Anharmonic Raman spectra in high-pressure ice from ab initio simulations

Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials Including Host-Guest Interactions

Layered framework materials, a rapidly advancing class of porous materials, are composed of molecular components stitched together via covalent bonds and are usually synthesized through wet-chemical methods. Computational infrared (IR) and Raman spectra are among the most important characterization tools for this material class. Besides the a priori known spectra of the molecular building blocks and the solvent, they allow for in situ monitoring of the framework formation during synthesis. Therefore, they need to capture the additional peaks from host-guest interactions and the bands from emerging bonds between the molecular building blocks, verifying the successful synthesis of the desired material. In this work, we propose a robust computational framework based on ab initio molecular dynamics (AIMD), where we compute IR and Raman spectra from the time-correlation functions of dipole moments and polarizability tensors, respectively. As a case study, we apply our methodology to a covalent organic framework (COF) material, COF-1, and present its AIMD-computed IR and Raman spectra with and without 1,4-dioxane solvent molecules in its pores. To determine robust settings, we meticulously validate our model and explore how stacking disorder and different methods for computing dipole moments and polarizabilities affect IR and Raman intensities. Using our robust computational protocol, we achieve excellent agreement with experimental data. Furthermore, we illustrate how the computed spectra can be dissected into individual contributions from the solvent molecules, the molecular building blocks of COF-1, and the bonds connecting them.

Accuracy and limitations of the bond polarizability model in modeling of Raman scattering from molecular dynamics simulations

Calculation of Raman scattering from molecular dynamics (MD) simulations requires accurate modeling of the evolution of the electronic polarizability of the system along its MD trajectory. For large systems, this necessitates the use of atomistic models to represent the dependence of electronic polarizability on atomic coordinates. The bond polarizability model (BPM) is the simplest such model and has been used for modeling the Raman spectra of molecular systems but has not been applied to solid-state systems. Here, we systematically investigate the accuracy and limitations of the BPM parameterized from the density functional theory results for a series of simple molecules, such as CO2, SO2, H2S, H2O, NH3, and CH4; the more complex CH2O, CH3OH, CH3CH2OH, and thiophene molecules; and the BaTiO3 and CsPbBr3 perovskite solids. We find that BPM can reliably reproduce the overall features of the Raman spectra, such as shifts of peak positions. However, with the exception of highly symmetric systems, the assumption of non-interacting bonds limits the quantitative accuracy of the BPM; this assumption also leads to qualitatively inaccurate polarizability evolution and Raman spectra for systems where large deviations from the ground state structure are present.

Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities

Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.

Tensorial Properties via the Neuroevolution Potential Framework: Fast Simulation of Infrared and Raman Spectra

Infrared and Raman spectroscopy are widely used for the characterization of gases, liquids, and solids, as the spectra contain a wealth of information concerning, in particular, the dynamics of these systems. Atomic scale simulations can be used to predict such spectra but are often severely limited due to high computational cost or the need for strong approximations that limit the application range and reliability. Here, we introduce a machine learning (ML) accelerated approach that addresses these shortcomings and provides a significant performance boost in terms of data and computational efficiency compared with earlier ML schemes. To this end, we generalize the neuroevolution potential approach to enable the prediction of rank one and two tensors to obtain the tensorial neuroevolution potential (TNEP) scheme. We apply the resulting framework to construct models for the dipole moment, polarizability, and susceptibility of molecules, liquids, and solids and show that our approach compares favorably with several ML models from the literature with respect to accuracy and computational efficiency. Finally, we demonstrate the application of the TNEP approach to the prediction of infrared and Raman spectra of liquid water, a molecule (PTAF-), and a prototypical perovskite with strong anharmonicity (BaZrO3). The TNEP approach is implemented in the free and open source software package gpumd, which makes this methodology readily available to the scientific community.

CRYSTAL23: A Program for Computational Solid State Physics and Chemistry

The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.

Phonon-Phonon Interactions in the Polarization Dependence of Raman Scattering

We have found that the polarization dependence of Raman scattering in organic crystals at finite temperatures can only be described by a fourth-rank tensor formalism. This generalization of the second-rank Raman tensor stems from the effect of off-diagonal components in the crystal self-energy on the light scattering mechanism. We thus establish a novel manifestation of phonon-phonon interaction in inelastic light scattering, markedly separate from the better-known phonon lifetime.

Raman Optical Activity of N-Acetyl-L-Cysteine in water and in methanol: the "clusters-in-a-liquid" model and ab initio molecular dynamics simulations

Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.

