Multi-component orbital interactions during oxyacyl radical addition reactions involving imines and electron-rich olefins

Ab initio and DFT calculations reveal that oxyacyl radicals add to imines and electron-rich olefins through simultaneous SOMO-pi*, SOMO-pi and pi*-HOMO interactions between the radical and the radicalophile. At the BHandHLYP/aug-cc-pVDZ level, energy barriers of 20.3 and 22.0 kJ mol(-1) are calculated for the attack of methoxycarbonyl radical at the carbon and nitrogen ends of methanimine, respectively. In comparison, barriers of 22.0 and 8.6 kJ mol(-1) are calculated at BHandHLYP/aug-cc-pVDZ for reaction of methoxycarbonyl radical at the 1- and 2-positions in aminoethylene, respectively. Natural bond orbital (NBO) analysis at the BHandHLYP/6-311G** level of theory reveals that SOMO-pi*, SOMO-pi and pi*-LP interactions are worth 111, 394 and 55 kJ mol(-1) respectively in the transition state (8) for reaction of oxyacyl radical at the nitrogen end of methanimine; similar interactions are observed for the chemistry involving aminoethylene. These multi-component interactions are responsible for the unusual motion vectors associated with the transition states involved in these reactions.     

Theoretical approach to the mechanism of reactions between halogen atoms and unsaturated hydrocarbons: the Cl + propene reaction

The potential energy surface for the Cl + propene reaction was analyzed at the MP2 level using Pople's 6-31G(d,p) and 6-311+G(d,p), and Dunning's cc-pVDZ and aug-cc-pVDZ basis sets. Two different channels for the addition reaction leading to chloroalkyl radicals and five alternative channels for the abstraction reaction leading to C(3)H(5) (.) + HCl were explored. The corresponding energy profiles were computed at the QCISD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level of theory. Theoretical results suggest that the previously established mechanism consisting of (1) direct abstraction and (2) addition-elimination steps is instead made up of (1) addition through an intermediate and (2) two-step abstraction processes. No direct abstraction mechanism exists on the potential energy surface. The kinetic equations derived for the new mechanism are consistent with the pressure dependence experimentally observed for this reaction.     

Multiorbital interactions during Acyl radical addition reactions involving imines and electron-rich olefins

Ab initio and DFT calculations reveal that acyl radicals add to imines and electron-rich olefins through simultaneous SOMO --> pi*, pi --> SOMO, and HOMO --> pi*C=O interactions between the radical and the radicalophile. At the CCSD(T)/aug-cc-pVDZ//QCISD/cc-pVDZ level, energy barriers of 15.6 and 17.9 kJ mol(-1) are calculated for the attack of the acetyl radical at the carbon and nitrogen ends of methanimine, respectively. These barriers are 17.1 and 20.4 kJ mol(-1) at BHandHLYP/cc-pVDZ. In comparison, barriers of 34.0 and 23.4 kJ mol(-1) are calculated at BHandHLYP/cc-pVDZ for reaction of the acetyl radical at the 1- and 2-positions in aminoethylene, repectively. Natural bond orbital (NBO) analysis at the BHandHLYP/6-311G** level of theory reveals that SOMO --> pi*imine, pi imine--> SOMO, and LPN --> pi*C=O interactions are worth 90, 278, and 138 kJ mol-1, respectively, in the transition state (2) for reaction of acetyl radical at the nitrogen end of methanimine; similar interactions are observed for the chemistry involving aminoethylene. These multiorbital interactions are responsible for the unusual motion vectors associated with the transition states involved in these reactions. NBO analyses for the remaining systems in this study support the hypothesis that the acetyl radical is ambiphilic in nature.     

Scavenging mechanism of curcumin toward the hydroxyl radical: a theoretical study of reactions producing ferulic acid and vanillin

Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.     

