Complete Basis Set Model Research Articles

Stereoelectronic Properties of 1,2,4-Triazole-Derived N-heterocyclic Carbenes - A Theoretical Study

Stereoelectronic Properties of 1,2,4-Triazole-Derived N-heterocyclic Carbenes - A Theoretical Study

Understanding the molecular mechanism of thio-Claisen rearrangement of allyl phenyl sulfide and allyl vinyl sulfide using bonding evolution theory coupled with NCI analysis

ABSTRACTA joint application of bonding evolution theory (BET) and non-covalent interaction (NCI) analysis provides a powerful tool to explain the molecular mechanism of organic reactions. Thio-Claisen rearrangements (TCR) of allyl phenyl sulfide and allyl vinyl sulfide have been studied energetically using the MPWB1K/6-311G(2d,d,p), M06-2x/6-311G(2d,d,p) and the complete basis set model chemistry CBS-QB3 to predict activation barriers and thermodynamic parameters. Loss of aromaticity within the benzene ring along the TCR of allyl phenyl sulfide leads to a higher activation barrier and its endergonicity (endothermicity) nature, while TCR of allyl vinyl sulfide is an exergonic (exothermic) rearrangement with lower activation barrier. The molecular mechanisms are described by using MPWB1K/6-311G(2d,d,p) wavefunctions and energy profiles. The TCR of allyl phenyl sulfide and allyl vinyl sulfide can be described by the sequence of catastrophes 6-[C†C]F[F†F†F]TS[C†C]C†-0 and 8-C†CC[F†F†F]TSFCC†-0, respectively, by the following chemical events: (a) homolytic bond breaking of C−S single bond and formation of pseudoradical centers on the atoms; (b) annihilation of the pseudoradical centers and reorganization in covalent bonds; (c) appearance of the pseudoradical centers on the terminal carbon atoms; (d) formation of new C−C single bond by the C-to-C coupling of pseudoradical centers when the TS of the reaction is reached and left behind. NCI isosurface appears in the region of broken C−S bond and forming C−C bond where the monosynaptic basins were localized.

Theoretical Investigation of the Radical–Radical Reaction of O(3P) + C2H3 and Comparison with Gas-Phase Crossed-Beam Experiments

Herein, we present an ab initio study of the prototypal radical-radical reactions of ground-state atomic oxygen [O((3)P)] with the vinyl (C2H3) radical using density functional theory and a complete basis set model. Two distinctive pathways on the lowest doublet potential energy surfaces (PESs) were predicted to be in competition: addition and abstraction. The barrierless addition of O((3)P) to the hydrocarbon radicals leads to energy-rich intermediate formation followed by subsequent isomerization and decomposition to yield various products: CH2CO (ketene) + H, CO + CH3, C2HOH (acetylenol) + H, (3,1)CCHOH + H, H2O + C2H, (3,1)CH2 + HCO, H2CO (formaldehyde) + CH, C2H2 (acetylene) + OH, and (3,1)CCH2 + OH. The competing but minor H-atom abstraction mechanisms produce C2H2 + OH and (1,3)CCH2 + OH. The optimized structures of the reactants, products, intermediates, and transition states and the reaction mechanisms were obtained on the lowest doublet PESs. The major pathway was predicted to be the formation of CH2CO + H through the low-barrier, single-step cleavages of the addition intermediates. The Levine-Bernstein prior method, statistical surprisal approach, and microcanonical Rice-Ramsperger-Kassel-Marcus theory were applied to deduce the energy distributions of H atoms and OH products and quantitative rate constants. On the basis of the statistical theory and the population analysis, the predicted energy distributions were compared to the kinetic energy release of H and the preferential population of the Π(A') component of OH products reported in recent gas-phase crossed-beam investigations (Park, M. J.; Jang, S. C.; Choi, J. H. J. Chem. Phys. 2012, 137, 204311), and their kinetic and dynamic characteristics were discussed.

Methane adsorption on porous nano-silica in the presence of water: An experimental and ab initio study

This study investigated the effects of silanol groups and water content on methane adsorption on hydrophilic nano-silica H-380 through experiments and ab initio calculations. Fourier transform infrared (FTIR) spectroscopy was used to confirm the presence of silanol groups on the solid surface, and the pore size distribution between 0 and 40nm was determined using CO2 and N2 sorption experiments. Ab initio MP2 and complete basis set model (CBS-4) calculations were performed to optimize four different silica surfaces with and without silanol groups using different basis sets. The theoretical calculations and experiments indicated that the adsorption of methane slightly decreased when the water content was low. As the water content increased from 29.03wt% to 40.54wt%, the confined water molecules (water within the pores) promoted the adsorption of CH4 by forming deeper adsorption potential energy wells, thus rendering the system more stable. The experimental isotherms at 308.15–318.15K were obtained over a wide range of water contents up to 75.05wt%. The experimental data are consistent with the theoretical analysis, indicating an increase in the adsorption of CH4 as the water content increased from 39.75wt% to 50.35wt%. Additionally, the adsorption of CH4 sharply decreased when the water content was greater than 63.12wt%. This study contributes essential data on methane-confined H2O interactions on nano-silica surfaces to the scientific literature.