On the Cartesian Representation of the Molecular Polarizability Tensor Surface by Polynomial Fitting to Ab Initio Data

We describe an approach to constructing an analytic Cartesian representation of the molecular dipole polarizability tensor surface in terms of polynomials in interatomic distances with a training set of ab initio data points obtained from a molecular dynamics (MD) simulation or by any other available means. The proposed formulation is based on a perturbation treatment of the unmodified point dipole polarizability model of Applequist [ J. Am. Chem. Soc. 1972, 94, 2952] and is shown here to be, by construction (i) free of short-range or other singularities or discontinuities, (ii) symmetric and translationally invariant, and (iii) nonreliant on a body-fixed coordinate system. Permutational invariance of like nuclei is demonstrated to be readily applicable, making this approach useful for highly fluxional and reactive systems. Derivation of the method is described in detail, adding brief didactic numerical examples of H₂ and H₂O and concluding with an MD simulation of the Raman spectrum of H₅O₂⁺ at 300 K with the polarizability tensor fitted to CCSD(T)/aug-cc-pVTZ data obtained using the HBB-4B potential [ J. Chem. Phys. 2005, 122, 044308].

Full Assignment of Ab-Initio Raman Spectra at Finite Temperatures Using Wannier Polarizabilities: Application to Cyclohexane Molecule in Gas Phase

We demonstrate how to fully ascribe Raman peaks simulated using ab initio molecular dynamics to specific vibrations in the structure at finite temperatures by means of Wannier functions. Here, we adopt our newly introduced method for the simulation of the Raman spectra in which the total polarizability of the system is expressed as a sum over Wannier polarizabilities. The assignment is then based on the calculation of partial Raman activities arising from self- and/or cross-correlations between different types of Wannier functions in the system. Different types of Wannier functions can be distinguished based on their spatial spread. To demonstrate the predictive power of this approach, we applied it to the case of a cyclohexane molecule in the gas phase and were able to fully assign the simulated Raman peaks.

TAO-DFT-Based Ab Initio Molecular Dynamics

Recently, AIMD (ab initio molecular dynamics) has been extensively employed to explore the dynamical information of electronic systems. However, it remains extremely challenging to reliably predict the properties of nanosystems with a radical nature using conventional electronic structure methods (e.g., Kohn-Sham density functional theory) due to the presence of static correlation. To address this challenge, we combine the recently formulated TAO-DFT (thermally-assisted-occupation density functional theory) with AIMD. The resulting TAO-AIMD method is employed to investigate the instantaneous/average radical nature and infrared spectra of n-acenes containing n linearly fused benzene rings (n = 2-8) at 300 K. According to the TAO-AIMD simulations, on average, the smaller n-acenes (up to n = 5) possess a nonradical nature, and the larger n-acenes (n = 6-8) possess an increasing radical nature, showing remarkable similarities to the ground-state counterparts at 0 K. Besides, the infrared spectra of n-acenes obtained with the TAO-AIMD simulations are in qualitative agreement with the existing experimental data.

"On-The-Fly" Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface

In the present work, we provide an electronic structure based method for the "on-the-fly" determination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polarizability are approximated to be proportional to the second moment of Wannier functions. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Raman spectrum and polarizability of liquid water from deep neural networks

Using deep neural networks to model the polarizability and potential energy surfaces, we compute the Raman spectrum of liquid water at several temperatures with ab initio molecular dynamics accuracy.

Computing Bulk Phase Resonance Raman Spectra from ab Initio Molecular Dynamics and Real-Time TDDFT

We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase systems from ab initio molecular dynamics, including solvent influence and some anharmonic effects. Based on real-time time-dependent density functional theory, we obtain the RR spectra for all laser wavelengths in one pass. We compute the RR spectrum of uracil in aqueous solution, which is in good agreement with experiment. This is the first simulation of a bulk phase RR spectrum.

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Exotic Spectra and Lattice Vibrations of Ice X Using the DFT Method

A typical vibrational spectrum in the ice phase has four separate bands: Translation, libration, bending, and stretching. Ice X, the final ice phase under high pressure, shows an exotic vibrational spectrum. Based on harmonic approximation, an ideal crystal of ice X has one peak, at 998 cm^-1, for Raman scattering and two peaks, at 450 cm^-1 and 1507 cm^-1, for infrared absorption in this work. These three characteristic peaks are indicators of the phase transition between ice VII and VIII and ice X. Despite many experimental and theoretical works on ice X, only this study has clearly indicated these characteristic peaks in the region of the IR band. The phonon density of states shows quite different features than ice VIII, which could be verified by inelastic neutron scattering in the future. The dynamic processes of 15 vibrational normal modes are discussed and the typical hydrogen bonds are missing.

Computing Bulk Phase Raman Optical Activity Spectra from ab initio Molecular Dynamics Simulations

We present our novel methodology for computing Raman optical activity (ROA) spectra of liquid systems from ab initio molecular dynamics (AIMD) simulations. The method is built upon the recent developments to obtain magnetic dipole moments from AIMD and to integrate molecular properties by using radical Voronoi tessellation. These techniques are used to calculate optical activity tensors for large and complex periodic bulk phase systems. Only AIMD simulations are required as input, and no time-consuming perturbation theory is involved. The approach relies only on the total electron density in each time step and can readily be combined with a wide range of electronic structure methods. To the best of our knowledge, these are the first computed ROA spectra for a periodic bulk phase system. As an example, the experimental ROA spectrum of liquid (R)-propylene oxide is reproduced very well.

