Benchmarking quantum chemical methods for accurate gas-phase structure predictions of carbonyl compounds: the case of ethyl butyrate.

High-resolution spectroscopy techniques play a pivotal role to validate and efficiently benchmark available methods from quantum chemistry. In this work, we analyzed the microwave spectrum of ethyl butyrate within the scope of a systematic investigation to benchmark state-of-the-art exchange-correlation functionals and ab initio methods, to accurately predict the lowest energy conformers of carbonyl compounds in their isolated state. Under experimental conditions, we observed two distinct conformers, one of Cs and one of C1 symmetry. As reported earlier in the cases of some ethyl and methyl alkynoates, structural optimizations of the most abundant conformer that exhibits a C1 symmetry proved extremely challenging for several quantum chemical levels. To probe the sensitivity of different methods and basis sets, we use the identified soft-degree of freedom in proximity to the carbonyl group as an order parameter. The results of our study provide useful insight for spectroscopists to select an adapted method for structure prediction of carbonyl compounds based on their available computational resources, suggesting a reasonable trade-off between accuracy and CPU cost. At the same time, our observations and the resulting sets of highly accurate experimental constants from high-resolution spectroscopy experiments give an appeal to theoretical groups to look further into this seemingly simple family of chemical compounds, which may prove useful for the further development and parametrization of theoretical methods in computational chemistry.

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth.

Many proteins have the potential to aggregate into amyloid fibrils, protein polymers associated with a wide range of human disorders such as Alzheimer's and Parkinson's disease. The thermodynamic stability of amyloid fibrils, in contrast to that of folded proteins, is not well understood: the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using a combination of theory, in vitro experiments, simulations of a coarse-grained protein model and meta-data analysis, we delineate the enthalpic and entropic contributions that dominate amyloid fibril elongation. Our prediction of a characteristic temperature-dependent enthalpic signature is confirmed by the performed calorimetric experiments and a meta-analysis over published data. From these results we are able to define the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability.

Large Amplitude Motions in Fruit Flavors: The Case of Alkyl Butyrates.

To accurately characterize the large amplitude motions and soft degrees of freedom of isolated molecules, sampling their conformational landscape by molecular mechanics and quantum chemical calculations may provide a valuable insight into the structure and dynamics. However, the resulting models need to be validated by a reliable experimental counterpart. For ethyl pentanoates, which belong to the family of fruit esters, benchmark calculations at different levels of theory showed that the C-C bond in proximity to the ester carbonyl group exhibits a large amplitude motion that is extremely sensitive to the choice of quantum chemical method and basis set. In such cases, insights from high-resolution molecular jet techniques are ideal to accurately identify and characterize soft degrees of freedom. Here, we report on the most abundant conformer of ethyl 2-ethyl butyrate using Fourier-transform microwave spectroscopy. We show that - unlike other structurally related pentanoates for which gas-phase and crystallographic data is available - ethyl 2-ethyl butyrate possesses a Cs symmetry plane under molecular jet conditions.

Quantifying soft degrees of freedom in volatile organic compounds: insight from quantum chemistry and focused single molecule experiments.

Sampling of the vast conformational landscape of organic compounds remains a challenging task in computational chemistry, especially when it comes to the characterization of soft-degrees of freedom and relatively small energy barriers between different local minima. Therefore, studying the intrinsic properties of isolated molecules using focused experiments such as high-resolution molecular spectroscopy provides a powerful approach to validate and improve available quantum chemical methods. Here, we report on the most abundant gas-phase structure of ethyl 2-methyl pentanoate under molecular jet conditions, which we used to benchmark several exchange-correlation functionals and ab initio methods at the quantum chemical level. The observed conformer of ethyl 2-methyl pentanoate in the gas-phase is of C1 symmetry and exhibits a large amplitude motion around the C-C bond in proximity to the carbonyl moiety, which, unlike in the case of its structural isomer ethyl 2-ethyl butyrate, is very sensitive to the applied quantum chemical method and basis set. Depending on the applied quantum chemical method, the dihedral angle of the lowest energy conformer is optimized to absolute values of ±20°. This is far above the usual convergence error of the theoretical methods and has a tremendous impact on the rotational constants of this conformer, which complicates the prediction of rotational spectra and the assignment of experimental data. We show that the loss of symmetry in the aliphatic chain bound to the carboxylic moiety of ethyl esters results in a shift of the dihedral angle value due to a flat potential well around the corresponding C-C bond. Our benchmark calculations further indicate the potential relevance of the wB97X-D functional for this ethyl pentanoate and other related ethyl esters.

