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Special Issue "Describing Bulk Phase Effects with Ab Initio Methods"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (30 September 2020).

Special Issue Editor

Dr. Martin Brehm
Website
Guest Editor
Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
Interests: molecular dynamics; electron structure methods; condensed matter; vibrational spectroscopy; solubility; microheterogeneity; statistical mechanics; free energy methods

Special Issue Information

Dear Colleagues,

With the advent of electronic computers in the 1950s, the field of computational quantum chemistry experienced an impressive evolution over the following decades. Many powerful methods, both for computing electron structure and for deriving molecular properties, have been developed during that time. However, most calculations were limited to single molecules or small clusters in vacuum and to one single conformer—usually a minimum energy structure. A first step toward bulk phase systems was achieved by the development of band structure calculations of periodic crystals. Still, these methods were not well-suited for disordered systems and did not take into account entropic effects. In the 1990s, DFT-based ab initio molecular dynamics (AIMD) simulations became feasible, allowing for the first time to accurately describe complex disordered bulk phase systems, including the full effects of temperature and entropy. Based on such approaches, it is now possible to precisely compute many properties of “real life” condensed phase systems, including physicochemical data, vibrational spectra, NMR, EPR, and XPS spectra, structure factors, ion mobility, and even free energy profiles of processes. Most of these properties are significantly influenced by bulk phase effects and can therefore only be accurately determined by a full condensed phase description. As ab initio methods, these approaches are truly predictive and can typically yield reliable predictions for systems that have not been synthesized yet.

Contributions to this Special Issue should highlight recent developments for describing bulk phase effects—covering the development of methods as well as applications and theoretical–experimental collaborations. Both original research articles and reviews are highly welcome.

Dr. Martin Brehm
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Molecular dynamics
  • Monte Carlo
  • Electron structure calculations
  • Density functional theory
  • Computational spectroscopy
  • Dispersion interaction
  • Bulk phase
  • Disordered systems
  • Soft matter
  • Solutions
  • Microheterogeneity
  • Statistical mechanics
  • Free energy sampling
  • Metadynamics

Published Papers (12 papers)

