Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Atmospheric Oxidation of Hydroperoxy Amides

Recently, hydroperoxy amides were identified as major products of OH-initiated autoxidation of tertiary amines in the atmosphere. The formation mechanism is analogous to that found for ethers and sulfides but substantially faster. However, the atmospheric fate of the hydroperoxy amides remains unknown. Using high-level theoretical methods, we study the most likely OH-initiated oxidation pathways of the hydroperoxy and dihydroperoxy amides derived from trimethylamine autoxidation. Overall, we find that the OH-initiated oxidation of the hydroperoxy amides predominantly leads to the formation of imides under NO-dominated conditions and more highly oxidized hydroperoxy amides under HO2-dominated conditions. Unimolecular reactions are found to be surprisingly slow, likely due to the restricting, planar structure of the amide moiety.

Raising the benchmark potential of a simple alcohol-ketone intermolecular balance

2-Butanone offers two hydrogen bond docking variants to a solvating methanol which are cleanly separated by supersonic jet infrared absorption spectroscopy in the OH-stretching range, resolving earlier action spectroscopy indeterminacies for this elementary case of an intermolecular alcohol-ketone balance. The solvent preference for the shorter chain side is unambiguously derived from the spectra of homologous compounds. It is analysed in terms of competing steric and dispersion interactions and the resulting energy differences across a low interconversion barrier. Fortuitous cancellations are discussed and quantitative energy deficiencies of the employed DFT approaches are suggested. Some benchmarkable experimental observations: at low temperature, a single methanol molecule prefers the methyl-sided oxygen lone pair of 2-butanone over the ethyl-sided lone pair by 1-2 kJ mol^-1, the trans butane backbone is conserved in both low-lying isomers, the OH-stretching fundamentals differ by 47(2) cm^-1.

Study on ozonolysis of asymmetric alkenes with matrix isolation and FT-IR spectroscopy

O₃ and alkenes are important reactants in the formation of SOA in the atmosphere. The intermediates and reaction mechanism of ozonation of alkene is an important topic in atmospheric chemistry. In this study, the low-temperature matrix isolation was used to capture the intermediates such as Primary ozonides (POZs), Criegee Intermediates (CIs), and Secondary ozonides (SOZs) generated from ozonation of 2-methyl-1-butene (2M1B) and 2-methyl-2-butene (2M2B). The results have been identified by the vacuum infrared spectroscopy and theoretical calculation. Our results show that during the ozonation of asymmetric alkenes, two kinds of CIs and more than two kinds of SOZs were generated due to the different decomposition modes of POZs. The infrared absorption peaks of (CH₃)₂COO and CH₃CH₂C(CH₃)OO for O-O telescopic vibration was determined to be 889 cm^-1 and 913 cm^-1, respectively. Using the merged jet method, it was found that a large amount of HCHO was produced during the ozonation of 2M1B, and glyoxal and methylglyoxal were produced in the ozonation of 2M2B. Our findings highlight the importance of asymmetric alkene ozonolysis reactions in producing CIs, further improving the understanding of the generation of CIs from ozonation of alkenes.

Temperature- and Pressure-induced Structural Transition of Binary Clathrate Hydrates

We discover new structure II (sII) hydrate forming agents of two C₄ H₈ O molecules (2-methyl-2-propen-1-ol and 2-butanone) and report the abnormal structural transition of binary C₄ H₈ O+CH₄ hydrates between structure I (sI) and sII with varying temperature and pressure conditions. In both (2-methyl-2-propen-1-ol+CH₄ ) and (2-butanone+CH₄ ) systems, the phase boundary of the two different hydrate phases (sI and sII) exists at the slope change of the phase-equilibrium curve in the semi-logarithmic plots. We confirm the crystal structures of two hydrates synthesized at low (278 K and 6 MPa) and high (286 K and 15 MPa) temperature and pressure conditions by using high-resolution powder diffraction and Raman spectroscopy. 2-Methyl-2-propen-1-ol and 2-butanone can occupy the large cages of sII hydrate at low temperature and pressure conditions; however, they are excluded from the hydrate phase at high temperature and pressure conditions, resulting in the formation of pure sI CH₄ hydrate.

Pressure-selected reactivity between 2-butyne and water induced by two-photon excitation

High-pressure photochemistry between 2-butyne (H3CC≡CCH3) and trace amount of H2O was investigated at room temperature using multiline UV radiation at λ ≈ 350 nm and monitored by FTIR spectroscopy. Instead of the expected polymerization of 2-butyne, the IR spectral analysis suggests the formation of cis- and trans-2-butene, as well as 2-butanone, as the primary products. The possible reaction mechanisms and production pathways of these products were examined, where the dissociation of water molecule as the other reactant is believed as the essential step of the photochemical reaction. We further found that initial loading pressure of the mixture can not only substantially influence the reaction kinetics, but also regulate the accessibilities to some reaction channels, which was evidenced by quantitative analysis of the characteristic IR bands of 2-butene and 2-butanone. The relative abundance of two products is found to be highly dependent on pressure and radiation time. This study provides attractive physical routes in the absence of solvents, catalysts, and radical initiators, to synthesis the relevant products with a great selectivity and feasibility.

Structural and spectroscopic characterisation of C4 oxygenates relevant to structure/activity relationships of the hydrogenation of α,β-unsaturated carbonyls

In the present work, we have investigated the conformational isomerism and calculated the vibrational spectra of the C4 oxygenates: 3-butyne-2-one, 3-butene-2-one, 2-butanone and 2-butanol using density functional theory. The calculations are validated by comparison to structural data where available and new, experimental inelastic neutron scattering and infrared spectra of the compounds. We find that for 3-butene-2-one and 2-butanol the spectra show clear evidence for the presence of conformational isomerism and this is supported by the calculations. Complete vibrational assignments for all four molecules are provided and this provides the essential information needed to generate structure/activity relationships for the sequential catalytic hydrogenation of 3-butyne-2-one to 2-butanol.

Ab initio study of the barriers to methyl torsion and torsional frequencies of acetyl molecules

A wide range of ab initio and hybrid density functional methods and basis sets have been employed to calculate the barriers to methyl internal rotation in a range of molecules with the acetyl moiety. Comparison is made of the computed torsional frequency with the experimental torsional frequency, nu(obs), for each molecule. With the MP2/6-311+G(3df,2p) combination of method and basis set, the agreement is better than 4 cm-1 for most of the molecules, where nu(obs) or the V3 barrier is well-determined experimentally.

Reactive Intermediates in Olefin Oxidations with Chromyl Chloride. IR-Spectroscopic Proof for O=CrCl(2)-Epoxide Complexes

After photolytic induction (411 nm) of the reaction between chromyl chloride and olefins in low-temperature matrixes, for the first time primary products of this system have been isolated and identified: the reaction of propylene yields O=CrCl(2).O=CHCH(2)CH(3) and while in the case of trans- and cis-2-butylene, OCrCl(2).O=C(CH(3))(CH(2)CH(3)) as well as OCrCl(2).(trans-2,3-butylene oxide) and OCrCl(2).(cis-2,3-butylene oxide) are obtained, respectively. Epoxide formation proceeds under complete retention of stereochemistry, and the regioselective reaction route leading to the carbonyl products can be suppressed if all hydrogen atoms at the olefinic bond are substituted: tetramethylethylene is selectively oxidized to tetramethylethylene oxide, which forms a complex with OCrCl(2). All products were characterized by IR spectroscopy, which was further supported by DFT calculations in certain cases. The mechanism leading to the formation of these products, their electronic states, and the implications of the matrix results on the thermal reactions of chromyl chloride are discussed.