A Remodeled Protein Arginine Methyltransferase 1 (PRMT1) Generates Symmetric Dimethylarginine

Protein arginine methylation is emerging as a significant post-translational modification involved in various cell processes and human diseases. As the major arginine methylation enzyme, protein arginine methyltransferase 1 (PRMT1) strictly generates monomethylarginine and asymmetric dimethylarginine (ADMA), but not symmetric dimethylarginine (SDMA). The two types of dimethylarginines can lead to distinct biological outputs, as highlighted in the PRMT-dependent epigenetic control of transcription. However, it remains unclear how PRMT1 product specificity is regulated. We discovered that a single amino acid mutation (Met-48 to Phe) in the PRMT1 active site enables PRMT1 to generate both ADMA and SDMA. Due to the limited amount of SDMA formed, we carried out quantum mechanical calculations to determine the free energies of activation of ADMA and SDMA synthesis. Our results indicate that the higher energy barrier of SDMA formation (ΔΔG(‡) = 3.2 kcal/mol as compared with ADMA) may explain the small amount of SDMA generated by M48F-PRMT1. Our study reveals unique energetic challenges for SDMA-forming methyltransferases and highlights the exquisite control of product formation by active site residues in the PRMTs.

A theoretical study on the reaction mechanism of O2 with C4H9• radical

Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C(4)H(9)•) with oxygen (O(2)). On the calculated potential energy surface, the addition of O(2) to C(4)H(9)• forms three intermediates barrierlessly, which can undergo subsequent isomerization or decomposition reaction leading to various products: HOO• + C(4)H(8), C(2)H(5)• + CH(2)CHOOH, OH• + C(3)H(7)CHO, OH• + cycle-C(4)H(8)O, CH(3)• + CH(3)CHCHOOH, CH(2)OOH• + C(3)H(6). Five pathways are supposed in this study. After taking into account the reaction barrier and enthalpy, the most possible reaction pathway is C(4)H(9)• + O(2) → IM1 → TS5 → IM3 → TS6 → IM4 → TS7 → OH• + cycle-C(4)H(8)O.

A computational study of the radical–radical reaction of O(3P) + C2H5 with comparisons to gas-phase kinetics and crossed-beam experiments

We present density functional theory (DFT) and complete basis set (CBS) calculations of the prototypical radical–radical reaction of ground–state atomic oxygen [O(3P)] with ethyl (C2H5) radicals. The respective reaction mechanisms and dynamics were investigated on the doublet potential energy surfaces using the DFT method and CBS model. In the title reaction, the barrierless addition of O(3P) to C2H5 led to the formation of energy-rich intermediates that underwent subsequent isomerization and decomposition to yield various products. The products predicted to be found were: H2CO + CH3, CH3CHO + H, c–CH2OCH2 + H, 1,3CH3COH + H, 1,3HCOH + CH3, CH2CHOH + H, C2H3 + H2O, and CH2CH2 + OH. In particular, unlike previous kinetic results, proposed to proceed only through the direct H-atom abstraction process, two distinctive pathways to the formation of CH2CH2 + OH were predicted to be in competition: direct, barrierless H-atom abstraction mechanism versus addition process. The competition was consistent with the recent crossed-beam investigations, and their microscopic dynamic characteristics are discussed at the molecular level.

Quantum chemical investigation of the reaction of O(3 P 2) with certain hydrocarbon radicals

The reaction of ground-state atomic oxygen [O(3 P 2)] with methyl, ethyl, n-propyl and isopropyl radicals has been studied using the density functional method and the complete basis set model. The energies of the reactants, products, reaction intermediates and various transition states as well as the reaction enthalpies have been computed. The possible product channels and the reaction pathways are identified in each case. In the case of methyl radical the minimum energy reaction pathway leads to the products CO + H2 + H. In the case of ethyl radical the most facile pathway leads to the products, methanal + CH3 radical. For propyl radical (n- and iso-), the minimum energy reaction pathways would lead to the channel containing ethanal + methyl radical.

