First-principles calculation of ideal-gas thermodynamic properties of long-chain molecules by R1SM approach—Application to n-alkanes

Accurate Enthalpies of Formation for Bioactive Compounds from High-Level Ab Initio Calculations with Detailed Conformational Treatment: A Case of Cannabinoids

Our recently developed approach based on the local coupled-cluster with single, double, and perturbative triple excitation [LCCSD(T)] model gives very efficient means to compute the ideal-gas enthalpies of formation. The expanded uncertainty (95% confidence) of the method is about 3 kJ·mol-1 for medium-sized compounds, comparable to typical experimental measurements. Larger compounds of interest often exhibit many conformations that can significantly differ in intramolecular interactions. Although the present capabilities allow processing even a few hundred distinct conformer structures for a given compound, many systems of interest exhibit numbers well in excess of 1000. In this study, we investigate how to reduce the number of expensive LCCSD(T) calculations for large conformer ensembles while controlling the error of the approximation. The best strategy found was to correct the results of the lower-level, surrogate model (density functional theory, DFT) in a systematic manner. It was also found that the error in the conformational contribution introduced by a surrogate model is mainly driven by a systematic (bias) rather than a random component of the DFT energy deviation from the LCCSD(T) target. This distinction is usually overlooked in DFT benchmarking studies. As a result of this work, the enthalpies of formation for 20 cannabinoid and cannabinoid-related compounds were obtained. Comprehensive uncertainty analysis suggests that the expanded uncertainties of the obtained values are below 4 kJ·mol-1.

A dual-cutoff machine-learned potential for condensed organic systems obtained via uncertainty-guided active learning

Machine-learned potentials (MLPs) trained on ab initio data combine the computational efficiency of classical interatomic potentials with the accuracy and generality of the first-principles method used in the creation of the respective training set. In this work, we implement and train a MLP to obtain an accurate description of the potential energy surface and property predictions for organic compounds, as both single molecules and in the condensed phase. We devise a dual descriptor, based on the atomic cluster expansion (ACE), that couples an information-rich short-range description with a coarser long-range description that captures weak intermolecular interactions. We employ uncertainty-guided active learning for the training set generation, creating a dataset that is comparatively small for the breadth of application and consists of alcohols, alkanes, and an adipate. Utilizing that MLP, we calculate densities of those systems of varying chain lengths as a function of temperature, obtaining a discrepancy of less than 4% compared with experiment. Vibrational frequencies calculated with the MLP have a root mean square error of less than 1 THz compared to DFT. The heat capacities of condensed systems are within 11% of experimental findings, which is strong evidence that the dual descriptor provides an accurate framework for the prediction of both short-range intramolecular and long-range intermolecular interactions.

Thermodynamic Study of N-Methylformamide and N,N-Dimethyl-Formamide

An extensive thermodynamic study of N-methylformamide (CAS RN: 123-39-7) and N,N-dimethylformamide (CAS RN: 68-12-2), is presented in this work. The liquid heat capacities of N-methylformamide were measured by Tian-Calvet calorimetry in the temperature interval (250-300) K. The vapor pressures for N-methylformamide and N,N-dimethylformamide were measured using static method in the temperature range 238 K to 308 K. The ideal-gas thermodynamic properties were calculated using a combination of the density functional theory (DFT) and statistical thermodynamics. A consistent thermodynamic description was developed using the method of simultaneous correlation, where the experimental and selected literature data for vapor pressures, vaporization enthalpies, and liquid phase heat capacities and the calculated ideal-gas heat capacities were treated together to ensure overall thermodynamic consistency of the results. The resulting vapor pressure equation is valid from the triple point to the normal boiling point temperature.

New Method of NPOH Equation-Based to Estimate the Physicochemical Properties of Noncyclic Alkanes

Changes in various physicochemical properties (P _(n)) of noncyclic alkanes can be roughly classified as linear and nonlinear changes. In our previous study, the NPOH equation was proposed to express nonlinear changes in the properties of organic homologues. Until now, there has been no general equation to express nonlinear changes in the properties of noncyclic alkanes involving linear and branched alkane isomers. This work, on the basis of NPOH equation, proposes a general equation to express nonlinear changes in the physicochemical properties of noncyclic alkanes, including a total of 12 properties, boiling point, critical temperature, critical pressure, acentric factor, heat capacity, liquid viscosity, and flash point, named as the "NPNA equation", as follows: ln(P _(n)) = a + b(n - 1) + c(S _CNE) + d (ΔAOEI) + f(ΔAIMPI), where a, b, c, and f are coefficients, and P _(n) represents the property of the alkane with n carbon atom number. n, S _CNE, ΔAOEI, and ΔAIMPI are number of carbon atoms, sum of carbon number effects, average odd-even index difference, and average inner molecular polarizability index difference, respectively. The obtained results show that various nonlinear changes in the properties of noncyclic alkanes can be expressed by the NPNA equation. Nonlinear and linear change properties of noncyclic alkanes can be correlated with four parameters, n, S _CNE, ΔAOEI, and ΔAIMPI. The NPNA equation has the advantages of uniform expression, usage of fewer parameters, and high estimation accuracy. Furthermore, using the above four parameters, a quantitative correlation equation can be established between any two properties of noncyclic alkanes. Employing the obtained equations as model equations, the property data of noncyclic alkanes, involving 142 critical temperatures, 142 critical pressures, 115 acentric factors, 116 flash points, 174 heat capacities, 142 critical volumes, and 155 gas enthalpies of formation, a total of 986 values, were predicted, which have not be experimentally measured. NPNA equation not only can provide a simple and convenient estimation or prediction method for the properties of noncyclic alkanes but also can provide new perspectives for studying quantitative structure-property relationships of branched organic compounds.

