Dipole Autocorrelation Function Research Articles

Slowdown of solvent structural dynamics in aqueous DMF solutions

This study presents a comprehensive investigation into the molecular dynamics of solvation environments through an integrated approach combining Fourier-transform infrared (FTIR) spectroscopy, molecular dynamics (MD) simulations, and two-dimensional infrared (2D IR) spectroscopy. We explore the solvation of an ionic solute (ammonium thiocyanate) in various solvent systems, including N,N-dimethylformamide (DMF), water, and a 0.5 mole fraction of DMF in water, aiming to unravel the intricate interplay between solute-solvent interactions and solvent dynamics across diverse solvation environments. By integrating FTIR spectral analysis with radial distribution functions and coordination numbers obtained from MD simulations, we decipher the solvent composition around the solute molecule. Analysis of 2D IR spectra and hydrogen bond, as well as dipolar autocorrelation function from MD simulations, further elucidates the nuances of solute-solvent interactions, highlighting the impact of solvent dynamics on solvation structures. Our results reveal a significant slowdown of the solvent structural dynamics in the equimolar binary solvent mixture compared to the neat solvents. This slowdown underscores the complex relationship between solute-solvent interactions and solvent dynamics. The integration of FTIR, MD simulations, and 2D IR spectroscopy provides a unified framework for obtaining a holistic understanding of solvation dynamics, offering valuable insights into the underlying molecular mechanisms governing solute-solvent interactions in complex systems. These results pave the way for future studies to delve deeper into the molecular intricacies of solvation phenomena.

Collaborative polarization in a solution of coupled hydroxychloroquine-graphene oxide: Optoelectrical measurements

Optical UV–vis and electrical impedance measurements were conducted at room temperature on aqueous solutions with hydroxychloroquine (HCQ) and graphene oxide (GO) molecules. Remarkably, at sufficiently high GO concentration, the HCQ-GO solution exhibited the least loss factor and the Debye relaxation process, suggesting that the polarization of coupled HCQ-GO molecules is cooperative and, hence, correlated within the Debye relaxation time. Indeed, our systematic molecular dynamic calculations of the equilibrium Dipole Auto-Correlation Function (DACF) showed that adding GO enhances the decay relaxation time of DACF for HCQ samples. Moreover, the depression of the characteristic UV absorption peak (at ∼ 342 nm) with increasing GO concentration validated the presence of the HCQ-GO interaction in our samples, agreeing with our calculation based on the simplified time-dependent density functional theory. Our work is, thus, timely regarding the current high demand for a method to remove HCQ from the aqueous environment. It is also relevant to drug delivery applications considering the anticancer efficacy of HCQ and the biocompatible GO as a potential drug carrier.

Computational dielectric spectroscopy on solid-solution interface by time-dependent voltage applied molecular dynamics simulation.

A frequency-dependent dielectric constant characterizes the dielectric response of a medium and also represents the time scale of system's collective dynamics. Although it is valuable not only academically but also practically for developing advanced devices, getting the value of a solution at the interface with a solid or electrode surface is challenging both experimentally and computationally. Here, we propose a computational method that imitates the dielectric spectroscopy and AC impedance measurement. It combines a time-dependent voltage applied molecular dynamics simulation with an equivalent circuit representation of a system composed of a solution confined between two identical electrodes. It gives the frequency-dependent dielectric constants of the bulk solution and the interface simultaneously. Unlike the conventional method, it does not require computation of a dipole autocorrelation function and its Fourier transformation. Application of the method on a system of water confined between polarizable Pt electrodes gives the static dielectric constant and the relaxation time of the bulk water in good agreement with previous simulation results and experimental values. In addition, it gives a much smaller static dielectric constant at the interface, consistent with previous observations. The outline of the dielectric dispersion curve of the interface seems similar to that of the bulk, but the relaxation time is several times faster.

Non-impact effects in the absorption spectra of HCl diluted in CO2, air, and He: Measurements and predictions.

Non-impact effects in the absorption spectra of HCl in various collision-partners are investigated both experimentally and theoretically. Fourier transform spectra of HCl broadened by CO2, air, and He have been recorded in the 2-0 band region at room temperature and for a wide pressure range, from 1 to up to 11.5 bars. Comparisons between measurements and calculations using Voigt profiles show strong super-Lorentzian absorptions in the troughs between successive lines in the P and R branches for HCl in CO2. A weaker effect is observed for HCl in air, while for HCl in He, Lorentzian wings are in very good agreement with measurements. In addition, the line intensities retrieved by fitting the Voigt profile on the measured spectra decrease with the density of the perturber. This perturber-density dependence decreases with the rotational quantum number. For HCl in CO2, the decrease in the retrieved line intensity can reach 2.5% per amagat for the first rotational quantum numbers. This number is about 0.8% per amagat for HCl in air, while for HCl in He, no density dependence of the retrieved line intensity is observed. Requantized classical molecular dynamics simulations have been performed for HCl-CO2 and HCl-He in order to simulate the absorption spectra for various perturber-density conditions. The density dependence of the intensities retrieved from the simulated spectra and the predicted super-Lorentzian behavior in the troughs between lines are in good agreement with experimental determinations for both HCl-CO2 and HCl-He. Our analysis shows that these effects are due to incomplete or ongoing collisions, which govern the dipole auto-correlation function at very short times. The effects of these ongoing collisions strongly depend on the details of the intermolecular potential: they are negligible for HCl-He but significant for HCl-CO2 for which a line-shape model beyond the impact approximation will be needed to correctly model the absorption spectra from the center to the far wings.