A Theoretical Investigation of the Gas‐Phase Oxidation Reaction of the Saturated tert‐Butyl Radical

The radical-radical reaction mechanisms and dynamics of ground-state atomic oxygen [O(3P)] with the saturated tert-butyl radical (t-C4H9) are investigated using the density functional method and the complete basis set model. Two distinctive reaction pathways are predicted to be in competition: addition and abstraction. The barrierless addition of O(3P) to t-C4H9 leads to the formation of an energy-rich intermediate (OC4H9) on the lowest doublet potential energy surface, which undergoes subsequent direct elimination or isomerization-elimination leading to various products: C3H6O + CH3, iso-C4H8O + H, C3H7O + CH2, and iso-C4H8 + OH. The respective microscopic reaction processes examined with the aid of statistical calculations, predict that the major addition pathway is the formation of acetone (C3H6O) + CH3 through a low-barrier, single-step cleavage. For the direct, barrierless H-atom abstraction mechanism producing iso-C4H8 (isobutene) + OH, which was recently reported in gas-phase crossed-beam investigations, the reaction is described in terms of both an abstraction process (major) and a short-lived addition dynamic complex (minor).

Quantum Chemical and Statistical Rate Study of the Reaction of O(3P) with Allene: O-Addition and H-Abstraction Channels

The lowest-lying triplet and singlet potential energy surfaces for the O(3P) + CH2=C=CH2 reaction were theoretically characterized using the complete basis set model chemistry, CBS-QB3. The primary product distributions for the multistate multiwell reactions on the individual surfaces were then determined by RRKM statistical rate theory and weak-collision master equation analysis using the exact stochastic simulation method. The results predict that the electrophilic O-addition pathways on the central and terminal carbon atom are dominant up to combustion temperatures. Major predicted end-products for the addition routes include CO + C2H4, 3CH2 + H2CCO, and CH2=C*-CHO + H*, in agreement with experimental evidence. CO + C2H4 are mainly generated from the lowest-lying singlet surface after an intersystem crossing process from the initial triplet surface. Efficient H-abstraction pathways are newly identified and occur on two different electronic state surfaces, 3A'' and 3A', resulting in OH + propargyl radicals; they are predicted to play an important role at higher temperatures in hydrocarbon combustion chemistry and flames, with estimated contributions of ca. 35% at 2000 K. The overall thermal rate coefficient k(O + C3H4) at 200-1000 K was computed using multistate transition state theory: k(T) = 1.60 x 10(-17) x T (2.05) x exp(-90 K/T) cm3 molecule(-1) s(-1), in good agreement with experimental data available for the 300-600 K range.

Ab initio investigations of the radical-radical reaction of O(P3)+C3H3

We present ab initio calculations of the reaction of ground-state atomic oxygen [O(P3)] with a propargyl (C3H3) radical based on the application of the density-functional method and the complete basis-set model. It has been predicted that the barrierless addition of O(P3) to C3H3 on the lowest doublet potential-energy surface produces several energy-rich intermediates, which undergo subsequent isomerization and decomposition steps to generate various exothermic reaction products: C2H3+CO, C3H2O+H, C3H2+OH, C2H2+CHO, C2H2O+CH, C2HO+CH2, and CH2O+C2H. The respective reaction pathways are examined extensively with the aid of statistical Rice-Ramsperger-Kassel-Marcus calculations, suggesting that the primary reaction channel is the formation of propynal (CHCCHO)+H. For the minor C3H2+OH channel, which has been reported in recent gas-phase crossed-beam experiments [H. Lee et al., J. Chem. Phys. 119, 9337 (2003); 120, 2215 (2004)], a comparison on the basis of prior statistical calculations is made with the nascent rotational state distributions of the OH products to elucidate the mechanistic and dynamic characteristics at the molecular level.

Kinetic Modeling of the Propyl Radical β-Scission Reaction: An Application of Composite Energy Methods

In this work, propyl radical β-scission reaction kinetics and energetics were investigated using quantum chemical Gaussian-3 (G3) and complete basis set (CBS) composite energy methods. Experimental thermodynamic and kinetic data were used to assess the accuracy of these calculations. The CBS model proved to have good agreement with the experimental data, which indicates that it is a good method for studying other hydrocarbon cracking reactions involving large species. Furthermore, a kinetic model with pressure and temperature effects was proposed. For P ≤ P0, k = (2.59 × 1011) × P0.40 × e(-13618.16/T); for P > P0, k = (2.70 × 1013) × e(-15117.33/T), where k is the reaction rate constant (in units of s-1), P is the pressure (in units of kPa), T is the temperature (in units of Kelvin), and the switching pressure P0 can be calculated as P0 = (1.53 × 109) × e(-10610.24/T).

