scholarly journals Nonenzymatic Deamidation Mechanism on a Glutamine Residue with a C-Terminal Adjacent Glycine Residue: A Computational Mechanistic Study

AppliedChem ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 142-155
Author(s):  
Haruka Asai ◽  
Koichi Kato ◽  
Tomoki Nakayoshi ◽  
Yoshinobu Ishikawa ◽  
Eiji Kurimoto ◽  
...  
Keyword(s):  
Transition State ◽  
Density Functional ◽  
Protein Denaturation ◽  
Activation Barrier ◽  
Single Point ◽  
Mechanistic Study ◽  
Amino Acid Residues ◽  
Hydrogen Bond Formation ◽  
Point Energy ◽  
Physiological Conditions

The deamidation of glutamine (Gln) residues, which occurs non-enzymatically under physiological conditions, triggers protein denaturation and aggregation. Gln residues are deamidated via the cyclic glutarimide intermediates to l-α-, d-α-, l-β-, and d-β-glutamate residues. The production of these biologically uncommon amino acid residues is implicated in the pathogenesis of autoimmune diseases. The reaction rate of Gln deamidation is influenced by the C-terminal adjacent (N +1) residue and is highest in the Gln-glycine (Gly) sequence. Here, we investigated the effect of the (N + 1) Gly on the mechanism of Gln deamidation and the activation barrier using quantum chemical calculations. Energy-minima and transition-state geometries were optimized by the B3LYP density functional theory, and MP2 calculations were used to obtain the single-point energy. The calculated activation barrier (85.4 kJ mol−1) was sufficiently low for the reactions occurring under physiological conditions. Furthermore, the hydrogen bond formation between the catalytic ion and the main chain of Gly on the C-terminal side was suggested to accelerate Gln deamidation by stabilizing the transition state.

scholarly journals Photolysis-induced scrambling of PAHs as a mechanism for deuterium storage

2020 ◽  
Vol 635 ◽  
pp. A9 ◽  
Author(s):  
Sandra D. Wiersma ◽  
Alessandra Candian ◽  
Joost M. Bakker ◽  
Jonathan Martens ◽  
Giel Berden ◽  
...  
Keyword(s):  
Transition State ◽  
Ir Spectra ◽  
Density Functional ◽  
Zero Point ◽  
Reaction Rates ◽  
Ion Cyclotron Resonance ◽  
Point Energy ◽  
Polycyclic Aromatic ◽  
Atom Loss ◽  
Ground State Structures

Aims. We investigate the possible role of polycyclic aromatic hydrocarbons (PAHs) as a sink for deuterium in the interstellar medium (ISM) and study UV photolysis as a potential underlying chemical process in the variations of the deuterium fractionation in the ISM. Methods. The UV photo-induced fragmentation of various isotopologs of deuterium-enriched, protonated anthracene and phenanthrene ions (both C14H10 isomers) was recorded in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Infrared multiple photon dissociation spectroscopy using the Free-Electron Laser for Infrared eXperiments was applied to provide IR spectra. Infrared spectra calculated using density functional theory were compared to the experimental data to identify the isomers present in the experiment. Transition-state energies and reaction rates were also calculated and related to the experimentally observed fragmentation product abundances. Results. The photofragmentation mass spectra for both UV and IRMPD photolysis only show the loss of atomic hydrogen from [D − C14H10]+, whereas [H − C14D10]+ shows a strong preference for the elimination of deuterium. Transition state calculations reveal facile 1,2-H and -D shift reactions, with associated energy barriers lower than the energy supplied by the photo-excitation process. Together with confirmation of the ground-state structures via the IR spectra, we determined that the photolytic processes of the two different PAHs are largely governed by scrambling where the H and the D atoms relocate between different peripheral C atoms. The ∼0.1 eV difference in zero-point energy between C–H and C–D bonds ultimately leads to faster H scrambling than D scrambling, and increased H atom loss compared to D atom loss. Conclusions. We conclude that scrambling is common in PAH cations under UV radiation. Upon photoexcitation of deuterium-enriched PAHs, the scrambling results in a higher probability for the aliphatic D atom to migrate to a strongly bound aromatic site, protecting it from elimination. We speculate that this could lead to increased deuteration as a PAH moves towards more exposed interstellar environments. Also, large, compact PAHs with an aliphatic C–HD group on solo sites might be responsible for the majority of aliphatic C–D stretching bands seen in astronomical spectra. An accurate photochemical model of PAHs that considers deuterium scrambling is needed to study this further.