Non-Markovian collisional dynamics probed with laser-aligned molecules

The Markov, as well as the secular, approximations are key assumptions that have been widely used to model decoherence in a large variety of open quantum systems, but, as far as intermolecular collisions are considered, very little has been done in the time domain. In order to probe the limits of both approximations, we here study the influence of pressure on the alignment revivals (echoes) created in properly chosen gas mixtures (HCl and ${\mathrm{CO}}_{2}$, pure and diluted in He) by one (two) intense and short laser pulse(s). Experiments and direct predictions using molecular-dynamics simulations consistently demonstrate, through analyses at very short times $(<15 \mathrm{ps})$ after the laser kick(s), the breakdown of these approximations in some of the selected systems. We show that the nonadiabatic laser-induced molecular alignment technique and model used in this paper directly provide detailed information on the physical mechanisms involved in the collisional dissipation. Besides this ``fundamental'' interest, our findings also have potential practical applications for radiative heat transfer in planetary atmospheres and climate studies. Indeed, short time delays in the dipole autocorrelation function monitoring the light absorption spectrum correspond to large detunings from the optical resonances in the frequency domain, thus influencing the atmospheric transparency windows. Furthermore, the fact that the approach tested here for linear rotors can potentially be applied to almost any gas mixture (including, for instance, nonlinear and/or reacting molecules) further strengthens and broadens the perspectives that it opens.

Calculation of infrared spectra for adsorbed molecules from the dipole autocorrelation function

Calculation of infrared spectra for adsorbed molecules from the dipole autocorrelation function

Influence of Specific Structure on the Dielectric and Thermal Performance of Bulk Polymers: Atomistic Molecular Dynamics Simulations of XNBR

In this work, we investigate the influence of the molecular structure of carboxylated acrylonitrile-butadiene rubber (XNBR) on the dielectric properties through non-equilibrium molecular dynamics (NEMD) simulations. The NEMD simulations are performed for calculating the permittivity (ε) of XNBR under different alternating electric field strength (Ei), alternating electric field frequency (Ef), and temperature. The simulation results show a similar change trend with the reported experimental consequence of dielectric elastomer. Interestingly, a critical alternating Ei at which the dielectric properties of XNBR with different acrylonitrile contents change seriously is found. Moreover, a deep insight into the mechanisms of the dielectric and thermal performance of XNBR is explored through the analysis from the atomistic level, including intermolecular interaction, fractional free volume, molecular chain migration ability, hydrogen bonds breaking and re-formation, dipole autocorrelation function, phonon vibration power spectrum, and kinetic energy. The research results will inspire the design of polymer structures to obtain high-performance polymer materials. This article is protected by copyright. All rights reserved

Mechanical Properties of Amide Functionalized CNT/NBR at Different Temperatures: A Molecular Dynamics Study.

A comprehensive study on the mechanical properties of a pure carbon nanotube (PCNT)/nitrile butadiene rubber (NBR) composite and an amide-functionalized carbon nanotube (CONH2–CNT)/nitrile butadiene rubber (NBR) composite was carried out using molecular dynamics (MDs) simulations at different temperatures. The effects of temperature on the mechanical properties, fractional free volume (FFV), MSD, dipole autocorrelation function, number of hydrogen bonds of PCNT composites, and functionalized CNT composites were analyzed and compared, and the pull-out behavior of the composites under different condition temperatures was simulated. The enhancement mechanism of the interface interaction between the functionalized carbon nanotubes and the NBR matrix was explained from an atomic point of view. The results show that, due to the existence of hydrogen bonds, higher interfacial binding energies were formed between PCNT and NBR, and FFVs and MSDs were restricted at each temperature, with the mechanical properties of the composites being improved by 5.02–25.93%.