Application of compound models for estimating rate constants of hydrocarbon thermal cracking reactions: The neopentyl radical β-scission reaction

In this work, neopentyl radical β-scission reaction kinetics and energetics are investigated using quantum chemical G3 and Complete Basis Set (CBS) compound models. Experimental thermodynamic and kinetic data are employed to assess the accuracy of these calculations. The CBS model proves to have good agreement with the experimental data, indicating it is a good method for studying other hydrocarbon cracking reactions involving large species. A kinetic model of the reaction with pressure and temperature effects is proposed. For for where P is in the units of kPa, T in the units of Kelvin, and These equations can be easily applied to different reaction conditions without performing additional costly calculations.

A theoretical study of the reaction of O(3P) with an allyl radical C3H5

Ab initio calculations of the reaction of ground-state atomic oxygen [O(3P)] with an allyl radical (C3H5) have been carried out using the density functional method and the complete basis set model. On the calculated lowest doublet potential energy surface, the barrierless association of O(3P) to C3H5 forms three energy-rich addition intermediates, which are predicted to undergo subsequent isomerization and decomposition steps leading to various products: C3H4O+H, CH2O+C2H3, C2H4+CHO, C2H2O+CH3, C2H5+CO, C3H4+OH, and C2H4O+CH. The respective reaction mechanisms through the three addition intermediates are presented, and it has been found that the barrier height, reaction enthalpy, and the number of intermediates involved along the reaction coordinate are of extreme importance in understanding such reactive scattering processes. With the aid of Rice–Ramsperger–Kassel–Marcus calculations, the major reaction pathway is predicted to be the formation of acrolein (C3H4O)+H, which is consistent with the previous gas-phase bulk kinetic experiment performed by Gutman et al. [J. Phys. Chem. 94, 3652 (1990)]. For the minor C3H4+OH channel, which has been newly found in the recent crossed beam investigations, a second barrierless, direct H-atom abstraction from the central carbon of C3H5 is calculated to compete with the addition process due to the little C–H bond dissociation energy and the formation of a stable allene product. The dynamic and kinetic characteristics of the reaction mechanism are discussed on the basis of the comparison of prior statistical calculations to the nascent internal distributions of the observed OH product.

Extension of complete basis set model chemistries to molecules containing third row atoms Ga–Kr

The complete basis set methods, CBS-4, CBS-q, CBS-Q and CBS-QB3, have been extended to molecules containing the third row elements Ga–Kr and their performance is assessed on 40 energies (atomization energies, ionization energies, electron affinities, and proton affinities) from the third row G2 test set. The mean absolute deviation from experiment for the highly accurate methods, CBS-Q and CBS-QB3, are 1.15 kcal/mol and 1.12 kcal/mol, respectively, both lower than for the G2 method, but not as low as the G3 method. The mean absolute deviation from experiment for the more affordable methods, CBS-4 and CBS-q, are 2.23 kcal/mol and 1.81 kcal/mol, respectively. The set of methods, CBS-4(d), CBS-q(d), CBS-Q(d), and CBS-QB3(d), with the d orbitals included in the correlation space is also investigated, giving results in poorer agreement with experiment. Problems with the CBS extrapolation step when the d orbitals are included in the correlation space are also discussed.

Accurate pK(a) calculations for carboxylic acids using complete basis set and Gaussian-n models combined with CPCM continuum solvation methods.

Complete Basis Set and Gaussian-n methods were combined with CPCM continuum solvation methods to calculate pK(a) values for six carboxylic acids. An experimental value of -264.61 kcal/mol for the free energy of solvation of H(+), DeltaG(s)(H(+)), was combined with a value for G(gas)(H(+)) of -6.28 kcal/mol to calculate pK(a) values with Cycle 1. The Complete Basis Set gas-phase methods used to calculate gas-phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed-phase free energies are slightly less accurate than the gas-phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. The use of Cycle 1 and the Complete Basis Set models combined with the CPCM solvation methods yielded pK(a) values accurate to less than half a pK(a) unit.

Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using complete basis set and Gaussian‐n models combined with CPCM continuum solvation methods

AbstractComplete basis set and Gaussian‐n methods were combined with Barone and Cossi's implementation of the polarizable conductor model (CPCM) continuum solvation methods to calculate pKa values for six carboxylic acids. Four different thermodynamic cycles were considered in this work. An experimental value of −264.61 kcal/mol for the free energy of solvation of H+, ΔGs(H+), was combined with a value for Ggas(H+) of −6.28 kcal/mol, to calculate pKa values with cycle 1. The complete basis set gas‐phase methods used to calculate gas‐phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed‐phase free energies are slightly less accurate than the gas‐phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. Thermodynamic cycles that include an explicit water in the cycle are not accurate when the free energy of solvation of a water molecule is used, but appear to become accurate when the experimental free energy of vaporization of water is used. This apparent improvement is an artifact of the standard state used in the calculation. Geometry relaxation in solution does not improve the results when using these later cycles. The use of cycle 1 and the complete basis set models combined with the CPCM solvation methods yielded pKa values accurate to less than half a pKa unit. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Symmetry Breaking and the Molecular Structure of NO3+

The equilibrium structure and vibrational frequencies of the nitrate cation, NO3+, have been investigated with an extensive set of ab initio calculations. Two stationary points were identified on the NO3+ potential energy surface: a symmetric D3h structure and a C2v ring structure similar to that found for the isoelectronic CO3 molecule. Geometry optimizations executed at the CCSD(T)/aug-cc-pVTZ level of theory yielded the following data. NO3+(D3h): Erel = 2130 cm-1, re = 1.238 Å. NO3+(C2v): Erel = 0 cm-1, r1 = 1.131 Å, r2 = r3 = 1.309 Å, θ = 142.3°. Calculations performed at the B3LYP, QCISD, CCSD, and CCSD(T) levels of theory all predict the C2v structure to be lower in energy than the D3h structure. Relative energy calculations performed with the Gaussian and complete basis set model chemistry algorithms also predict the C2v structure to be the most stable NO3+ conformation. These results are supported by vibrational frequency calculations which suggest that the D3h structure may correspond to a second-order saddle point rather than a true minimum on the NO3+ potential energy hypersurface. The symmetry breaking observed in the present NO3+ calculations is similar to that observed in ab initio studies of the NO3 equilibrium structure and is used to examine symmetry breaking across the nitrate series NO3-, NO3, NO3+.

A new complete basis set model (CBS-QB3) study on the possible intermediates in chemiluminescence

The new highly accurate complete basis set model, CBS-QB3, was employed here to elucidate the long experimentally discussed problem in a general class of chemiluminescent reactions involving peroxyoxalate systems. Both the stability comparison and the vibrational spectra favor that the intermediate is better to be recognized as the cyclic singlet 1,2-dioxetanedione with the C2v symmetry, which verifies the experimental suggestion yet provides more characterization information. Another two kinds of minimum species in its potential energy surface (PES) are two kinds of product: (1) two carbon dioxide and (2) two carbon monoxide and one oxygen, where the thermodynamic parameters correctly identify their relative yield in the experiment—the former is much more abundant than the latter. In a complete search of minimum states in its PES, the triplet C2v and D2h states were found, which is energetically unfavorable compared with the singlet C2v state. Their vibrational data also support some experimental conclusions of ruling out a radical intermediate. In contrast, the singlet D2h state was found to be a transition state for the “up” and “down” singlet C2v states. The complete active space self-consistent-field calculations with the second-order Möller–Plesset correlation energy correction also support that the most stable species is the singlet C2v state and the singlet D2h state is more energetically favorable than its triplet counterpart.

Thermochemical Property, Pathway and Kinetic Analysis on the Reactions of Allylic Isobutenyl Radical with O2: an Elementary Reaction Mechanism for Isobutene Oxidation

Kinetics for the reactions of allylic isobutenyl radical (CC(C)C) with molecular oxygen are analyzed by using quantum Rice−Ramsperger−Kassel (QRRK) theory for k(E) and master equation analysis for falloff. Thermochemical properties and reaction path parameters are determined by ab initio−Moller−Plesset (MP2(full)/6-31g(d) and MP4(full)/6-31g(d,p)//MP2(full)/6-31g(d)), complete basis set model chemistry (CBS-4 and CBS-q with MP2(full)/6-31g(d) and B3LYP/6-31g(d) optimized geometries), and density functional (B3LYP/6-31g(d) and B3LYP/6-311+g(3df,2p)//B3LYP/6-31g(d)) calculations. An elementary reaction mechanism is constructed to model the experimental system, isobutene oxidation. The forward and reverse rate constants for initiation reaction C2CC + O2 ↔ CC(C)C + HO2 are determined to be 1.86 × 109 T1.301 exp(−40939 cal/RT) (cm3 mol-1 s-1) and 6.39 × 108 T0.944 exp(−123.14 cal/RT) (cm3 mol-1 s-1), respectively. Calculations on 2,5-dimethylhexa-1,5-diene, methacrolein, isobutene oxides, and acetone product f...