Revealing substituent effects on the concerted interaction of pnicogen, chalcogen, and halogen bonds in substituted s-triazine ring

Quantum chemical calculations have been performed to gauge the effect of substituents on concerted interactions of pnicogen, chalcogen, and halogen bonds in the X–TAZ···Y complexes (X = CN, F, Cl, Br, H, CH₃, OH, and NH₂, where TAZ and Y denote s-triazine ring and P, S, and Cl atoms, respectively) at the M06-2X/aug-cc-pVDZ level. The mutual interplay of these interactions is also investigated. The results indicate that diminutive effects are observed when the three kinds of noncovalent interactions pnicogen, chalcogen, and halogen bonds are coexisted in the complexes. These effects are studied in terms of energetic and geometric features of the complexes. In addition, Bader’s theory of “atoms in molecules” is used to analyze their strength of varying electron density at bond critical points. Natural bond orbital (NBO) theory is used to characterize the orbital interactions. The results indicate that the electron-withdrawing/donating substituents decrease/increase the magnitude of the binding energies compared to the unsubstituted X–TAZ···Y (X = H) complex. Good correlations among binding energies, Hammett constants, geometrical, atoms in molecular and NBO parameters are established in X–TAZ···Y complexes. By taking advantage of all the aforementioned computational methods, this study examines how these interactions mutually influence each other.     

Aliphatic C-H/pi interactions: Methane-benzene, methane-phenol, and methane-indole complexes

Noncovalent C-H/pi interactions are prevalent in biochemistry and are important in molecular recognition. In this work, we present potential energy curves for methane-benzene, methane-phenol, and methane-indole complexes as prototypes for interactions between C-H bonds and the aromatic components of phenylalanine, tyrosine, and tryptophan. Second-order perturbation theory (MP2) is used in conjunction with the aug-cc-pVDZ and aug-cc-pVTZ basis sets to determine the counterpoise-corrected interaction energy for selected complex configurations. Using corrections for higher-order electron correlation determined with coupled-cluster theory through perturbative triples [CCSD(T)] in the aug-cc-pVDZ basis set, we estimate, through an additive approximation, results at the very accurate CCSD(T)/aug-cc-pVTZ level of theory. Symmetry-adapted perturbation theory (SAPT) is employed to determine the physically significant components of the total interaction energy for each complex.     

Theoretical investigation on the conformational space of perfluorohydroxylamine,F2NOF

The conformational space of perfluorohydroxylamine, F₂NOF, is studied using the CCSD/aug-cc-pVDZ level of theory. It is found that the lowest-energy form of F₂NOF exhibits an anti conformation. This finding agrees with other theoretical studies, which indicate that the anti form is the most stable conformation upon H₂NOH fluorination on oxygen and/or nitrogen takes place [L. Radom, W.J. Hehre, J.A. Pople, J. Am. Chem. Soc. 94 (1972) 2371]. On the other hand, the present result is in complete disagreement with recent theoretical studies, in which the syn form of F₂NOF is proposed to be the minimum-energy conformation [P. Antoniotti, F. Grandinetti, Chem. Phys. Lett. 366 (2002) 676]. An NBO analysis at the B3LYP/aug-cc-pVDZ level of theory reveals that the interaction between the nitrogen lone pair and the OF antibond on one hand, and interactions between one oxygen lone pair and the two NF antibonds on the other hand, are responsible for the deep minimum, in which the anti conformer lies. Only those stabilizing interactions originated in the abovementioned oxygen lone pair accounts for the very flat region, in which the syn form is located.     

Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed

Benzene dimer configurations namely T-shaped, parallel-displaced, sandwich, and V-shaped that were proposed by experimental studies are investigated using second- and fourth-order Møller–Plesset perturbation theory. The MP2 method with aug-cc-pVDZ and aug-cc-pVTZ basis sets unequivocally shows that the parallel-displaced configuration is considerably more stable than T-shaped structure. On the other hand, the MP4(SDTQ)/aug-cc-pVDZ level predicts that the T-shaped and parallel-displaced configurations are nearly isoenergetic, which is parallel to the previous results of estimated CCSD(T)/CBS level reported recently. The lowest energy T-shaped configuration is stabilized by 0.17 kcal/mol over the parallel-displaced configuration at the MP4(SDTQ)/aug-cc-pVDZ level. Although the structures of all the four different types of configurations are found to be stable at both MP2 and full MP4 methods, the V-shaped configuration is the least stable among them. The calculated interaction energy of ?2.3 kcal/mol for the lowest energy T-shaped structure at the MP4(SDTQ)/aug-cc-pVDZ level is in good agreement with the experimental value of ?2.4 ± 0.4 kcal/mol. We conclude that the MP4(SDTQ) with a reasonably good basis set can be used for systems involving π–π interactions to obtain qualitative and quantitative results.     

Theoretical study of the mechanism and rate constant of the B + CO2 reaction

The different stationary points on the potential energy surface relative to the title reaction have been reinvestigated at the B3LYP/aug-cc-pVDZ level with relative energies computed at the CCSD(T)/aug-cc-pVTZ level with B3LYP/aug-cc-pVDZ optimized geometries and by using the G3B3 composite method. Two entrance channels have been identified. The first one corresponds to boron addition at one of the oxygen atoms of the CO 2 molecule leading to trans-BOCO, which is found to be about 27 kcal/mol exothermic with a potential energy barrier of 16.4 kcal/mol (G3B3). The second channel, which has not been identified in previous theoretical works, corresponds to a direct insertion of the boron atom into a CO bond and leads to OBCO. The B + CO 2 --> OBCO step is found to be about 84 kcal/mol exothermic and needs to overcome a potential energy barrier of only 3.6 kcal/mol (G3B3). The rate constant at 300 K of the insertion step, calculated by using TST theory with G3B3 calculated activation energy value, is 5.4 10 (-14) cm (3) molecule (-1) s (-1), in very good agreement with the experimental data ((7.0 +/- 2.8) 10 (-14) cm (3) molecule (-1) s (-1), DiGiuseppe, T. G.; Davidovits, P. J. Chem. Phys. 1981, 74, 3287). The one corresponding to the addition process is found to be several orders of magnitude smaller because of a much higher potential energy barrier. The addition channel would not contribute to the title reaction even at high temperature. A modified Arrhenius equation has been fitted in the 300-1000 K temperature range, which might be useful for chemical models.     

Charge-assisted intramolecular hydrogen bonds in disubstituted cyclohexane derivatives

In this paper, the N(+)-H···N, N(+)-H···O, and O-H···O(-) charge-assisted intramolecular hydrogen bonds (CAHBs) are investigated using different theoretical approaches. Monocharged cyclohexyldiamines (CHDA), aminocyclohexanols (ACHO), and cyclohexanediols (CHDO) are used as model compounds. Geometry optimizations at the MP2/aug-cc-pVDZ level are used to find the equilibrium structures for all possible H-bonded conformers. CAHBs are characterized geometrically and spectroscopically, and their energy is evaluated by means of homodesmic reactions. By comparison with the neutral forms, the presence of the charge is found to have a deep influence on the geometric and energetic H-bond parameters. In addition, these parameters are strongly dependent on the type of the groups involved as well as on their relative position in the cyclohexyl ring. For the systems under study, the H-bond energies vary from -23 to -113 kJ mol(-1), being classified from moderate to strong H-bonds. These H-bonds are also characterized by the application of the NBO and AIM theories. NBO analysis reveals that the energy corresponding to the charge transfer between the lone-pairs of the electron donor group and the antibonding orbitals of the acceptor group represents an important contribution in the H-bond stabilization. From the application of the AIM theory it is possible to see that these H-bonds possess some covalence which varies according to the type and relative position of the intervenient groups.     