The first microsolvation step for furans: New experiments and benchmarking strategies.

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.

Communication through the furan ring: the conformational effect on the internal rotation of 5-methyl furfural studied by microwave spectroscopy.

Internal rotation is a fundamental motion of methyl groups that provides important insights into the molecular physics of isolated molecules. The barrier heights of such large amplitude motions are highly sensitive to their molecular and electronic environment. To date, it is still not possible to accurately determine these values using quantum chemical calculations. To probe the effect of molecular conformations on the barrier heights of substituted furan rings, the molecular jet Fourier transform microwave spectrum of 5-methyl furfural was recorded in the frequency range from 2.0 to 40.0 GHz. Quantum chemical calculations yielded two conformers with a trans and a cis orientation of the formyl group, which were both observed in the experimental spectrum. Torsional splittings due to the internal rotation of the methyl group were resolved and analyzed. The experimental spectrum is reproduced with standard deviations close to the experimental accuracy, yielding sets of highly accurate rotational and internal rotation parameters. The results, especially the V3 potentials, are compared to quantum chemical calculations and discussed within the scope of the current literature of other methyl substituted furans, where the methyl group is in close proximity of the furan oxygen atom. The present work provides an accurate evaluation of the different case studies and highlights the bottlenecks and future options of the currently available theoretical techniques.

The furan microsolvation blind challenge for quantum chemical methods: First steps.

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.

Methyl Internal Rotation in the Microwave Spectrum of o-Methyl Anisole.

The microwave spectrum of o-methyl anisole (2-methoxytoluene), CH3 OC6 H4 CH3, has been measured by using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Conformational analysis using quantum chemical calculations at the MP2/6-311++G(d,p) level of theory yields only one stable conformer with a Cs structure, which was assigned in the experimental spectrum. A-E splittings due to the internal rotation of the ring methyl group could be resolved and the barrier to internal rotation was determined to be 444.05(41) cm-1 . The experimentally deduced molecular parameters such as rotational and centrifugal distortion constants as well as the torsional barrier of the ring methyl group are in agreement with the calculated values.

Favored Conformations of Carbonyl Compounds: A Structural Study of n-Octanal.

We report on the molecular structures of the two most abundant conformers of n-octanal observed by molecular beam Fourier transform microwave spectroscopy. Next to limonene, which is the main component of citrus-oil, octanal and other n-alkyl aldehydes strongly enhance the typical fresh smell of lemon-oil. Due to the high flexibility of its n-alkyl chain and the high number of possible conformers, different semi-empirical methods (AM1, PM3, MMFF94) were used to sample the conformational space of octanal before performing more sophisticated quantum chemical calculations at the MP2 level of theory. This technique has previously been shown to be an ideal tool to characterize relevant odorant structures in fragrance chemistry. The structure of octanal and structurally related molecules is discussed in the context of the most abundant chain conformations and the potential use of the microwave validated structures for further studies in biological media.

From cats and blackcurrants: structure and dynamics of the sulfur-containing cassis odorant cat ketone.