Ferroelectricity in high-density H2O ice

The origin of longstanding anomalies in experimental studies of the dense solid phases of H2O ices VII, VIII, and X is examined using a combination of first-principles theoretical methods. We find that a ferroelectric variant of ice VIII is energetically competitive with the established antiferroelectric form under pressure. The existence of domains of the ferroelectric form within anti-ferroelectric ice can explain previously observed splittings in x-ray diffraction data. The ferroelectric form is stabilized by density and is accompanied by the onset of spontaneous polarization. The presence of local electric fields triggers the preferential parallel orientation of the water molecules in the structure, which could be stabilized in bulk using new high-pressure techniques.

Voronoi dipole moments for the simulation of bulk phase vibrational spectra

Voronoi tessellation of the electron density in ab initio molecular dynamics simulations is used to calculate vibrational spectra.

Evidence for the existence of Li2S2 clusters in lithium–sulfur batteries: ab initio Raman spectroscopy simulation

Using density functional theory calculations and ab initio molecular dynamics simulations, we have observed a clear evidence of Li₂S₄ → Li₂S₂ transition by studying systematic changes in the simulated Raman spectra of (Li₂S₄)_n, n = 1, 4, and 8, towards that of (Li₂S₂)₈.

Raman spectra from symmetric hydrogen bonds in water by high-intensity laser-induced breakdown

Raman spectra of ice VII and X were investigated using strong plasma shockwave generated by laser-induced breakdown (LIB) in liquid water. Simultaneously, the occurrence of the hydrogen emission lines of 656 nm (Hα), 486 nm (Hβ), 434 nm (Hγ) and 410 nm (Hδ) was observed. At 5 × 10(12) W/cm(2) optical power density, the O-H symmetric stretching, translational and librational modes of ice VII and a single peak at 785 cm(-1) appeared in the spectra. The band was assigned to the Raman-active O-O mode of the monomolecular phase, which was the symmetric hydrogen bond of cuprite ice X. The spectra indicated that ice VII and X structure were formed, as the trajectory of the strong plasma shockwave passes through the stable Pressure-Temperature range of ice VII and X. The shockwave temperature and pressure were calculated by the Grüneisen model.

Aqueous solutions: state of the art in ab initio molecular dynamics

The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.

Raman Spectra of Liquid Water from Ab Initio Molecular Dynamics: Vibrational Signatures of Charge Fluctuations in the Hydrogen Bond Network

We report the first ab initio simulations of the Raman spectra of liquid water, obtained by combining first principles molecular dynamics and density functional perturbation theory. Our computed spectra are in good agreement with experiments, especially in the low frequency region. We also describe a systematic strategy to analyze the Raman intensities, which is of general applicability to molecular solids and liquids, and it is based on maximally localized Wannier functions and effective molecular polarizabilities. Our analysis revealed the presence of intermolecular charge fluctuations accompanying the hydrogen bond (HB) stretching modes at 270 cm(-1), in spite of the absence of any Raman activity in the isotropic spectrum. We also found that charge fluctuations partly contribute to the 200 cm(-1) peak in the anisotropic spectrum, thus providing insight into the controversial origin of such peak. Our results highlighted the importance of taking into account electronic effects in interpreting the Raman spectra of liquid water and the key role of charge fluctuations within the HB network; they also pointed at the inaccuracies of models using constant molecular polarizabilities to describe the Raman response of liquid water.

Ab initio characterization of graphene nanoribbons and their polymer precursors

Bottom-up fabrication of graphene nanoribbons (GNRs) from halogen-terminated aromatic precursors is a promising method for achieving atomically precise nanoribbons at competitive yields. GNR fabrication proceeds via the polymerization of the precursors and successive dehydrogenation. By first principles density functional theory calculations, we perform a systematic characterization of the polymeric precursors and the corresponding graphene nanoribbons in terms of structural and electronic properties, and we compute the Raman and infrared spectra. The band structure properties are examined by considering the bonding features and the partial charge densities of the structures. The physical origin of the infrared and Raman peaks is investigated in terms of the morphology and vibrational properties of the precursors and products. We show that light spectroscopy provides a unique fingerprint for each type of GNR, which may be used to monitor the quality of the final products and the kinetics of the synthesis process.

Infrared and Raman line shapes for ice Ih. II. H2O and D2O

We present a theoretical study of infrared and Raman line shapes of polycrystalline and single crystal ice Ih, for both water and heavy water, at 1, 125, and 245 K. Our calculations involve a mixed quantum/classical approach, a new water simulation model with explicit three-body interactions, transition frequency and dipole maps, and intramolecular and intermolecular vibrational coupling maps. Our theoretical spectra are in reasonable agreement with experimental spectra (available only near the two higher temperatures). We trace the origins of the different spectral peaks to weak and strong intermolecular couplings. We also discuss the delocalization of the vibrational eigenstates in terms of the competing effects of disorder and coupling.