The Direct Oxidizing Mechanism for the Reaction of Ozone and Phenol: A DFT Study

2012 ◽  
Vol 554-556 ◽  
pp. 1632-1636
Author(s):  
Shuang Kou Chen ◽  
Jian Fang Zhu ◽  
Wen Zhang Huang ◽  
Bai He ◽  
Li Jun Xiang ◽  
...  
Keyword(s):  
Global Optimization ◽  
Transition State ◽  
Calculation Result ◽  
Substitution Reaction ◽  
Single Point ◽  
Vibrational Analysis ◽  
Ortho Position ◽  
Free Energies ◽  
Point Energy ◽  
Exothermic Reactions

Using DFT/6-31+G (d, p) method, the structure of phenol are gained in the global optimization and properties were theoretically studied. The atomic electric charges, activation of reaction and thermodynamics parameters are obtained. The calculation shows that benzene ring in phenol tends to have electrophonic attacking substitution reaction O3 directly and form catechol and hydroquinol. The calculation of thermodynamics properties indicate that two pathways are exothermic reactions, and the Gibbs free energies (ΔG) are always less than zero, two reactions are easily occurred spontaneously. Dynamics calculations show that there is only one transition state in each reaction; through vibrational analysis we confirm the transition state. After corrected single point energy, we find that the reaction activation energies of the two reactions are small (Ea1=4.48kcal/mol and Ea2=2.87kal/mol), indicating that ortho-position and para-position products exist simultaneously, which is in accordance with the thermodynamics calculation result.

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.

scholarly journals Comparison of computational chemistry methods for the discovery of quinone-based electroactive compounds for energy storage

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qi Zhang ◽  
Abhishek Khetan ◽  
Süleyman Er
Keyword(s):  
Energy Storage ◽  
Prediction Accuracy ◽  
Density Functional ◽  
Single Point ◽  
Computational Cost ◽  
Systematic Evaluation ◽  
Redox Potentials ◽  
Implicit Solvation ◽  
Point Energy ◽  
Computational Screening

AbstractHigh-throughput computational screening (HTCS) is a powerful approach for the rational and time-efficient design of electroactive compounds. The effectiveness of HTCS is dependent on accuracy and speed at which the performance descriptors can be estimated for possibly millions of candidate compounds. Here, a systematic evaluation of computational methods, including force field (FF), semi-empirical quantum mechanics (SEQM), density functional based tight binding (DFTB), and density functional theory (DFT), is performed on the basis of their accuracy in predicting the redox potentials of redox-active organic compounds. Geometry optimizations at low-level theories followed by single point energy (SPE) DFT calculations that include an implicit solvation model are found to offer equipollent accuracy as the high-level DFT methods, albeit at significantly lower computational costs. Effects of implicit solvation on molecular geometries and SPEs, and their overall effects on the prediction accuracy of redox potentials are analyzed in view of computational cost versus prediction accuracy, which outlines the best choice of methods corresponding to a desired level of accuracy. The modular computational approach is applicable for accelerating the virtual studies on functional quinones and the respective discovery of candidate compounds for energy storage.

