Intrinsic molecular vibration and rigorous vibrational assignment of benzene by first-principles molecular dynamics

Hitting the Trifecta: How to Simultaneously Push the Limits of Schrödinger Solution with Respect to System Size, Convergence Accuracy, and Number of Computed States

Methods for solving the Schrödinger equation without approximation are in high demand but are notoriously computationally expensive. In practical terms, there are just three primary factors that currently limit what can be achieved: 1) system size/dimensionality; 2) energy level excitation; and 3) numerical convergence accuracy. Broadly speaking, current methods can deliver on any two of these three goals, but achieving all three at once remains an enormous challenge. In this paper, we shall demonstrate how to "hit the trifecta" in the context of molecular vibrational spectroscopy calculations. In particular, we compute the lowest 1000 vibrational states for the six-atom acetonitrile molecule (CH₃CN), to a numerical convergence of accuracy 10^-2 cm^-1 or better. These calculations encompass all vibrational states throughout most of the dynamically relevant range (i.e., up to ∼4250 cm^-1 above the ground state), computed in full quantum dimensionality (12 dimensions), to near spectroscopic accuracy. To our knowledge, no such vibrational spectroscopy calculation has ever previously been performed.

Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor

Background

The study of drug–target interactions (DTIs) affinity plays an important role in safety assessment and pharmacology. Currently, quantitative structure–activity relationship (QSAR) and molecular docking (MD) are most common methods in research of DTIs affinity. However, they often built for a specific target or several targets, and most QSAR and MD methods were based either on structure of drug molecules or on structure of receptors with low accuracy and small scope of application. How to construct quantitative prediction models with high accuracy and wide applicability remains a challenge. To this end, this paper screened molecular descriptors based on molecular vibrations and took molecule-target as a whole system to construct prediction models with high accuracy-wide applicability based on dissociation constant (Kd) and concentration for 50% of maximal effect (EC50), and to provide reference for quantifying affinity of DTIs.

Results

After comprehensive comparison, the results showed that RF models are optimal models to analyze and predict DTIs affinity with coefficients of determination (R²) are all greater than 0.94. Compared to the quantitative models reported in literatures, the RF models developed in this paper have higher accuracy and wide applicability. In addition, E-state molecular descriptors associated with molecular vibrations and normalized Moreau-Broto autocorrelation (G3), Moran autocorrelation (G4), transition-distribution (G7) protein descriptors are of higher importance in the quantification of DTIs.

Conclusion

Through screening molecular descriptors based on molecular vibrations and taking molecule-target as whole system, we obtained optimal models based on RF with more accurate-widely applicable, which indicated that selection of molecular descriptors associated with molecular vibrations and the use of molecular-target as whole system are reliable methods for improving performance of models. It can provide reference for quantifying affinity of DTIs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04389-w.

Doublet-Singlet-Doublet Transition in a Single Organic Molecule Magnet On-Surface Constructed with up to 3 Aluminum Atoms

Starting from a long aza-starphene neutral and nonmagnetic organic molecule, a single-molecule magnet is on-surface constructed using up to 3 light nonmagnetic aluminum (Al) atoms. Seldom observed in solution with transition-metal atoms and going from 1 to 3 Al coordinated atoms, the doublet-singlet-doublet transition is easily on-surface accessible using the scanning tunneling microscope single-atom and single-molecule manipulations on a gold(111) surface. With 3 coordinated Al atoms, the lateral vibration modes of the Al3-aza-starphene molecule magnet are largely frozen. Using the Kondo states, this opens the observation of the in-phase Al vertical atom vibrations and out-of-phase central phenyl vibrations.