{"title":"Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations.","authors":"V S Sandeep Inakollu, Haibo Yu","doi":"10.1063/4.0000124","DOIUrl":null,"url":null,"abstract":"<p><p>Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, \"A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function,\" J. Comput. Chem. <b>39</b>, 2067 (2018)] of deprotonated serine, we observed a significant difference in the vibrational spectra with the classical MD simulations compared to the infrared multiple photon dissociation spectra. It was postulated that this is due to neglecting the nuclear quantum effects (NQEs). In this work, NQEs are considered in spectral calculation using the TRPMD simulations. With the help of potential of mean force calculations, the conformational space of deprotonated serine is analyzed and used to understand the difference in the spectra of classical MD and TRPMD simulations at 298.15 and 100 K. The high-frequency vibrational bands in the spectra are characterized using Fourier transform localized vibrational mode (FT-<i>ν<sub>N</sub></i> AC) and interatomic distance histograms. At room temperature, the quantum effects are less significant, and the free energy profiles in the classical MD and the TRPMD simulations are very similar. However, the hydrogen bond between the hydroxyl-carboxyl bond is slightly stronger in TRPMD simulations. At 100 K, the quantum effects are more prominent, especially in the 2600-3600 cm<sup>-1</sup>, and the free energy profile slightly differs between the classical MD and TRPMD simulations. Using the FT-<i>ν<sub>N</sub></i> AC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3000,"publicationDate":"2021-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443303/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Structural Dynamics-Us","FirstCategoryId":"101","ListUrlMain":"https://doi.org/10.1063/4.0000124","RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2021/9/1 0:00:00","PubModel":"eCollection","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0
Abstract
Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, "A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function," J. Comput. Chem. 39, 2067 (2018)] of deprotonated serine, we observed a significant difference in the vibrational spectra with the classical MD simulations compared to the infrared multiple photon dissociation spectra. It was postulated that this is due to neglecting the nuclear quantum effects (NQEs). In this work, NQEs are considered in spectral calculation using the TRPMD simulations. With the help of potential of mean force calculations, the conformational space of deprotonated serine is analyzed and used to understand the difference in the spectra of classical MD and TRPMD simulations at 298.15 and 100 K. The high-frequency vibrational bands in the spectra are characterized using Fourier transform localized vibrational mode (FT-νN AC) and interatomic distance histograms. At room temperature, the quantum effects are less significant, and the free energy profiles in the classical MD and the TRPMD simulations are very similar. However, the hydrogen bond between the hydroxyl-carboxyl bond is slightly stronger in TRPMD simulations. At 100 K, the quantum effects are more prominent, especially in the 2600-3600 cm-1, and the free energy profile slightly differs between the classical MD and TRPMD simulations. Using the FT-νN AC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.
Structural Dynamics-UsCHEMISTRY, PHYSICALPHYSICS, ATOMIC, MOLECU-PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
CiteScore
5.50
自引率
3.60%
发文量
24
审稿时长
16 weeks
期刊介绍:
Structural Dynamics focuses on the recent developments in experimental and theoretical methods and techniques that allow a visualization of the electronic and geometric structural changes in real time of chemical, biological, and condensed-matter systems. The community of scientists and engineers working on structural dynamics in such diverse systems often use similar instrumentation and methods.
The journal welcomes articles dealing with fundamental problems of electronic and structural dynamics that are tackled by new methods, such as:
Time-resolved X-ray and electron diffraction and scattering,
Coherent diffractive imaging,
Time-resolved X-ray spectroscopies (absorption, emission, resonant inelastic scattering, etc.),
Time-resolved electron energy loss spectroscopy (EELS) and electron microscopy,
Time-resolved photoelectron spectroscopies (UPS, XPS, ARPES, etc.),
Multidimensional spectroscopies in the infrared, the visible and the ultraviolet,
Nonlinear spectroscopies in the VUV, the soft and the hard X-ray domains,
Theory and computational methods and algorithms for the analysis and description of structuraldynamics and their associated experimental signals.
These new methods are enabled by new instrumentation, such as:
X-ray free electron lasers, which provide flux, coherence, and time resolution,
New sources of ultrashort electron pulses,
New sources of ultrashort vacuum ultraviolet (VUV) to hard X-ray pulses, such as high-harmonic generation (HHG) sources or plasma-based sources,
New sources of ultrashort infrared and terahertz (THz) radiation,
New detectors for X-rays and electrons,
New sample handling and delivery schemes,
New computational capabilities.