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.

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.

Quantum chemical study of inner-sphere complexes of trivalent lanthanide and actinide ions on the corundum (110) surface

2013 ◽  
Vol 101 (9) ◽  
pp. 561-570
Author(s):  
R. Polly ◽  
B. Schimmelpfennig ◽  
M. Flörsheimer ◽  
Th. Rabung ◽  
T. Kupcik ◽  
...  
Keyword(s):  
Metal Ions ◽  
Density Functional ◽  
Single Point ◽  
Quantum Chemical Study ◽  
Basis Sets ◽  
Water Molecules ◽  
Point Energy ◽  
Inner Sphere ◽  
Sphere Complex ◽  
Inner Sphere Complexes

Summary Sorption plays a major role in the safety assessment of nuclear waste disposal. In the present theoretical study we focused on understanding the interaction of trivalent lanthanides and actinides (La3+, Eu3+ and Cm3+) with the corundum (110) surface. Optimization of the structures were carried out using density functional theory with different basis sets. Additionally, Møller-Plesset perturbation theory of second order was used for single point energy calculations. We studied the structure of different inner-sphere complexes depending on the surface deprotonation and the number of water molecules in the first coordination shell. The most likely structure of the inner-sphere complex (tri- or tetradentate) was predicted. For the calculations we used a cluster model for the surface. By deprotonating the cluster a chemical environment at elevated pH values was mimicked. Our calculations predict the highest stability for a tetradentate inner-sphere surface complexes with five water molecules remaining in the first coordination sphere of the metal ions. The formation of the inner-sphere complexes is favored when a coordination takes place with at most one deprotonated surface aluminol group located beneath the inner-sphere complex. The mutual interaction between sorbing metal ions at the surface is studied as well. The minimal possible distance between two inner-sphere sorbed metal ions at the surface was determined to be 530 pm.

Computational study on the thermal decomposition and isomerization of the CH3OCF2O• radical

2012 ◽  
Vol 90 (4) ◽  
pp. 403-409 ◽  
Author(s):  
Hari Ji Singh ◽  
Bhupesh Kumar Mishra ◽  
Pradeep Kumar Rao
Keyword(s):  
Transition State Theory ◽  
Computational Study ◽  
Single Point ◽  
State Theory ◽  
Basis Set ◽  
Point Energy ◽  
B3lyp Level ◽  
Bond Scission ◽  
Decomposition Pathway ◽  
Thermal Rate Constant

The geometries of the reactant, products, and transition states involved in the decomposition pathways of the CH3OCF2O• radical formed during the photooxidation of CH3OCHF2 (HFE-152a) have been optimized and characterized at the DFT-B3LYP level of theory using the 6–311G(d,p) basis set. Single-point energy calculations have been made at the G2M (CC,MP2) level of theory. Out of the four prominent decomposition channels considered, the β-C–O bond scission is found to be the dominant path involving a barrier height of 9.78 kcal mol–1 (1 cal = 4.184 J). The thermal rate constant for the above decomposition pathway is evaluated using canonical transition state theory (CTST) and was found to be 5.27 × 104 s–1 at 298 K and 1 atm (1 atm = 101.325 kPa).

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.

scholarly journals Stable Occupancy of Hydrogen Molecules in Clathrate Hydrates and + THF Clathrate Hydrates Determined by Ab Initio Calculations

2010 ◽  
Vol 2010 ◽  
pp. 1-6 ◽  
Author(s):  
Prasad Yedlapalli ◽  
Sangyong Lee ◽  
Jae W. Lee
Keyword(s):  
Ab Initio ◽  
Binding Energies ◽  
Clathrate Hydrates ◽  
Basis Set ◽  
Large Cavity ◽  
Basis Sets ◽  
Pure Hydrogen ◽  
Point Energy ◽  
Small Cavity ◽  
Hydrogen Molecules

Structure II clathrate hydrates of pure hydrogen and binary hydrates of are studied using ab initio calculations to determine the stable occupancies of small cavities. Ab initio calculations are carried out for a double cavity consisting of one dodecahedron (small cavity) and one hexakaidecahedron (large cavity). These two cavities are attached to each other as in sII hydrates to form a double cavity. One or two molecules are placed in the small cavity and one THF (or 4 molecules) molecule is placed in the large cavity. We have determined the binding energies of the double cavities at the MP2 level using various basis sets (3-21G, 3-21G(2p), 3-21 G(2p), 6-31G, 6-31G(2p), and 6-31 G(2p)). Different basis sets yield different stable occupancies of the small cavity. The results from the highest basis set (6-31 G(2p) with zero point energy corrections) indicate that the single occupancy is slightly more favorable than the double occupancy in both the cases of pure hydrates and THF + double hydrates.

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.

A computational study of hexachlorobenzene-soil organic matter-interactions

2014 ◽  
Vol 13 (02) ◽  
pp. 1450009 ◽  
Author(s):  
Ashour A. Ahmed ◽  
Peter Leinweber ◽  
Oliver Kühn
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Computational Study ◽  
Basis Set ◽  
Basis Sets ◽  
Dispersion Correction ◽  
Test Set ◽  
Covalent Interaction ◽  
General Ability ◽  
Gromos Force Field

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.

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.

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