calculations have been carried out at the MPWB1K/6–311+G(3df,2p) level. The possible secondary reactions were also studied. Several energetically favorable reaction pathways were revealed for the first time.Key words: acenaphthene, NO3 radicals, reaction mechanism, product information, oxidation degradation.

Atmospheric oxidation mechanism of polyfluorinated sulfonamides — A quantum chemical and kinetic study

2013 ◽  
Vol 91 (6) ◽  
pp. 472-478 ◽  
Author(s):  
Xiaoyan Sun ◽  
Lei Ding ◽  
Qingzhu Zhang ◽  
Wenxing Wang
Keyword(s):  
Rate Constants ◽  
Density Functional ◽  
Single Point ◽  
Oxidation Mechanism ◽  
Basis Set ◽  
Atmospheric Oxidation ◽  
Oh Radicals ◽  
Oh Radical ◽  
Orbital Theory ◽  
Point Energy

Polyfluorinated sulfonamides (FSAs, F(CF2)nSO2NR1R2) are present in the atmosphere and may serve as the source of perfluorocarboxylates (PFCAs, CF3(CF2)nCOO–) in remote locations through long-range atmospheric transport and oxidation. Density functional theory (DFT) molecular orbital theory calculations were carried out to investigate OH radical-initiated atmospheric oxidation of a series of sulfonamides, F(CF2)nSO2NR1R2 (n = 4, 6, 8). Geometry optimizations of the reactants as well as the intermediates, transition states, and products were performed at the MPWB1K level with the 6-31G+(d,p) basis set. Single-point energy calculations were carried out at the MPWB1K/6-311+G(3df,2p) level of theory. The OH radical-initiated reaction mechanism is given and confirms that the OH addition to the sulfone double bond producing perfluoroalkanesulfonic acid directly cannot occur in the general atmosphere. Canonical variational transition-state (CVT) theory with small curvature tunneling (SCT) contribution was used to predict the rate constants. The overall rate constants were determined, k(T) (N-EtFBSA + OH) = (3.21 × 10−12) exp(–584.19/T), k(T) (N-EtFHxSA + OH) = (3.21 × 10−12) exp(–543.24/T), and k(T) (N-EtFOSA + OH) = (2.17 × 10−12) exp(–504.96/T) cm3 molecule−1 s−1, over the possible atmospheric temperature range of 180–370 K, indicating that the length of the F(CF2)n group has no large effect on the reactivity of FSAs. Results show that the atmospheric lifetime of FSAs determined by OH radicals will be 20–40 days, which agrees well with the experimental values (20–50 days), 20 thus they may contribute to the burden of perfluorinated pollution in remote regions.

Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

2013 ◽  
Vol 91 (7) ◽  
pp. 559-572 ◽  
Author(s):  
Jennifer L. Kellie ◽  
Stacey D. Wetmore
Keyword(s):  
Active Sites ◽  
Noncovalent Interactions ◽  
Single Point ◽  
Enzymatic Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dna Glycosylases ◽  
Dft Methods ◽  
Primary Focus ◽  
High Level

When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.

scholarly journals Computational Modeling and Theoretical Calculations on the Interactions between Spermidine and Functional Monomer (Methacrylic Acid) in a Molecularly Imprinted Polymer

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Yujie Huang ◽  
Qiujin Zhu
Keyword(s):  
Binding Energy ◽  
Methacrylic Acid ◽  
Molecularly Imprinted Polymer ◽  
Single Point ◽  
Basis Set ◽  
Stable Complex ◽  
Functional Monomer ◽  
Imprinted Polymer ◽  
Point Energy ◽  
Molecularly Imprinted

This paper theoretically investigates interactions between a template and functional monomer required for synthesizing an efficient molecularly imprinted polymer (MIP). We employed density functional theory (DFT) to compute geometry, single-point energy, and binding energy (ΔE) of an MIP system, where spermidine (SPD) and methacrylic acid (MAA) were selected as template and functional monomer, respectively. The geometry was calculated by using B3LYP method with 6-31+(d) basis set. Furthermore, 6-311++(d, p) basis set was used to compute the single-point energy of the above geometry. The optimized geometries at different template to functional monomer molar ratios, mode of bonding between template and functional monomer, changes in charge on natural bond orbital (NBO), and binding energy were analyzed. The simulation results show that SPD and MAA form a stable complex via hydrogen bonding. At 1 : 5 SPD to MAA ratio, the binding energy is minimum, while the amount of transferred charge between the molecules is maximum; SPD and MAA form a stable complex at 1 : 5 molar ratio through six hydrogen bonds. Optimizing structure of template-functional monomer complex, through computational modeling prior synthesis, significantly contributes towards choosing a suitable pair of template-functional monomer that yields an efficient MIP with high specificity and selectivity.