Kinetics and mechanism for chlorine-initiated atmospheric oxidation of ethyl formate

2014 ◽  
Vol 92 (7) ◽  
pp. 598-604 ◽  
Author(s):  
Yan Zhao ◽  
Xiaomin Sun ◽  
Wenxing Wang ◽  
Laixiang Xu
Keyword(s):  
Rate Constants ◽  
Density Functional ◽  
Single Point ◽  
Oxidation Mechanism ◽  
Density Functional Theory Method ◽  
Ethyl Formate ◽  
Stationary Points ◽  
Atmospheric Conditions ◽  
Point Energy ◽  
Rearrangement Reaction

The chlorine-initiated reaction mechanism of ethyl formate in the atmosphere was investigated using the density functional theory method. The geometry parameters and frequencies of all of the stationary points were calculated at the B3LYP/ 6-31G(d,p) level. The single-point energy calculations were carried out at different levels, including MP2/6-31G(d), MP2/6-311++G(d,p), and CCSD(T)/6-31G(d). A detailed oxidation mechanism is provided and discussed. Present results show that α-ester rearrangement reaction and the O2 direct abstraction from IM6 (HC(O)OCH(O)CH3) are the more favorable pathway and are competitive. The 1,4-H shift isomerization of IM6 proved to be feasible under general atmospheric conditions. The decomposition of IM18 (CH3CH2OC(O)O) is favorable both thermodynamically and kinetically. Canonical variational transition theory with small-curvature tunneling correction was employed to predict the rate constants. The overall rate constant of ethyl formate at 298 K is 8.63 × 10−12 cm3 molecule−1 s−1. The Arrhenius equations of rate constants at the temperature range of 200–380 K were fitted.

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.

Theoretical study on the reaction mechanism of vinyl acetate with OH radicals in the atmosphere

2013 ◽  
Vol 91 (4) ◽  
pp. 241-247 ◽  
Author(s):  
Yan Zhao ◽  
Haitao Sun ◽  
Renjun Wang ◽  
Fei Gao
Keyword(s):  
Vinyl Acetate ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Theoretical Study ◽  
Single Point ◽  
Density Functional Theory Method ◽  
Basis Sets ◽  
Stationary Points ◽  
Oh Radicals ◽  
Point Energy

The reaction mechanisms of vinyl acetate with OH radicals in the atmosphere have been studied using the density functional theory method. The geometry parameters and frequencies of all of the stationary points are calculated at the MPWB1K level with the 6-31G(d,p) basis sets. The single-point energy calculations are carried out at the MPWB1K/6-311+G(3df,2pd) level. The detailed profiles of the potential energy surfaces for the reactions are constructed. Two OH addition and three H abstraction reaction pathways are considered for the reaction of vinyl acetate with OH radicals. The theoretical study shows that the most energetically favorable isomer is that of OH addition to the terminal carbon positions (C1 atom). The α-ester rearrangement, which is characteristic of ester oxidation processes, is confirmed to be thermodynamically and kinetically favorable. The main products of the OH-initiated atmospheric oxidation of vinyl acetate are formaldehyde, formic acetic anhydride, and acetic acid.

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.

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.

scholarly journals Theoretical investigation of the Anti-Parkinson drug rasagiline and its salts: conformations and infrared spectra

2012 ◽  
Vol 10 (2) ◽  
pp. 395-406 ◽  
Author(s):  
U. Başköse ◽  
Sevgi Bayarı ◽  
Semran Sağlam ◽  
Hacı Özışık
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Normal Modes ◽  
Basis Set ◽  
Stable Conformer ◽  
Functional Theory ◽  
Point Energy ◽  
Vibrational Assignments ◽  
B3lyp Method ◽  
The Density Functional Theory

AbstractThe conformational analysis of rasagiline [N-propargyl-1(R)-aminoindan] was performed by the density functional theory (DFT) B3LYP method using the 6–31++G (d,p) basis set. A single point energy calculations based on the B3LYP optimized geometries were also performed at MP2/6-31++G (d, p) level. The vibrational frequencies of the most stable conformer of rasagiline was calculated at the B3LYP level and vibrational assignments were made for normal modes on the basis of scaled quantum mechanical force field (SQM) method. The influence of mesylate and ethanedisulfonate salts on the geometry of rasagiline free base and its normal modes are also discussed.

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