Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

Abstract

Two efficient methods, the Eckart frame algorithm and the multiorder derivative algorithm, for vibrational frequency calculation directly based on the raw data of atomic trajectory from the state-of-the-art first-principles molecular dynamics simulation are presented. The Eckart frame approach is robust to retrieve the full set of anharmonic fundamental frequencies of any molecule from the atomic trajectory for a sufficiently long molecular dynamics simulation at a temperature close to 0 K. In addition to the fundamental vibrational frequencies, the multiorder derivative approach is universal for the calculations of vibrational frequencies based on the molecular dynamics result in a wide range of temperatures. The accuracy, efficiency, and applicability of these two methods are demonstrated through several successful examples in calculating the anharmonic fundamental vibrational frequencies of methane, ethylene, water, and cyclobutadiene.

Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds

“…Standard Newtonian molecular dynamics simulations are not an option for anharmonic high frequency vibrations, although this is frequently claimed in the literature. [80][81][82] There will always be a specific simulation temperature for which the average classical frequency matches the quantum mechanical anharmonic value for a specific mode, but this temperature exceeds several 1000 K for a hydride stretching fundamental and changes from mode to mode. 44 At room temperature or even below, 80 hardly any high frequency mode anharmonicity is probed by Newtonian dynamics.…”

“…[80][81][82] There will always be a specific simulation temperature for which the average classical frequency matches the quantum mechanical anharmonic value for a specific mode, but this temperature exceeds several 1000 K for a hydride stretching fundamental and changes from mode to mode. 44 At room temperature or even below, 80 hardly any high frequency mode anharmonicity is probed by Newtonian dynamics. Agreement with experiment is then the result of a fortuitous cancellation between electronic structure error and vibrational error without any benchmarking insight.…”

Understanding the solubilization of Ca acetylide with a new computational model for ionic pairs

“…Accounting for anharmonic effects in calculations of free energies can be another option for incremental improvement of the methodology. Such effects can be incorporated in the solid state step (Figure 1, left), 93,94 as well as in the MD 95,96 and molecular DFT steps 97,98 (Figure 1, middle and right, correspondingly), although in the latter two cases this may be technically non-trivial. It was shown in recent studies of solid state and surface systems that anharmonic effects may be crucial.…”

"Dividing and Conquering" and "Caching" in Molecular Modeling

“…are problematic for anharmonic interactions, which are very common in many molecular systems. 23 It is well understood that properly parameterized Lennard-Jones potentials are accurate only near the bottom of its potential well. Frustration are ubiquitous in biomolecular systems and are likely fundamental driving force for conformational transformations.…”