A study of the rotational barriers for some organic compounds using the G3 and G3CEP theories

Universal Generalization of Density Functional Theory for Static Correlation

A major challenge for density functional theory (DFT) is its failure to treat static correlation, yielding errors in predicted charges, band gaps, van der Waals forces, and reaction barriers. Here we combine one- and two-electron reduced density matrix (1- and 2-RDM) theories with DFT to obtain a universal O(N^{3}) generalization of DFT for static correlation. Using the lowest unitary invariant of the cumulant 2-RDM, we generate a 1-RDM functional theory that corrects the convexity of any DFT functional to capture static correlation in its fractional orbital occupations. Importantly, the unitary invariant yields a predictive theory by revealing the dependence of the correction's strength upon the trace of the two-electron repulsion matrix. We apply the theory to the barrier to rotation in ethylene, the relative energies of the benzynes, as well as an 11-molecule, dissociation benchmark. By inheriting the computational efficiency of DFT without sacrificing the treatment of static correlation, the theory opens new possibilities for the prediction and interpretation of significant quantum molecular effects and phenomena.

Intramolecular hydrogen bonds interactions in the isomers of the bilirubin molecule: DFT and QTAIM analysis

CONTEXT

Bilirubin is an important molecule, used as a marker of some liver diseases, and it can also be toxic and cause jaundice, especially in newborns. The main treatment for neonatal jaundice is phototherapy with blue light, which is still widely studied because the photophysical processes involved are not fully understood.

METHODS

Calculations based on the density functional theory (DFT) at M062X/6-31G(d,p) level were performed in order to evaluate the structural, electronic, and topological properties of bilirubin isomers. It was found that the ZZ conformation can form a greater number of hydrogen bonds, which gives the isomer greater energy stabilization compared to the other ZE, EZ, and EE isomers, and that the EE isomer is the conformer with the lowest energy of stabilization. The hydrogen bonds were characterized by the quantum theory of atoms in molecules (QTAIM) and for the ZZ isomer four hydrogen bonds (HBs) were found classified as intermediate, ∇2ρ(r) > 0, H(r) > 0. The ZE, EZ, and EE isomers show weak HBs, ∇2ρ(r) > 0, H(r) > 0.

Theoretical and experimental study of the diastereoisomers (2S) and (2R)-naringenin-6-C-β-D-glucopyranoside obtained from Clitoria guianensis

In this work the diastereoisomers (2S) and (2R)-naringenin-6-C-β-D-glucopyroside, isolated for the first time from Clitoria guianensis, were studied using the density functional theory. The frontier molecular orbitals and structural properties showed that the diastereoisomers exhibit the same energy gap 166.61 kcal mol^-1 and structural properties different, where in the S diastereoisomer, the bond length between the chiral carbon and the phenolic group is greater (difference of 0.0126 Å). The HPLC data showed that the retention time of the S-diastereoisomer (16.7 min) is shorter than that of R, suggesting that the S compound is more polar than R. The HPLC results corroborates with the molecular electrostatic potential which showed that in the S configuration, the electronegative density was more intense overall, particularly in the glucose molecule. The reactivity indices showed that the diastereoisomers are good electrophiles and reactive species. Finally, the absolute configuration of the diastereoisomers were determined using electronic circular dichroism (ECD) spectroscopy and the theoretical spectra were similar to the experimental. METHODS : All calculations of Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) were performed using the program Gaussian 09 and the structures of the diastereoisomers were generated and analyzed using the GaussView program. The optimization and vibrational frequency calculations were performed using the functional CAM-B3LYP and 6-311 +  + G(2d,2p) basis set. Conformational searches were performed for R configuration, by molecular mechanics using the MM + , MMFF, and OPLS05 force fields; the entire molecular mechanics simulation was performed using the Maestro/MacroModel software. The calculations for the simulations of the ECD spectra were performed for the eight lowest energy conformers obtained in the geometric optimization step, and the TDDFT at the CAM-B3LYP/6-311 +  + G(2d,2p) theory level used. The effects of methanol and chloroform were calculated using the SMD implicit solvent model.

Brueckner Doubles variation of W1 theory (W1BD) adapted to pseudopotential: W1BDCEP theory

Composite methods are the combination of ab initio calculations used to achieve high precision in the face of a computational reduction. Weizmann-n theories (n = 1, 2, 3, and 4) stand out for presenting a high precision, and a version of the W1 theory is the W1BD theory that uses ab initio Brueckner Doubles (BD) methods. One way to reduce the computational cost of composite methods and maintain accuracy is to use pseudopotentials in the calculation steps; in this context, W1BDCEP composite method was developed from the respective W1BD all-electron version by considering the implementation of compact effective pseudopotential (CEP). The test set used to evaluate the theory were 8 proton affinities (PA₀), 46 electron affinities (EA₀), 54 ionization energies (IE₀), 80 enthalpies of formation (Δ_fH⁰), and 10 bond dissociation energies (BDE). The mean absolute deviation values (MADs) for W1BD and for the version adapted to the pseudopotential, W1BDCEP, were similar, with values of 0.97 kcal mol^-1 and 1.03 kcal mol^-1, respectively, when the properties PA₀, EA₀, IE₀, and Δ_fH⁰ were evaluated together. Comparing the versions of the theories that employ ab initio Brueckner Doubles calculations with the W1 and W1CEP theories, it is possible to observe that the W1BD and W1BDCEP theories are more accurate than the W1 theory (MAD_W1 = 1.25 kcal mol^-1) and W1CEP (MAD_W1CEP = 1.44 kcal mol^-1), proving the accuracy of using the BD method. Pseudopotential reduces computational time by up to 30% and thus enables more accurate calculations with less computational time.