Sulfur-containing odorants and flavors play an important role in flavor and food industry, especially when meaty, garlic, onion, and vegetable scents are needed. Still, many S-containing flavors also possess fruity scents and may be used in compositions of perfumes that require a fresh and fruity odor perception. They are naturally abundant in various fruits, essential oils, and food. Most of these compounds possess strong scents, and their scent composition is highly dependent on the concentration applied. At higher concentrations, they usually feature repellent off-odors, while their sweet and fruity nature is only experienced at very low concentrations. This represents a challenge for their application in perfumery, as well as in food industry. From a molecular point of view, the endless structural and scent variety of these compounds makes them fascinating, especially as their O-analogs are usually free of any malodors. Here, we report on the investigation of the gas-phase structure and dynamics of the S-containing blackcurrant odorant cat ketone (4-methyl-4-sulfanylpentan-2-one). The work was performed by combining quantum-chemical calculations and molecular-beam Fourier-transform microwave spectroscopy as complementary tools. Using this technique, we are able to determine the structures of sizeable molecules where energy differences are small and conformational distinction is not always possible by quantum-chemical calculations alone. The presented results can be used for further structure-activity correlation studies, as well as for benchmarks to improve theoretical models, especially, as there is still significant interest in characterizing the various conformers of organic molecules in terms of relative energies, structures, and dipole moments.

A touch of lavender: gas-phase structure and dynamics of the monoterpene linalool validated by microwave spectroscopy.

The microwave spectrum of linalool, an acyclic monoterpene, was recorded for the first time in the range from 9 to 16 GHz. The only conformer observed under molecular beam conditions was assigned. Fitting the rotational spectrum with two different programs treating internal rotation yielded the rotational constants A = 1.64674020(46) GHz, B = 0.68219862(16) GHz, C = 0.61875100(20) GHz, and the centrifugal distortion constants. The standard deviation of the fit was close to experimental accuracy. A-E splittings due to the internal rotation of one methyl group could be resolved and the internal rotation barrier was determined to be 400.20(64) cm(-1). The results from microwave spectroscopy were used to validate the molecular geometry obtained from quantum chemical calculations.

Conformational landscape of diisopropyl ketone: quantum chemical calculations validated by microwave spectroscopy.

We report on the gas-phase structure of the most abundant conformer of diisopropyl ketone, (CH(3))(2)HC-CO-CH(CH(3))(2), as observed by molecular beam Fourier transform microwave spectroscopy. The gas-phase structures of five conformers of diisopropyl ketone were optimized using ab initio calculations at the MP2/6-311++G(d,p) level of theory. The natures of the stationary points were verified using harmonic frequency calculations. The only conformer observed in the supersonic jet possesses C(2) symmetry and appears as an enantiomeric pair. From the microwave spectrum, a set of three highly accurate rotational constants, five centrifugal distortion constants, and three sextic centrifugal distortion constants were determined. The structure of the observed conformer was optimized again at different levels of theory using the HF, MP2, and B3LYP methods. The theoretical constants of the C(2) conformer were subsequently validated using the experimental constants. To understand the transitions of one conformer to the others, the isopropyl groups were rotated against each other. The resulting two-dimensional potential energy surface shows nicely the symmetry of the conformational landscape and also indicates the enantiomeric pairs of the conformers. The barriers to internal rotation of the methyl groups were determined to be 1052 and 905 cm(-1) at the MP2/6-311++G(d,p) and the B3LYP/6-311++G(d,p) levels, respectively. In agreement with the theoretical predictions, no internal rotation patterns could be observed in the microwave spectrum.

Sulfur-containing flavors: gas phase structures of dihydro-2-methyl-3-thiophenone.

Dihydro-2-methyl-3-thiophenone was investigated using a combination of quantum chemical calculations and molecular beam Fourier transform microwave spectroscopy. The substance is present in coffee, roasted peanuts, and whiskey. The microwave spectrum was recorded under molecular beam conditions in the frequency range from 9 to 14 GHz. We report on the two main conformers of dihydro-2-methyl-3-thiophenone, for which highly accurate rotational constants and centrifugal distortion constants were obtained. No splittings due to internal rotation of the methyl group could be observed in the microwave spectrum. This is in agreement with the theoretical predictions of the barrier heights, which have been determined to be more than 1000 cm(-1) at the MP2/6-311++G(d,p) level of theory. In addition to the most abundant (32)S-isotopologue of the main conformer, also the (34)S-isotopologue was assigned, which occurs with a natural abundance of about 4%. Using the experimental rotational constants, different quantum chemical calculations were validated for the two observed conformers. To complete the theoretical investigation of dihydro-2-methyl-3-thiophenone, different transition states were optimized to understand the intramolecular conversion between the two conformers at the MP2/6-311++G(d,p) level. The transition states were optimized using the Berny algorithm.