Direct method for MD simulations of collision-induced absorption: Application to an Ar–Xe gas mixture

With the reformulation of the classical equations of collision-induced absorption, we present a method to perform the direct computation of the spectral density function. This way the absorption coefficient can be computed from classical molecular dynamics (MD) without the computationally demanding evaluation of the dipole autocorrelation function. In addition, we have developed an algorithm to extract the bound-to-bound dimer contribution to the MD simulated absorption. The method has been tested on the Ar–Xe rare gas system. Comparisons with quantum mechanical (QM) and conventional MD methods validate the approach. The obtained MD bound-to-bound spectra generally agree in shape and magnitude with QM results, including features stemming from rotations and vibrations of the Ar–Xe dimer.

Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations.

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-νNAC) 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-νNAC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.

Molecular dynamics calculations of collision-induced absorption in a gas mixture of neon and krypton.

We continue the development of the in-house molecular dynamics software package SpaCIAL and test it for the computation of the collision-induced absorption coefficients for a neon (Ne) and krypton (Kr) gas mixture. An apodization procedure for the dipole autocorrelation function is implemented and tested. We also carry out a statistical study of the convergence rate with respect to ensemble size. The resulting absorption coefficients show a good accordance with quantum mechanical results. Comparison with laboratory measurements shows agreement within 10%-20% at T = 295 K. At T = 480 K, a larger difference of 40%-80% is observed, which can presumably be explained by experimental uncertainties. For the study, an empirical (Barker, Fisher, and Watts) interaction-potential [Mol. Phys. 21, 657 (1971)] for Ne-Kr has been developed. Ab initio {coupled cluster with singles and doubles (triples) [CCSD(T)]} potentials for Ne-Ne, Kr-Kr, and Ne-Kr have been computed, as well as the CCSD(T) interaction-induced Ne-Kr dipole moment curve.

Equation of motion coupled-cluster for core excitation spectra: Two complementary approaches.

This paper presents core excitation spectra from coupled-cluster (CC) theory obtained from both a time-independent and a new time-dependent formalism. The conventional time-independent CC formulation for excited states is the equation-of-motion (EOM-CC) method whose eigenvalues and eigenvectors describe the core excited states. An alternative computational procedure is offered by a time-dependent CC description. In that case, the dipole transition operator is expressed in the CC effective Hamiltonian form and propagated with respect to time. The absorption spectrum is obtained from the CC dipole autocorrelation function via a Fourier transformation. Comparisons are made among the time-dependent results obtained from second-order perturbation theory, to coupled cluster doubles and their linearized forms (CCD and LCCD), to CC singles and doubles (CCSD) and the linearized form (LCCSD). In the time-independent case, considerations of triples (EOM-CCSDT) and quadruples (EOM-CCSDTQ) are used to approach sub-electron volt accuracy. A particular target is the allyl radical, as an example of an open-shell molecule. As the results have to ultimately be the same, the two procedures offer a complementary approach toward analyzing experimental results.

Effect of Wave Collapse on Lyman and Balmer lines

The nonlinear coupling of Langmuir, ion sound and electromagnetic waves can create wave collapse conditions in a plasma, and modify the line shapes emitted by hydrogen atoms. Such conditions may appear in the presence of a strong source of energy, and create numerous regions where wave packets localize and the plasma density is decreased. We use a model of envelope solitons for the electric field acting on the emitter, and calculate the dipole autocorrelation function and the line shape with a numerical simulation. We investigate the role of the frequency of wave packets, and propose an approach retaining a dispersion relation ω(k).

Thermodynamic simulations of SrTiO3/epoxy nanocomposites with different mass fractions

Molecular dynamics simulations have been used to study the thermomechanical properties of SrTiO3/epoxy nanocomposites with different mass fractions. The calculation results revealed that thermal conductivity increased with mass fractions and temperature, which was consistent with the measured experiment value. Motion of molecular chain segment of pure epoxy resin became intense with temperature increase. With the increase in mass fractions of incorporated SrTiO3 nanoparticles, the mobility of molecular chain segment was significantly weakened below 500 K compared with pure epoxy resin model and the model of nanocomposite with a mass fraction of 25 wt% SrTiO3 showed best structure stability. Dipole autocorrelation functions (DACF) of pure epoxy resin fluctuated slightly under 350 K, but substantial fluctuation happened over 500 K. With the incorporation of SrTiO3 nanoparticles, the fluctuation of DACF of nanocomposites decreased drastically, maintaining a small value of 0.004 Debye, which demonstrated that structure stability of nanocomposites was strengthened under 500 K. Based on interface model between epoxy resin macromolecular ligands and crystal plane (110) of SrTiO3, interface interaction energy was calculated to be − 235.9 kcal/mol. To sum up, incorporation of SrTiO3 nanoparticles could significantly improve the thermomechanical properties of epoxy resin and enhance structure stability of nanocomposites.

A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function.