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Research

Open AccessArticle
Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite
Molecules 2021, 26(1), 160; https://doi.org/10.3390/molecules26010160 - 31 Dec 2020
Abstract
Today’s fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future, and therefore effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to [...] Read more.
Today’s fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future, and therefore effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end, we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate (GP) and inositol hexaphosphate (IHP)) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite–IHP/GP–water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the 3M motif being most stable. The order of goethite–IHP/GP interaction energies is GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite–IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
TiCl4 Dissolved in Ionic Liquid Mixtures from Аb Initio Molecular Dynamics Simulations
Molecules 2021, 26(1), 79; https://doi.org/10.3390/molecules26010079 - 26 Dec 2020
Abstract
To gain a deeper understanding of the TiCl4 solvation effects in multi-component ionic liquids, we performed ab initio molecular dynamics simulations of 1-butyl-3-methylimidazolium [C4C1Im]+, tetrafluoroborate [BF4], chloride [Cl] both with and [...] Read more.
To gain a deeper understanding of the TiCl4 solvation effects in multi-component ionic liquids, we performed ab initio molecular dynamics simulations of 1-butyl-3-methylimidazolium [C4C1Im]+, tetrafluoroborate [BF4], chloride [Cl] both with and without water and titanium tetrachloride TiCl4. Complex interactions between cations and anions are observed in all investigated systems. By further addition of water and TiCl4 this complex interaction network is extended. Observations of the radial distribution functions and number integrals show that water and TiCl4 not only compete with each other to interact mainly with [Cl], which strongly influences the cation-[BF4] interaction, but also interact with each other, which leads to the fact that in certain systems the cation-anion interaction is enhanced. Further investigations of the Voronoi polyhedra analysis have demonstrated that water has a greater impact on the nanosegregated system than TiCl4 which is also due to the fact of the shear amount of water relative to all other components and its higher mobility compared to TiCl4. Overall, the polar network of the IL mixture collapses by including water and TiCl4. In the case of [Cl] chloride enters the water continuum, while [BF4] remains largely unaffected, which deeply affects the interaction of the ionic liquid (IL) network. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Exploring Free Energy Profiles of Enantioselective Organocatalytic Aldol Reactions under Full Solvent Influence
Molecules 2020, 25(24), 5861; https://doi.org/10.3390/molecules25245861 - 11 Dec 2020
Abstract
We present a computational study on the enantioselectivity of organocatalytic proline-catalyzed aldol reactions between aldehydes in dimethylformamide (DMF). To explore the free energy surface of the reaction, we apply two-dimensional metadynamics on top of ab initio molecular dynamics (AIMD) simulations with explicit solvent [...] Read more.
We present a computational study on the enantioselectivity of organocatalytic proline-catalyzed aldol reactions between aldehydes in dimethylformamide (DMF). To explore the free energy surface of the reaction, we apply two-dimensional metadynamics on top of ab initio molecular dynamics (AIMD) simulations with explicit solvent description on the DFT level of theory. We avoid unwanted side reactions by utilizing our newly developed hybrid AIMD (HyAIMD) simulation scheme, which adds a simple force field to the AIMD simulation to prevent unwanted bond breaking and formation. Our condensed phase simulation results are able to nicely reproduce the experimental findings, including the main stereoisomer that is formed, and give a correct qualitative prediction of the change in syn:anti product ratio with different substituents. Furthermore, we give a microscopic explanation for the selectivity. We show that both the explicit description of the solvent and the inclusion of entropic effects are vital to a good outcome—metadynamics simulations in vacuum and static nudged elastic band (NEB) calculations yield significantly worse predictions when compared to the experiment. The approach described here can be applied to a plethora of other enantioselective or organocatalytic reactions, enabling us to tune the catalyst or determine the solvent with the highest stereoselectivity. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
ab-Initio Study of Hydrogen Bond Networks in 1,2,3-Triazole Phases
Molecules 2020, 25(23), 5722; https://doi.org/10.3390/molecules25235722 - 03 Dec 2020
Abstract
The research in storage and conversion of energy is an everlasting process. The use of fuel cells is very tempting but up to now there are still several conceptual challenges to overcome. Especially, the requirement of liquid water causes difficulties due to the [...] Read more.
The research in storage and conversion of energy is an everlasting process. The use of fuel cells is very tempting but up to now there are still several conceptual challenges to overcome. Especially, the requirement of liquid water causes difficulties due to the temperature limit. Therefore, imidazoles and triazoles are increasingly investigated in a manifold of experimental and theoretical publications as they are both very promising in overcoming this problem. Recently, triazoles were found to be superior to imidazoles in proton conduction. An ab-initio molecular dynamics simulation of pure triazole phases for investigating the behavior of both tautomer species of the triazole molecule has never been done. In this work, we investigate the structural and dynamical properties of two different solid phases and the liquid phase at two different temperatures. We are able to show how the distinct tautomers contribute to the mechanism of proton conduction, to compute dynamical properties of the four systems and to suggest a mechanism of reorientation in solid phase. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ
Molecules 2020, 25(23), 5505; https://doi.org/10.3390/molecules25235505 - 24 Nov 2020
Abstract
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics–statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1 [...] Read more.
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics–statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides
Molecules 2020, 25(22), 5415; https://doi.org/10.3390/molecules25225415 - 19 Nov 2020
Abstract
Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the [...] Read more.
Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the product formation by the variation in initial conditions. In the present study, we use Car–Parrinello molecular dynamics to simulate the fastest reaction steps under such circumstances. We investigate the behavior of amino acids and peptides under anodic conditions. Such highly reactive situations lead to chemical reactions within picoseconds, and we can model the reaction mechanisms in full detail. The role of the electric current is to discharge charged species and, hence, to produce radicals from ions. This leads to ultra-fast radical reactions in a bulk environment, which can also be seen as redox reactions as the oxidation states change. In the case of amino acids, the educts can be zwitterionic, so we also observe complex acid–base chemistry. Hence, we obtain the full spectrum of condensed-phase chemistry. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
