Determination of molecular structure of succinic acid in a very complex conformational landscape: Gas-phase electron diffraction (GED) and ab initio studies

Elucidating the Infrared Spectral Properties of Succinic Molecular Acid Crystals: Illustration of the Structure and the Hydrogen Bond Energies of the Crystal and Its Deuterated Analogs

Herein, the infrared spectroscopic properties of molecular succinic acid crystals (SA) and their four isotopic analogs [C₂H₄(COOH)₂, h₆-SA; C₂H₄(COOD)₂, d₂-SA; C₂D₄(COOH)₂, d₄-SA; C₂D₄(COOD)₂, d₆-SA] are reported. The correlation between the structure of succinic acid molecules and their corresponding hydrogen bond energies is elucidated. The effects related to the isotopic dilution as well as the changes in the spectrum recording temperature on the fine structures of the v_O-H and v_O-D bands are interpreted. The infrared spectral anomalies detected in the spectra of isotopically neat succinic nanocrystal acids are confirmed by theoretical calculations using density functional theory (DFT). According to previous spectroscopic studies of succinic acid and those carried out for α,ω-dicarboxylic acids, a decent agreement between the experimental results and the theoretical DFT simulations is obtained. Moreover, the spectra of single crystals of the h₆ and d₄ succinic acid variants prove that the vibrational coupling mechanism between the (COOH)₂ cycles is rigorously convergent to that detected in the spectra of aromatic carboxylic acids, suggesting thereby that the promotion of symmetry-forbidden high stretching IR transitions plays a crucial role. Furthermore, the obtained experimental results reveal that the succinic acid shows a spectral behavior significantly different from that characteristic of hydrogen associations of other acids of homologous series, such as the glutaric, adipic, malonic, and pimelic acid crystals. The results obtained herein shed light on the way to explore the revealed structure of isotopic derivatives of succinic acid crystals and may prove to be useful results for understanding the nature of unconventional interactions as well as the macroscopic energy effects directing the development of hydrogen associations.

Revised values for the X23 benchmark set of molecular crystals

A revised reference value set for molecular crystals: X23b; new cell volumes and lattice energies including volumetric expansion due to zero-point energy and thermal effects.

Conformational steering in dicarboxy acids: the native structure of succinic acid

Succinic acid, a dicarboxylic acid molecule, has been investigated spectroscopically with computational support to elucidate the complex aspects of its conformational composition. Due to the torsional freedom of the carbon backbone and hydroxy groups, a large number of potentially plausible conformers can be generated with an indication that the gauche conformer is favored over the trans form. The microwave and millimeter wave spectra have been analyzed and accurate spectroscopic constants have been derived that correlate best with those of the lowest energy gauche conformer. For an unambiguous conformational identification measurements were extended to the monosubstituted isotopologues, precisely determining the structural properties. Besides bond distances and angles, particularly the dihedral angle has been determined to be 67.76(11)°, confirming the anomalous tendency of the methylene units to favor gauche conformers when a short aliphatic segment is placed between two carbonyl groups.

Benchmarking Compound Methods (CBS-QB3, CBS-APNO, G3, G4, W1BD) against the Active Thermochemical Tables: A Litmus Test for Cost-Effective Molecular Formation Enthalpies

The theoretical atomization energies of some 45 CxHyOz molecules present in the Active Thermochemical Tables compilation and of particular interest to the combustion chemistry community have been computed using five composite model chemistries as titled. The species contain between 1-8 "heavy" atoms, and a few are conformationally diverse with up to nine conformers. The enthalpies of formation at 0 and 298.15 K are then derived via the atomization method and compared against the recommended values. In general, there is very good agreement between our averaged computed values and those in the ATcT; those for 1,3-cyclopentadiene exceptionally differ considerably, and we show from isodesmic reactions that the true value for 1,3-cyclopentadiene is closer to 134 kJ mol(-1) than the reported 101 kJ mol(-1). If one is restricted to using a single method, statistical measures indicate that the best methods are in the rank order G3 ≈ G4 > W1BD > CBS-APNO > CBS-QB3. The CBS-x methods do on average predict ΔfH(⊖)(298.15 K) within ≈5 kJ mol(-1) but are prone to occasional lapses. There are statistical advantages to be gained from using a number of methods in tandem, and all possible combinations have been tested. We find that the average formation enthalpy coming from using CBS-APNO/G4, CBS-APNO/G3, and G3/G4 show lower mean signed and mean unsigned errors, and lower standard and root-mean-squared deviations, than any of these methods in isolation. Combining these methods also leads to the added benefit of providing an uncertainty rooted in the chemical species under investigation. In general, CBS-APNO and W1BD tend to underestimate the formation enthalpies of target species, whereas CBS-QB3, G3, and G4 have a tendency to overestimate the same. Thus, combining CBS-APNO with a G3/G4 combination leads to an improvement in all statistical measures of accuracy and precision, predicting the ATcT values to within 0.14 ± 4.21 kJ mol(-1), thus rivalling "chemical accuracy" (±4.184 kJ mol(-1)) without the excessive cost associated with higher-level methods such as W1BD.

Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals

The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013)], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.

Interplay of experiment and theory: determination of an accurate equilibrium structure of 1-methyluracil by the gas electron diffraction method and coupled-cluster computations

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.