Diffusion Monte Carlo Calculations of Zero-Point Energies of Methanol and Deuterated Methanol

Diffusion Monte Carlo (DMC) simulations have been used to obtain quantum zero-point energies of methanol and all its isotopologs and isotopomers, using a new, accurate semi-global potential energy surface. This potential energy surface is a precise, permutationally invariant fit to 6676 ab initio energies, obtained at the CCSD(T)-F12b/aug-cc-pVDZ level of theory. Quantum zero-point energies of deuterated methanol isotopomers are very close to each other and so a simple statistical argument can be used to estimate the populations of each isotopomer at very low-temperatures. The DMC simulations also indicate that there is virtually zero probability for H/D exchange in the zero-point state. © 2019 Wiley Periodicals, Inc.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

Spectra and integrated band intensities of the low order OH stretching overtones in peroxyformic acid: an atmospheric molecule with prototypical intramolecular hydrogen bonding

The gas phase spectra of several vibrational bands of peroxyformic acid (PFA), an atmospheric molecule exhibiting intramolecular hydrogen bonding, are presented. In the fundamental region, Fourier transform infrared (FT-IR) spectroscopy is used to probe the C-O, O-H and C-H stretching vibrations, while in the region of the first and second OH-stretching overtones (2ν(OH) and 3ν(OH)) photoacoustic spectroscopy is used. Integrated absorption cross sections for the PFA vibrational bands are determined by comparing their respective peak areas with that for the OH-stretching bands of n-propanol for which the absorption cross section is known. The measured integrated intensities of the OH stretching bands are then compared with a local mode model using a one-dimensional dipole moment function in conjunction with the OH stretching potential computed at both the MP2/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The data allow us to investigate changes in the OH stretch band position and intensity as a function of overtone order arising from the influence of hydrogen bonding. Furthermore, calculations at the MP2/aug-cc-pVDZ level show that there are three stable conformers of PFA with relative energies of 0, 13.54, and 13.76 kJ/mol, respectively. In the room temperature spectra, however, we see evidence for transitions from only the lowest energy conformer. The geometrical parameters and vibrational frequencies of the most stable conformer are presented.     

Theoretical Study on Dissociation Potential Energy Surface of Peroxynitric Acid

The lowest energy structures of peroxynitric acid have been studied with B3LYP/6-311+ G(2d,2p) method. The potential energy surfaces (PES) along the O-N and O-Obonds have been scanned at CCSD(T)/aug-cc-pVDZ level, respectively. The calculated results show that on the O-N PES, the O3-N4 bond length of the loose transition state is 2.82 ? and the corresponding energy barrier is 25.6 kcal/mol, while on the O-O PES, the loose transition state with of O2-O3 bond length of 2.35 ? has the energy barrier of 37.4 kcal/mol. Thus the primary reaction path for peroxynitric acid is the dissociation into HO₂ and NO₂.     

Theoretical investigation of adenine–BX3 (X=F,Cl) complex

Geometries and binding energies are predicted at B3LYP/6-311+G* level for the adenine–BX₃ (X=F,Cl) systems and four conformers with no imaginary frequencies have been obtained for both adenine–BF₃ and adenine–BCl₃, respectively, and single energy calculations using much larger basis sets (6-311+G(2df,p)) and aug-cc-pVDZ were carried out as well. The most stable conformer is BF₃ or BCl₃ connected to N₃ of adenine and with the stabilization energy of 22.55 or 20.59 kcal/mol at B3LYP/6-311+G* level (BSSE corrected). The analyses for the combining interaction between BX₃ and adenine with natural bond orbital method (NBO) and the atom-in-molecules theory (AIM) have been performed. The results indicate that all the conformers were formed with σ–p type interactions between adenine and BX₃, in which pyridine-type nitrogen or nitrogen atom of amino group offers its lone pair electron to the empty p orbital of boron atom and the concomitances of charge transference from adenine to BX₃ were occurred. Frequency analysis suggested that the stretching vibration of BX₃ underwent a red shift in complexes. Adenine–BF₃ complex was more stable than adenine–BCl₃ although the distance of B–N is shorter in the later.     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