A Review of Density Functional Models for the Description of Fe(II) Spin-Crossover Complexes
Molecules 2020, 25(21), 5176; https://doi.org/10.3390/molecules25215176 - 06 Nov 2020
Abstract
Spin-crossover (SCO) materials have for more than 30 years stood out for their vast application potential in memory, sensing and display devices. To reach magnetic multistability conditions, the high-spin (HS) and low-spin (LS) states have to be carefully balanced by ligand field stabilization [...] Read more.
Spin-crossover (SCO) materials have for more than 30 years stood out for their vast application potential in memory, sensing and display devices. To reach magnetic multistability conditions, the high-spin (HS) and low-spin (LS) states have to be carefully balanced by ligand field stabilization and spin-pairing energies. Both effects could be effectively modelled by electronic structure theory, if the description would be accurate enough to describe these concurrent influences to within a few kJ/mol. Such a milestone would allow for the in silico-driven development of SCO complexes. However, so far, the ab initio simulation of such systems has been dominated by general gradient approximation density functional calculations. The latter can only provide the right answer for the wrong reasons, given that the LS states are grossly over-stabilized. In this contribution, we explore different venues for the parameterization of hybrid functionals. A fitting set is provided on the basis of explicitly correlated coupled cluster calculations, with single- and multi-dimensional fitting approaches being tested to selected classes of hybrid functionals (hybrid, range-separated, and local hybrid). Promising agreement to benchmark data is found for a rescaled PBE0 hybrid functional and a local version thereof, with a discussion of different atomic exchange factors. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation
Molecules 2020, 25(21), 5174; https://doi.org/10.3390/molecules25215174 - 06 Nov 2020
Abstract
Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, [...] Read more.
Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Clusters of Hydroxyl-Functionalized Cations Stabilized by Cooperative Hydrogen Bonds: The Role of Polarizability and Alkyl Chain Length
Molecules 2020, 25(21), 4972; https://doi.org/10.3390/molecules25214972 - 27 Oct 2020
Abstract
We explore quantum chemical calculations for studying clusters of hydroxyl-functionalized cations kinetically stabilized by hydrogen bonding despite strongly repulsive electrostatic forces. In a comprehensive study, we calculate clusters of ammonium, piperidinium, pyrrolidinium, imidazolium, pyridinium, and imidazolium cations, which are prominent constituents of ionic [...] Read more.
We explore quantum chemical calculations for studying clusters of hydroxyl-functionalized cations kinetically stabilized by hydrogen bonding despite strongly repulsive electrostatic forces. In a comprehensive study, we calculate clusters of ammonium, piperidinium, pyrrolidinium, imidazolium, pyridinium, and imidazolium cations, which are prominent constituents of ionic liquids. All cations are decorated with hydroxy-alkyl chains allowing H-bond formation between ions of like charge. The cluster topologies comprise linear and cyclic clusters up to the size of hexamers. The ring structures exhibit cooperative hydrogen bonds opposing the repulsive Coulomb forces and leading to kinetic stability of the clusters. We discuss the importance of hydrogen bonding and dispersion forces for the stability of the differently sized clusters. We find the largest clusters when hydrogen bonding is maximized in cyclic topologies and dispersion interaction is properly taken into account. The kinetic stability of the clusters with short-chained cations is studied for the different types of cations ranging from hard to polarizable or exhibiting additional functional groups such as the acidic C(2)-H position in the imidazolium-based cation. Increasing the alkyl chain length, the cation effect diminishes and the kinetic stability is exclusively governed by the alkyl chain tether increasing the distance between the positively charged rings of the cations. With adding the counterion tetrafluoroborate (BF4) to the cationic clusters, the binding energies immediately switch from strongly positive to strongly negative. In the neutral clusters, the OH functional groups of the cations can interact either with other cations or with the anions. The hexamer cluster with the cyclic H-bond motive and “released” anions is almost as stable as the hexamer built by H-bonded ion pairs exclusively, which is in accord with recent IR spectra of similar ionic liquids detecting both types of hydrogen bonding. For the cationic and neutral clusters, we discuss geometric and spectroscopic properties as sensitive probes of opposite- and like-charge interaction. Finally, we show that NMR proton chemical shifts and deuteron quadrupole coupling constants can be related to each other, allowing to predict properties which are not easily accessible by experiment. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair
Molecules 2020, 25(21), 4942; https://doi.org/10.3390/molecules25214942 - 26 Oct 2020
Abstract
Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its stability, and to obtain clues on the mechanism of the incorporation of mercury(II) [...] Read more.
Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its stability, and to obtain clues on the mechanism of the incorporation of mercury(II) into the DNA. The dynamic distance constraint was employed to find initial structures, control the dissociation process in an unbiased fashion and to determine the free energy required. A strong influence of the exocyclic carbonyl or amino groups of neighbouring base pairs on both the bonding pattern and the mechanism of incorporation was observed. During the dissociation simulation, an amino group of an adenine moiety of the adjacent base pair acts as a turnstile to rotate the mercury(II) ion out of the DNA core region. The calculations provide an important insight into the mechanism of formation of this dinuclear metal-mediated base pair and indicate that the exact location of a transition metal ion in a metal-mediated base pair may be more ambiguous than derived from simple model building. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessArticle
Regulatory Impact of the C-Terminal Tail on Charge Transfer Pathways in Drosophila Cryptochrome
Molecules 2020, 25(20), 4810; https://doi.org/10.3390/molecules25204810 - 19 Oct 2020
Abstract
Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an [...] Read more.
Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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Open AccessFeature PaperArticle
“On-The-Fly” Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface
Molecules 2020, 25(17), 3939; https://doi.org/10.3390/molecules25173939 - 28 Aug 2020
Cited by 1
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
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