Quantum Theory of Atoms in Molecules Analysis on the Conformational Preferences of Vinyl Alcohol and Related Ethers

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.

Conformer-Specific Heavy-Atom Tunneling in the Rearrangement of Benzazirines to Ketenimines

5-Methoxy-2H-benzazirine was prepared via irradiation of the corresponding phenyl azide, isolated in an argon matrix at cryogenic temperatures. It undergoes ring expansion to the corresponding ketenimine in the dark at T < 30 K despite a calculated activation barrier of 4.9 kcal mol^-1 [B3LYP/6-311++G(d,p)]. Since this rearrangement proceeds with a rate constant in the order of 10^-4 s^-1, exhibiting only a shallow temperature dependence, the results are interpreted in terms of heavy-atom tunneling. Of the four isomeric benzazirines resulting from the initial photolysis, only one can be observed to rearrange; this conformer specificity is explained by the other potentially observable rearrangements being either too fast or too slow to be detected due to the differences in heights and widths of their respective activation barriers.

Attractive Nonbonded Interactions Help Stabilize the Z Form of Alkenyl Anions

Alkenyl anions (^(-)H₂C-CH═CH-Y; Y = aliphatic, aromatic, amine, ether) are often thermodynamically stable in the sterically congested Z form. This preference for Z structures is used to control regiochemistry in organometallic and Grignard reactions, allyl amine rearrangements to enamines, and allyl ether rearrangements to enol ethers. Explanations for Z stability in alkenes (Y = CH₂R) typically invoke through-space attraction (Coulomb or charge transfer) between the formally anionic carbon C1 and the Y = CH₂R hydrogens. However, this explanation is difficult to generalize to amines and ethers. We suggest that the orbital-driven so-called "attractive nonbonded interactions" suggested to stabilize the Z forms of 1,2-difluoroethylene and 1-substituted propenes also help stabilize Z alkenyl anions. We present electronic structure calculations and surveys of the experimental literature to show these effects' relevance for alkenyl anions. Our results suggest new approaches for regiocontrol in reactions with alkenyl anion intermediates and motivate revisiting older orbital-based theories of "attractive nonbonded interactions".

How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules

This article compares molecular properties and atomic properties defined by the quantum theory of atoms in molecules (QTAIM) obtained from three underlying levels of theory: MP2(full), density functional theory (DFT) (B3LYP), and Hartree-Fock (H-F). The same basis set (6-311++G(d,p)) has been used throughout the study. The calculations and comparisons were applied to a set of 30 small molecules representing common fragments of biological molecules. The molecular properties investigated are the energies and the electrostatic moments (up to and including the quadrupoles), and the atomic properties include electron populations (and atomic charge), atomic dipolar and quadrupolar polarizations, atomic volumes, and corrected and raw atomic energies. The Cartesian distance between dipole vectors and the Frobenius distance between the quadrupole tensors calculated at the three levels of theory provide a measure of their correlation (or lack thereof). With the exception of energies (atomic and molecular), it is found that both DFT and H-F are in excellent agreement with MP2, especially with regards to the electrostatic mutipoles up to the quadrupoles, but DFT and MP2 agree better in almost all studied properties (with the exception of molecular geometries). QTAIM properties whether obtained from H-F, DFT(B3LYP), or MP2 calculations when used in the construction of empirical correlations with experiment such as quantitative structure-activity-(or property)-relationships (QSAR/QSPR) are equivalent (because the properties calculated at the three levels are very highly correlated among themselves with r(2) typically >0.95, and therefore preserving trends). These results suggest that the massive volume of results that were published in the older literature at the H-F level is valid especially when used to study trends or in QSAR or QSPR studies, and, as long as our test set of molecules is representative, there is no pressing need to re-evaluate them at other levels of theory except when inadequate basis sets were used by today's standards. Extensive tabulation of molecular and atomic properties at the three theoretical levels is available in the Supporting Information, including optimized geometries, molecular energies, virial ratios, molecular electrostatic moments up to and including hexadecapoles, atomic populations, atomic volumes, atomic electrostatic moments up to and including the quadrupoles, and atomic energies.