Computational vibrational spectroscopy serves as an important tool in the interpretation of experimental infrared (IR) spectra. In this article, we present a systematic benchmarking study of DFTB3 with two different computational vibrational spectroscopic methods, based on either normal mode analysis (NMA) or fast Fourier transform dipole autocorrelation function (FT-DAC). The results were compared with experimental data and theoretical calculations with B3LYP/cc-pVTZ. The empirical scaling factors for DFTB3/NMA, DFTB3-freq/NMA, and DFTB3/FT-DAC methods are 0.9993, 1.0059, and 0.9982, respectively. We also demonstrate the significance of anharmonicity and conformational sampling in vibrational spectroscopic calculations on flexible molecules. As expected, DFTB3/FT-DAC predicted the anharmonic vibrational peaks more accurately than DFTB3/NMA and NMA spectra are highly dependent on the initial structures. The potential limitations of DFTB3 for vibrational spectroscopic calculations and the challenges in assigning the FT-DAC spectral peaks were noted. DFTB3/FT-DAC is expected to serve as a promising technique in computational spectroscopy in complex biomolecular systems. © 2018 Wiley Periodicals, Inc.

Communication: Symmetrical quasi-classical analysis of linear optical spectroscopy.

The symmetrical quasi-classical approach for propagation of a many degree of freedom density matrix is explored in the context of computing linear spectra. Calculations on a simple two state model for which exact results are available suggest that the approach gives a qualitative description of peak positions, relative amplitudes, and line broadening. Short time details in the computed dipole autocorrelation function result in exaggerated tails in the spectrum.

Influence of Helical Trajectories of Perturbers on Stark Line Shapes in Magnetized Plasmas

In plasmas subject to a strong magnetic field, the dynamical properties of the microfield are affected by the cyclotron motion, which can alter Stark-broadened lines. We illustrate this effect through calculations of the hydrogen Lyman α line in an ideal one-component plasma. A focus is put on the central Zeeman component. It is shown that the atomic dipole autocorrelation function decreases more slowly if the cyclotron motion is retained. In the frequency domain, this denotes a reduction of the line broadening. A discussion based on numerical simulations and analytical estimates is done.

Simulation of Near-Edge X-ray Absorption Fine Structure with Time-Dependent Equation-of-Motion Coupled-Cluster Theory.

An explicitly time-dependent (TD) approach to equation-of-motion (EOM) coupled-cluster theory with single and double excitations (CCSD) is implemented for simulating near-edge X-ray absorption fine structure in molecular systems. The TD-EOM-CCSD absorption line shape function is given by the Fourier transform of the CCSD dipole autocorrelation function. We represent this transform by its Padé approximant, which provides converged spectra in much shorter simulation times than are required by the Fourier form. The result is a powerful framework for the blackbox simulation of broadband absorption spectra. K-edge X-ray absorption spectra for carbon, nitrogen, and oxygen in several small molecules are obtained from the real part of the absorption line shape function and are compared with experiment. The computed and experimentally obtained spectra are in good agreement; the mean unsigned error in the predicted peak positions is only 1.2 eV. We also explore the spectral signatures of protonation in these molecules.

Super- and sub-Lorentzian effects in the Ar-broadened line wings of HCl gas.

Using previously recorded spectra of HCl diluted in Ar gas at room temperature for several pressure conditions, we show that the absorptions in between successive P and R transitions are significantly different from those predicted using purely Lorentzian line shapes. Direct theoretical predictions of the spectra are also made using requantized classical molecular dynamics simulations and an input HCl-Ar interaction potential. They provide the time evolution of the dipole auto-correlation function (DAF) whose Fourier-Laplace transform yields the absorption spectrum. These calculations very well reproduce the observed super-Lorentzian behavior in the troughs between the intense lines in the central part of the band and the tendency of absorption to become sub-Lorentzian in the band wings between high J lines. The analysis shows that the former behavior is essentially due to incomplete collisions which govern the DAF at very short times. In addition, the increasing influence of line-mixing when going away from the band center explains the tendency of absorption to become more and more sub-Lorentzian in the wings.

Line shapes in turbulent plasmas

The fluctuations and oscillations observed in turbulent plasmas may affect the line shapes emitted by atoms and ions. We investigate several plasma conditions for which a spectroscopic signature of plasma turbulence can be observed. Starting from the simple model of microturbulence for Doppler profile, we examine how information on turbulent fluctuations is obtained in astrophysics and magnetic fusion plasmas. We recall the potential of a formalism which expresses the measured line shape in function of the probability density function of the fluctuating plasma parameters. New calculations of hydrogen dipole autocorrelation functions and line shapes are presented for plasmas affected by strong Langmuir turbulence and nonlinear wave collapse. We propose a model using a sequence of envelope solitons for the electric field created by the wave packets and felt by the emitters, and show that the line shape may be dominated by the effect of strong Langmuir turbulence.