Structural studies on ethyl isovalerate by microwave spectroscopy and quantum chemical calculations.

We observed the microwave spectrum of ethyl isovalerate by molecular beam Fourier transform microwave spectroscopy. The rotational and centrifugal distortion constants of the most abundant conformer were determined. Its structure was investigated by comparison of the experimental rotational constants with those obtained by ab initio methods. In a first step, the rotational constants of various conformers were calculated at the MP2/6-311++G** level of theory. Surprisingly, no agreement with the experimental results was found. Therefore, we concluded that in the case of ethyl isovalerate more advanced quantum chemical methods are required to obtain a reliable molecular geometry. Ab initio calculations carried out at MP3/6-311++G**, MP4/6-311++G**, and CCSD/6-311++G** levels and also density functional theory calculations using the B3LYP/6-311++G** method gave similar results for the rotational constants, but they were clearly distinct from those obtained at the MP2/6-311++G** level. With use of these more advanced methods, the rotational constants of the lowest energy conformer were in good agreement with those obtained from the microwave spectrum.

Structural insight from intermolecular interactions and energy framework analyses of 2-substituted 6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-ones.

The crystal structures of three mackinazolinone derivatives (2-amino-6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one at room temperature, and 2-nitro-6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one and N-(11-oxo-6,8,9,11-tetrahydro-7H-pyrido[2,1-b]quinazolin-2-yl)benzamide at 100 K) are explored using X-ray crystallography. To delineate the different intermolecular interactions and the respective interaction energies in the crystal architectures, energy framework analyses were carried out using the CE-B3LYP/6-31G(d,p) method implemented in the CrystalExplorer software. In the structures the different molecules are linked by C-H...O, C-H...N and N-H...O hydrogen bonds. Together with these hydrogen bonds, C-H...π and C-O...π interactions are involved in the formation of a three-dimensional crystal network. A Hirshfeld surface analysis allows the visualization of the two-dimensional fingerprint plots and the quantification of the contributions of H...H, H...C/C...H and H...O/O...H contacts throughout the different crystal structures. To obtain additional information on the intrinsic properties of our targets and to compare the experimental crystal structures with their respective conformations in the gas phase, quantum chemical calculations at the B3LYP-D3BJ/6-311++G(d,p) level of theory, including Grimme's D3 correction term and BJ damping functions, were carried out to account for intramolecular dispersion interactions. The identified energy gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO gap) of our targets in the gas phase and in two implicit solvents (methanol and dimethyl sulfoxide) allow us to quantify the impact of different substituents on the reactivity of mackinazolinone derivatives.

Highlights from the Faraday Discussion 296: quantum effects in small molecular systems, 10-12 September 2018, Edinburgh, United Kingdom.

Exciting discussions on the impact of quantum effects in small molecular systems took place in the historical city of Edinburgh this fall 2018 in the unique conference format of the Faraday Discussions. During this three day conference meeting close to Holyrood Park, 65 leading experts from all over the world came together to discuss the developments, advances and challenges in the wide field of quantum effects in small molecular systems, either isolated or embedded into clusters, clathrates or cold matrices. The meeting clearly reflected the importance of the accurate description, characterization and prediction of quantum effects in isolated, solvated and complexed molecular systems, while allowing the community to crystallize future perspectives and directions in the field, as well as applications in chemistry, physics, biology, environmental sciences and industry.

Competing Dispersive Interactions: From Small Energy Differences to Large Structural Effects in Methyl Jasmonate and Zingerone.

Modern structural studies of biologically relevant molecules require an exhaustive interplay between experiment and theory. In this work, we present two examples where a poor choice of the theoretical method led to a misinterpretation of experimental results. We do that by performing a rotational spectroscopy study on two large and flexible biomolecules: methyl jasmonate and zingerone. The results show the enormous potential of rotational spectroscopy as a benchmark to evaluate the performance of theoretical methods.