A comparison of the energetic and topological properties of weak interactions in molecular organic crystals

Several molecular organic crystals [tetraphenylphosphonium squarate, bianthrone, and bis(benzophenone) azine] have been analyzed topologically following a multipole refinement of each compound. This has resulted in the complete characterization of all the weak interactions present in these systems (C-H···O, C-H···C, and C-Hδ+···δ+H-C). Correlations have been found to exist between the energetic and topological properties for each type of interaction. The coexistence of the three types of interactions provides a unique opportunity to examine their energetic differences and similarities. This examination can also be used to help understand the complex nature of C-Hδ+···δ+H-C type interactions, in particular those characterized as H–H bonds. All this leads to a better understanding of the role H–H bonds play in molecular organic crystals compared with other weak interactions such as hydrogen bonds and van der Waals interactions.Key words: energetics, multipole refinement, H–H bonds, hydrogen bonds.

Experimental and Theoretical Electron Density Study of a Highly Twisted Polycyclic Aromatic Hydrocarbon: 4-Methyl-[4]helicene

Helicenes are molecules of considerable interest in view of their aromaticity which persists despite a marked departure from planarity and because of the extreme potency of some of their metabolites as tumor and mutation promoters. In this study, the electron density of 4-methyl-[4]helicene (or 4-methylbenzo[c]phenanthrene) is studied topologically with an emphasis on the fjord region since this region is where metabolic activation is initiated. The molecule consists of four fused aromatic rings that assume a twisted geometry. This geometry brings two hydrogen atoms into close proximity in the fjord region of the molecule accompanied by the appearance of an intramolecular C-Hdelta+...delta+H-C bond path (an interaction termed hydrogen-hydrogen or H- H bonding to distinguish it from dihydrogen bonding from which it is qualitatively distinct). In addition to the intramolecular H-H interaction, a number of intermolecular interactions are shown to be involved in the packing of this molecule in the crystalline state. The effect of the nonplanarity of the molecule on the local aromaticity of each ring is also discussed.

Thermodynamic Properties (Enthalpy, Bond Energy, Entropy, and Heat Capacity) and Internal Rotor Potentials of Vinyl Alcohol, Methyl Vinyl Ether, and Their Corresponding Radicals

Vinyl alcohols (enols) have been discovered as important intermediates and products in the oxidation and combustion of hydrocarbons, while methyl vinyl ethers are also thought to occur as important combustion intermediates. Vinyl alcohol has been detected in interstellar media, while poly(vinyl alcohol) and poly(methyl vinyl ether) are common polymers. The thermochemical property data on these vinyl alcohols and methyl vinyl ethers is important for understanding their stability, reaction paths, and kinetics in atmospheric and thermal hydrocarbon-oxygen systems. Enthalpies , entropies , and heat capacities (C(p)()(T)) are determined for CH(2)=CHOH, C(*)H=CHOH, CH(2)=C(*)OH, CH(2)=CHOCH(3), C(*)H=CHOCH(3), CH(2)=C(*)OCH(3), and CH(2)=CHOC(*)H(2). Molecular structures, vibrational frequencies, , and C(p)(T) are calculated at the B3LYP/6-31G(d,p) density functional calculation level. Enthalpies are also determined using the composite CBS-Q, CBS-APNO, and G3 methods using isodesmic work reactions to minimize calculation errors. Potential barriers for internal rotors are calculated at the B3LYP/6-31G(d,p) level and used to determine the hindered internal rotational contributions to entropy and heat capacity. The recommended ideal gas phase values calculated in this study are the following (in kcal mol(-1)): -30.0, -28.9 (syn, anti) for CH(2)=CHOH; -25.6, -23.9 for CH(2)=CHOCH(3); 31.3, 33.5 for C(*)H=CHOH; 27.1 for anti-CH(2)=C(*)OH; 35.6, 39.3 for C(*)H=CHOCH(3); 33.5, 32.2 for CH(2)=C(*)OCH(3); 21.3, 22.0 for CH(2)=CHOC(*)H(2). Bond dissociation energies (BDEs) and group additivity contributions are also determined. The BDEs reveal that the O-H, O-CH(3), C-OH, and C-OCH(3) bonds in vinyl alcohol and methyl vinyl ether are similar in energy to those in the aromatic molecules phenol and methyl phenyl ether, being on average around 3 kcal mol(-1) weaker in the vinyl systems. The keto-enol tautomerization enthalpy for the interconversion of vinyl alcohol to acetaldehyde is determined to be -9.7 kcal mol(-1), while the activation energy for this reaction is calculated as 55.9 kcal mol(-1); this is the simplest keto-enol tautomerization and is thought to be important in the reactions of vinyl alcohol. Formation of the formyl methyl radical (vinoxy radical/vinyloxy radical) from both vinyl alcohol and methyl vinyl ether is also shown to be important, and its reactions are discussed briefly.