Theoretical study on the OH-initiated atmospheric reaction of N-methyl perfluorobutane sulfonamidoethanol (C4F9SO2N(CH3)CH2CH2OH)

2013 ◽  
Vol 91 (12) ◽  
pp. 1161-1167
Author(s):  
Juan Dang ◽  
Lei Ding ◽  
Xiaoyan Sun ◽  
Qingzhu Zhang ◽  
Wenxing Wang
Keyword(s):  
Reaction Mechanism ◽  
Degradation Products ◽  
Single Point ◽  
Basis Set ◽  
Stationary Points ◽  
Geometrical Parameters ◽  
Chemical Transformations ◽  
Point Energy ◽  
Range Transport ◽  
Perfluorinated Carboxylic Acids

N-methyl perfluorobutane sulfonamidoethanol (NMeFBSE), a new product of the 3M Company, is currently widely used in many countries and territories. It is prone to volatilize to the atmosphere where it can undergo long-range transport and chemical transformations. In this work, the reaction mechanism for the OH-initiated atmospheric oxidation of NMeFBSE was investigated. The geometrical parameters and vibrational frequencies of all of the stationary points were calculated at the MPWB1K level with the 6-31G+(d,p) basis set. Single-point energy calculations were carried out at the MPWB1K/6-311+G(3df,2p) level. The results indicate that the channel of the formation of C4F9 and HSO3N(CH3)CH2CH2OH resulting from OH addition to NMeFBSE and hydrogen abstractions from the −CH3 group in NMeFBSE are energetically favorable. The main degradation products include perfluorinated carboxylic acids (C3F7COOH, C2F5COOH, CF3COOH), HSO3N(CH3)CH2CH2OH, NMeFBSA (C4F9SO2NH(CH3)), C4F9SO2N(CH3)CH2CHO, and C4F9SO2N(CH3)CH2COOH. The reaction mechanism for the formation of NMeFBSA is reported for the first time. Using the atmospheric fate of NMeFBSE as a guide, it seems that N-methyl perfluorooctane sulfonamidoethanol (NMeFOSE) contributes to the ubiquity of perfluoroalkyl sulfonate and carboxylate compounds in the atmosphere.

scholarly journals Computational Study of the Dissociation Reactions of Secondary Ozonide

Atmosphere ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 100 ◽  
Author(s):  
Mansour H. Almatarneh ◽  
Shefa’ F. Alrebei ◽  
Mohammednoor Altarawneh ◽  
Yuming Zhao ◽  
Abd Al-Aziz Abu-Saleh
Keyword(s):  
Barrier Height ◽  
Computational Study ◽  
Reaction Pathway ◽  
Single Point ◽  
Water Dimer ◽  
Basis Set ◽  
Basis Sets ◽  
Water Molecules ◽  
Point Energy ◽  
Secondary Ozonide

This contribution presents a comprehensive computational study on the reactions of secondary ozonide (SOZ) with ammonia and water molecules. The mechanisms were studied in both a vacuum and the aqueous medium. All the molecular geometries were optimized using the B3LYP functional in conjunction with several basis sets. M06-2X, APFD, and ωB97XD functionals with the full basis set were also used. In addition, single-point energy calculations were performed with the G4MP2 and G3MP2 methods. Five different mechanistic pathways were studied for the reaction of SOZ with ammonia and water molecules. The most plausible mechanism for the reaction of SOZ with ammonia yields HC(O)OH, NH3, and HCHO as products, with ammonia herein acting as a mediator. This pathway is exothermic and exergonic, with an overall barrier height of only 157 kJ mol−1 using the G3MP2 method. All the reaction pathways between SOZ and water molecules are endothermic and endergonic reactions. The most likely reaction pathway for the reaction of SOZ with water involves a water dimer, in which the second water molecule acts as a mediator, with an overall barrier height of only 135 kJ mol−1 using the G3MP2 method. Solvent effects were found to incur a significant reduction in activation energies. When the second H2O molecule acts as a mediator in the reaction of SOZ with water, the barrier height of the rate-determining step state decreases significantly.

Quantum chemical study on the atmospheric photooxidation of ethyl acetate

2014 ◽  
Vol 92 (9) ◽  
pp. 814-820 ◽  
Author(s):  
Yan Zhao ◽  
Xiaomin Sun ◽  
Wenxing Wang ◽  
Laixiang Xu
Keyword(s):  
Acetic Anhydride ◽  
Ethyl Acetate ◽  
Density Functional ◽  
Single Point ◽  
Quantum Chemical Study ◽  
Density Functional Theory Method ◽  
Basis Set ◽  
Oh Radicals ◽  
Point Energy ◽  
Rearrangement Reaction

The mechanism for OH radical initiated atmospheric photoxidation reaction of ethyl acetate was carried out by using the density functional theory method. Geometries have been optimized at the B3LYP level with a standard 6-31G(d,p) basis set. The single-point energy calculations have been performed at the MP2/6-31G(d), MP2/6-311++G(d,p), and CCSD(T)/6-31G(d) levels, respectively. All of the possible degradation channels involved in the oxidation of ethyl acetate by OH radicals have been presented and discussed. Among the five possible hydrogen abstraction pathways of the reaction of ethyl acetate with OH radicals, the hydrogen abstractions from the C1–H3 and C2–H5 bonds are the dominant reaction pathways due to the low potential barriers and strong exothermicity. The β-ester rearrangement of IM6 is energetically favorable but is not expected to be important. The α-ester rearrangement reaction and O2 direct abstraction from IM17 are the more favorable pathways and are strongly competitive. In addition, the α-ester rearrangement reaction is confirmed to be a one-step process. Acetic acid, formic acetic anhydride, acetoxyacetaldehyde, and acetic anhydride are the main products for the reaction of ethyl acetate with OH radicals.