On the intensity of light scattered by molecular liquids-Comparison of experiment and quantum chemical calculations

The intensity of light scattered by liquids has been studied for over a century since the valuable microscopic information about the molecules can be obtained, such as the anisotropy of the molecular polarizability tensor or preferred orientations of neighboring molecules. However, in modern dynamic light scattering experiments, the scattering intensity is usually disregarded, unlike in dielectric spectroscopy, which can be considered as a complementary experimental method, where the dielectric strength is routinely evaluated. The reason lies partly on the fact that the exact form of the equations relating the macroscopically measured light scattering intensity to the microscopic properties of the molecules is debated in the literature. Therefore, as a first step, we compare anisotropy parameters from the literature, calculated from light scattering intensities using different equations, with quantum chemical calculations for over 150 medium-sized molecules. This allows us to identify a consistent form of equations. In a second part, we turn to the depolarized light scattering spectra of 13 van der Waals liquids and some mixtures thereof, recorded with a combination of Tandem-Fabry-Perót and Raman spectroscopies, giving direct access to the reorientational dynamics of the molecules. We discuss how the strength of the structural α-relaxation is connected to the anisotropy parameter, what implication this has for the shape of the α-relaxation, how the components of a mixture-also for the case of ionic liquids-can be identified in this way, and how orientational correlation parameters can be extracted. Additionally, we point out for the example of n-alkanes that for highly flexible molecules, the reorientational motion might not be the decisive source of the depolarized scattered light. We also show that light scattering might serve as a sensitive tool to check the accuracy of a conformer ensemble obtained by quantum chemical calculations.

Sublimation Properties of α,ω-Diamines Revisited from First-Principles Calculations

Sublimation enthalpies of alkane-α,ω-diamines exhibit an odd-even pattern within their homologous series. First-principles calculations coupled with the quasi-harmonic approximation for crystals and with the conformation mixing model for the ideal gas are used to explain this phenomenon from the theoretical point of view. Crystals of the odd and even alkane-α,ω-diamines distinctly differ in their packing motifs. However, first-principles calculations indicate that it is a delicate interplay of the cohesive forces, phonons, molecular vibrations and conformational equilibrium which governs the odd-even pattern of the sublimation enthalpies within the homologous series. High molecular flexibility of the alkane-α,ω-diamines predetermines higher sensitivity of the computational model to the quality of the optimized geometries and relative conformational energies. Performance of high-throughput computational methods, such as the density functional tight binding (DFTB, GFN2-xTB) and the explicitly correlated dispersion-corrected Møller-Plesset perturbative method (MP2C-F12), are benchmarked against the consistent state-of-the-art calculations of conformational energies and interaction energies, respectively.

Volatility Study of Amino Acids by Knudsen Effusion with QCM Mass Loss Detection

This work presents a new Knudsen effusion apparatus employing continuous monitoring of sample deposition using a quartz-crystal microbalance sensor with internal calibration by gravimetric determination of the sample mass loss. The apparatus was tested with anthracene and 1,3,5-triphenylbenzene and subsequently used for the study of sublimation behavior of several proteinogenic amino acids. Their low volatility and thermal instability strongly limit possibilities of studying their sublimation behavior and available literature data. The results presented in this work are unique in their temperature range and low uncertainty required for benchmarking theoretical studies of sublimation behavior of molecular crystals. The possibility of dimerization in the gas phase that would invalidate the effusion experiments is addressed and disproved by theoretical calculations. The enthalpy of sublimation of each amino acid is analyzed based on the contributions in two hypothetical sublimation paths involving the proton transfer in the solid and in the gas phase.

Ideal-gas thermodynamic properties of proteinogenic aliphatic amino acids calculated by R1SM approach

In this work, a R1SM approach was applied for the calculation of ideal-gas thermodynamic properties of five amino acids with aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine. The first step of the calculation was an extensive conformational analysis that located several conformers not reported previously. A new systematic and user-friendly nomenclature of the conformers was introduced, and the stable conformers were clearly assigned with the previously used labeling where possible. Stability and calculated relative energies of the conformers were compared between various levels of theory and with several experimental studies, demonstrating a good performance of the selected B3LYP-D3/6-311+G(2df,p) level of theory. As a second step, the theoretically calculated vibrational frequencies were compared to the previously reported experimental spectra to verify the performance of the applied double-linear scaling factor. Finally, ideal-gas heat capacities, enthalpies, and absolute entropies were calculated, accounting for all stable conformers using the R1SM model. The resulting thermodynamic data are presented for the first time, since they cannot be determined experimentally and their rigorous calculation requires a complex thermodynamic model.