Conformational analysis of melatonin at Hartree–Fock ab initio level

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5-18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

Dipole moments of trans- and cis-(4-methylcyclohexyl)methanol (4-MCHM): obtaining the right conformer for the right reason

Accurate computational estimates of fundamental physical properties can be used as inputs in the myriad of extant models employed to predict toxicity, transport, and fate of contaminants. However, as molecular complexity of contaminants increases, it becomes increasingly difficult to determine the magnitude of the errors introduced by ignoring the 3D conformational space averaging within group-additivity and semi-empirical approaches. The importance of considering 3D molecular structure is exemplified for the dipole moments of cis and trans isomers of (4-methylcyclohexyl)methanol (4-MCHM). When 10 000 gallons of 4-MCHM was spilled into the Elk River in January 2014, a lack of toxicological data and environmental partitioning coefficients hindered the immediate protection of human health and the local water supply in West Virginia, USA. Post-spill analysis of the contaminants suggested that the cis and trans isomers had observably different partitioning coefficients and solubility, and thus differing environmental fates. Obtaining high-quality dipole moments using ab initio quantum chemical methods for the isomeric pair was crucial in validating their experimental differences in solubility [Environ. Sci. Technol. Lett., 2015, 2, 127]. The use of first principles electronic structure theory is further explored here to obtain accurate conformer relative energies and dipole moments of cis- and trans-4-MCHM. Overall, the MP2 aug-cc-pVDZ level of theory affords the best balance between accuracy and computational cost.

Exploring the Accuracy Limits of Local Pair Natural Orbital Coupled-Cluster Theory

The domain based local pair natural orbital coupled cluster method with single-, double-, and perturbative triple excitations (DLPNO–CCSD(T)) is an efficient quantum chemical method that allows for coupled cluster calculations on molecules with hundreds of atoms. Because coupled-cluster theory is the method of choice if high-accuracy is needed, DLPNO–CCSD(T) is very promising for large-scale chemical application. However, the various approximations that have to be introduced in order to reach near linear scaling also introduce limited deviations from the canonical results. In the present work, we investigate how far the accuracy of the DLPNO–CCSD(T) method can be pushed for chemical applications. We also address the question at which additional computational cost improvements, relative to the previously established default scheme, come. To answer these questions, a series of benchmark sets covering a broad range of quantum chemical applications including reaction energies, hydrogen bonds, and other noncovalent interactions, conformer energies, and a prototype organometallic problem were selected. An accuracy of 1 kcal/mol or better can readily be obtained for all data sets using the default truncation scheme, which corresponds to the stated goal of the original implementation. Tightening of the three thresholds that control DLPNO leads to mean absolute errors and standard deviations from the canonical results of less than 0.25 kcal/mol (<1 kJ/mol). The price one has then to pay is an increased computational time by a factor close to 3. The applicability of the method is shown to be independent of the nature of the reaction. On the basis of the careful analysis of the results, three different sets of truncation thresholds (termed “LoosePNO”, “NormalPNO”, and “TightPNO”) have been chosen for “black box” use of DLPNO–CCSD(T). This will allow users of the method to optimally balance performance and accuracy.

Vibrational and electronic spectroscopic studies of melatonin

We report the infrared absorption and Raman spectra of melatonin recorded with 488 and 632.8 nm excitations in 3600-2700 and 1700-70 cm(-1) regions. Further, we optimized molecular structure of the three conformers of melatonin within density functional theory calculations. Vibrational frequencies of all three conformers have also been calculated. Observed vibrational bands have been assigned to different vibrational motions of the molecules on the basis of potential energy distribution calculations and calculated vibrational frequencies. Observed band positions match well with the calculated values after scaling except NH stretching mode frequencies. It is found that the observed and calculated frequencies mismatch of NH stretching is due to intermolecular interactions between melatonin molecules.