A Theoretical Study of the OH + HN2 Reaction

2013 ◽  
Vol 321-324 ◽  
pp. 314-317
Author(s):  
Tian Cheng Xiang ◽  
Hong Yan Si
Keyword(s):  
Dft Calculations ◽  
Theoretical Study ◽  
Potential Surface ◽  
Single Point ◽  
Point Energy ◽  
Energy Calculations ◽  
High Level

The singlet potential surface of the OH + HN2 reaction has been investigated at the B3LYP/6-311++G (3df, 3pd) level. The single-point energy calculations are performed at the high-level CCSD (T) / 6-311++G (3df, 3pd) for more accurate energy values. DFT calculations show that the most favorable association way starts with a barrierless addition of the OH to HN2 leading to HNN-OH (im6). The adduct im6 goes through an H shift from N atom to O atom, forming the product of H2O and N2.

COMPUTATION OF LARGE SYSTEMS WITH AN ECONOMIC BASIS SET: AB INITIO CALCULATIONS OF BIOLOGICAL NUCLEIC ACID BASE PAIRS

2006 ◽  
Vol 05 (spec01) ◽  
pp. 411-420 ◽  
Author(s):  
WENJIE FAN ◽  
RUIQIN ZHANG
Keyword(s):  
Nucleic Acid ◽  
Single Point ◽  
Basis Set ◽  
Basis Sets ◽  
Mulliken Charge ◽  
Acid Base ◽  
Base Pairs ◽  
Point Energy ◽  
Economic Basis ◽  
Nucleic Acid Base

We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.

scholarly journals Probing the mechanism of xanthine oxidase and 2-amino xanthine: an implication of energy, charge bond order and wave function.

2018 ◽  
Vol 6 (1) ◽  
pp. 95
Author(s):  
Mamaru Bitew
Keyword(s):  
Wave Function ◽  
Xanthine Oxidase ◽  
Single Point ◽  
Energy Charge ◽  
Dft Method ◽  
Theoretical Work ◽  
Electronic Energy ◽  
Basis Set ◽  
Energy Output ◽  
Point Energy

Xanthine oxidase (XO) is an important molybdenum-containing enzyme catalyzing the hydroxylation of hypoxanthine to xanthine and xanthine to uricacid. The mechanistic action by which xanthine oxidase oxidizes purine derivatives is not well understood. A better understanding of the overall mechanism is supposed to enhance our ability to control the metabolic properties of potential drug molecules metabolized by this enzyme. In this work a model substrate, 2-Amino Xanthine has been used to study the mechanistic action of the enzyme. For this reason, the present theoretical work was intended to probe a unified mechanism for the oxidation of 2-Amino Xanthine by xanthine oxidase. Parameters like total electronic energy, Mulliken atomic charges, wave functions, and percent contribution of chemical fragments were generated using a DFT method employing B3LYP level of theory with 6-31G(d',p') basis set for nonmetals and LanL2DZ basis set for molybdenum. AOmix software package that employs single point energy output as an input file was employed for wave function and percent fragment analysis. From these result new reaction intermediates and plausible reaction mechanism root has been reported for reductive and oxidative half reaction using 2-Amino Xanthine as model substrate. In this work it can be concluded that a stepwise mechanistic route with hydrogen bonding reaction complex and active site resemble very rapid Mo (V) intermediate is most plausible.     

scholarly journals Study on the Product Formation of the Reaction between Criegee Compound and Propargyl Radical

2021 ◽  
Vol 31 (4) ◽  
pp. 80-84
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Product Formation ◽  
Basis Set ◽  
Functional Theory ◽  
Point Energy ◽  
Propargyl Radical ◽  
The Density Functional Theory ◽  
Stable Product ◽  
Mechanism Of The Reaction

Mechanism of the reaction between Criegee compound (CH2OO) and Propargyl radical (C3H3) has been studied by using the density functional theory DFT/M06-2X in conjunction with the 6-311++G(3df,2p) basis set for both optimization and single-point energy calculations. The calculated results indicate that mechanism of the C3H3 + CH2OO reaction can occur in two different directions: H-atom abstraction and/or addition. As a result, 11 various products have been created from this reaction; in which, P10 (OCHCHCHCHO + H) is the most thermodynamically stable product and the reaction path leading to the P7 (CH2-[cyc-CCHCHOO] + H) product is the most energetically and kinetically favorable channel.

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