Theoretical study of internal rotational barriers of electrons donating and electrons withdrawing groups in aromatic compounds

The presence of internal rotation in sigma bonds is essential for conformational analysis of organic molecules and its understanding is of great relevance in chemistry, as well as in several other areas. However, for aromatic compounds that have substituent groups, withdrawers or donors of electron, there are no data in the literature to explain their rotational barriers. In this context, the work studied the internal rotational barriers of electron donating and withdrawing groups in aromatic compounds using the MP3, MP4, and CCSD(T) methods and the influence of substituents' nature on barrier heights was investigated through calculations based on the theory of Natural Bond Orbitals (NBO) and Quantum Theory of Atoms in Molecules (QTAIM). The results obtained showed that the CCSD(T) method is the one that best describes the internal rotational barriers, followed by MP4 and MP3 and the electron donating groups decrease the barrier, whereas electron withdrawing groups increase. Through the NBO analysis it was possible to observe that for withdrawing groups the interaction of the molecular orbitals is more accentuated promoting the increase of the rotational barrier of these compounds. Through the QTAIM analysis it was possible to show that, for electron donating groups, the internal rotation is influenced by the loss of electronic density when the substituents is perpendicular to the ring plane, however, for withdrawing groups the density is little influenced, regardless of the two conformations (minimum and maximum energy). Two molecules showed free rotation, trichloromethylbenzene and methylbenzene, and the theoretical calculations NBO and QTAIM showed that for these species there is no difference in the properties studied when there is rotation of the dihedral angle.

Peracetic acid: Structural elucidation for applications in wastewater treatment

Peracetic acid (PAA) is an oxidizer widely used for the sterilization of equipment in hospitals, pharmaceutical, cosmetic and food industries and also for water and wastewater disinfection. Even with its increasing applications, there have been no previous theoretical studies that explain the experimental results based on its molecular behavior. In this context, this work used calculations based on the density functional theory (DFT) combined with experimental results to elucidate the decomposition mechanisms of PAA for predicting its stability and the possible products generated from its decomposition. The results obtained showed that the protonation of PAA promoted its spontaneous decomposition in acetic acid and molecular oxygen. The hydrolysis mechanism of PAA in acidic medium indicated that the low energy difference involved in the mechanism's stages is responsible for the equilibrium between PAA and H₂O₂. The structural and electronic comparison of PAA with H₂O₂ showed that the O-O bond length of PAA is longer than that of H₂O₂ and is also weaker, therefore may demonstrate greater efficiency in advanced oxidative processes by photocatalysis.

Assessment of pKa Determination for Monocarboxylic Acids with an Accurate Theoretical Composite Method: G4CEP

For 22 monoprotic acids, pK_a values were calculated using the G4CEP composite theory. The solvation effect was included considering the continuous SMD solvation model; SMD and one explicit water molecule; and SMD, one water molecule, and linear correction with respect to the experimental pK_a values. The three tests provided mean absolute errors equal to 0.83, 0.51, and 0.30 pK_a units, respectively, indicating excellent performance of the G4CEP method. Comparison with density functional theory at the B3LYP and BMK levels showed that these results are quickly obtained but with a significant error. The best performance of the functionals was obtained from the combination of SMD, one explicit water molecule, linear regression correction, and basis set including diffuse functions. However, the dispersion of the results with DFT can lead to deviations of up to two pK_a units, whereas for G4CEP the largest deviations seldom exceed one pK_a unit.

Reactivity, vibrational spectroscopy, internal rotation and thermochemical aspects of methylarsine

The aim of this investigation was to perform a characterization of the spectroscopic and thermodynamic properties of methylarsine (CH₃AsH₂). Post-Hartree-Fock, 29 DFT methods and eight different composite methodologies were employed in these analyses. A comparison between harmonic and anharmonic frequency accuracies in reproducing the observable frequencies was performed here. In addition, the CH₃AsH₂→CH₂AsH₃ isomerization barrier energy was estimated in 100kcalmol^-1, whereas the H₂-release routes barrier heights were in the 45-107kcalmol^-1 range. A rate constant of 10^-66s^-1 was predicted regarding the isomerization route, while the CH₂AsH₃ hydrogen elimination mechanism is faster than the methylarsine one. The transition state structure of the CH₃AsH₂ internal rotational barrier energy varied between 1.0 and 1.4kcalmol^-1. For the CH₂AsH₃ internal rotation the estimated barrier heights varied 0.6-2.5kcalmol^-1. The adiabatic ionization energy and the heat of formation each structure was also calculated here.

An interpretation of the phenol nitration mechanism in the gas phase using G3(MP2)//B3-CEP theory

G3(MP2)//B3-CEP theory was applied to study the mechanism of phenol nitration in the gas phase, as promoted by the electrophile NO2 (+). The results of studying this mechanism at the G3(MP2)//B3-CEP level pointed to the occurrence of a single-electron transfer (SET) from the aromatic π-system to the nitronium ion prior to σ-complex formation. The formation of an initial π-complex between the nitronium ion and phenol was not observed. Excellent agreement between the activation barriers predicted by G3(MP2)//B3-CEP and those yielded by other, more accurate, versions of the G3 theory showed that the former is a useful tool for studying reaction mechanisms, as G3(MP2)//B3-CEP is much less computationally expensive than other high-level methods.