LFMO和NBO的定域性和作用能解析

为分析苯并分子C12H6的垂直共振能(VRE), 建立了定域片断分子轨道(LFMO)和自然键轨道(NBO)两种基组, 并在两种基组之上进行NBO能量分析和Morokuma能量分解. 在NBO能量分析中, 两种基组的VRE都是稳定的; 而在Morokuma能量分解中, VRE的稳定性取决于基组. 在NBO能量分析中, Fock矩阵的一次性对角化忽视了σ体系和π体系之间的电子耦合作用. 故NBO基组和NBO能量分析方法在计算VRE时似乎都不合理.     

Effect of dimer formation via hydrogen bonding on static and dynamic nonlinear optical characteristics of chromophores

The effect of head-to-tail azochromophore dimer formation on the values of static and dynamic first hyperpolarizability is studied on the basis of calculations performed at M06-2X/aug-cc-pVDZ and ωB97X-D/aug-cc-pVDZ computational levels; the results are compared with those obtained at second-order Moller-Plesset pertubation theory (MP2)/aug-cc-pVDZ. Azochromophores DO3 and AAB-DCV , participating in the dimer formation, contain nitro- or dicyanovinylene acceptor moieties. The structure of the studied dimers is obtained at the B3LYP-D3/6-31++G (d,p) level with basis set superposition error (BSSE) correction. Dynamic first hyperpolarizabilities are calculated at radiation frequencies of 0.65 eV, 0.918 eV and 1.165 eV. The essential effect of dimer formation is demonstrated: it results in almost a 3.5 times increase of the first hyperpolarizability. In the series D1 - D2 - D3 , β(2ω) values at 0.65 eV increase in a way similar to the static case: β(2ω) for D2 and D3 are 1.5 and 1.8 times higher than that for D1 . The notable resonance enhancement of β(2ω) for the studied hydrogen-bonded dimers is demonstrated at radiation frequency of 1.165 eV.     

Perturbation expansion theory corrected from basis set superposition error II. Charge transfer,pair correlationand dispersion terms

The second-order perturbation theory based on the locally projected molecular orbitals is developed. A few test calculations with cc-pVDZ and aug-cc-pVDZ basis sets are carried out for the dimers, (H₂O)₂ and (HF)₂. The charge transfer terms remove the deficiency of the locally projected self-consistent field method for molecular interaction (LP SCF MO MI), and the potential energy curves calculated with aug-cc-pVDZ are very close to the corresponding curves of the counterpoise-corrected SCF energy. Only after adding the spin-exchanged dispersion type to the dispersion and intra-molecular pair correlation terms, the calculated potential energy curves become close to those of the counterpoise-corrected second-order Møller–Plesset (MP2). Pragmatic approaches for reducing the influence of the basis set superposition error are proposed.     

Methyl radical also reacts by the frontside mechanism: an ab initio study of some homolytic substitution reactions of methyl radical at silicon,germanium and tin

Ab initio calculations using 6-311G**, cc-pVDZ, aug-cc-pVDZ, and a (valence) double-zeta pseudopotential (DZP) basis sets, with (MP2, QCISD, CCSD(T)) and without (UHF) the inclusion of electron correlation, and density functional (B3LYO) calculations predict that homolytic substitution reactions of the methyl radical at the silicon atom in disilane can proceed via both backside and frontside attack mechanisms. At the highest level of theory (CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ), energy barriers (delta E) of 47.4 and 48.6 kJ mol-1 are calculated for the backside and frontside reactions respectively. Similar results are obtained for reactions involving germanium and tin with energy barriers (delta E) of between 46.5 and 67.3, and 41.0 and 73.3 kJ mol-1 for the backside and frontside mechanisms, respectively. These data suggest that homolytic substitution reactions of methyl radical at silicon, germanium, and tin can proceed via either homolytic substitution mechanism.