Unveiling Low THz Dynamics of Liquid Crystals: Identification of Intermolecular Interaction among Intramolecular Modes.

Liquid crystals have found a wide area of application over the last few decades, proving to be excellent materials for tunable optics from visible to near-infrared frequencies. Currently, much effort is devoted to demonstrating their applicability at THz frequencies (1-10 THz), where tremendous advances of broadband and intense sources have been achieved. Yet, a detailed understanding of THz-triggered dynamics in liquid crystals is incomplete. Here, we perform broadband THz time domain spectroscopy on 4-cyano-4'-alkyl-biphenyl (nCB) and 5-phenylcyclohexanes (PCH5) across mesophases. Density functional theory calculations on isolated molecules capture the majority of the response. In particular, the pronounced modes around 4.5 and 5.5 THz mainly originate from bending modes of the cyano group. In contrast, the broad response below 3 THz, linked to modes of the alkyl chain, disagrees with the single molecule calculation. Here, we identify a clear intermolecular character of the response, supported by dimer and trimer calculations.

Revealing the Unique Role of Water in the Formation of Benzothiazoles: an Experimental and Computational Study.

We present here a joint experimental and computational study on the formation of benzothiazoles. Our investigation reveals a green protocol for accessing benzothiazoles from acyl chlorides using either water alongside a reducing agent as the reaction medium or in combination with stoichiometric amounts of a weak acid, instead of the harsh conditions and catalysts previously reported. Specifically, we show that a protic solvent, particularly water, enables the formation of 2-substituted benzothiazoles from N-acyl 1,2-aminothiophenols already at room temperature, without the need for strong acids or metal catalysts. DFT Molecular Dynamics simulations coupled with advanced enhanced sampling techniques provide a clear understanding of the catalytic role of water. We demonstrate how bulk water - due to its extended network of hydrogen bonds and an efficient Grotthuss mechanism - provides a reaction path that strongly reduces the reaction barriers compared to aprotic environments, namely more than 80 kJ/mol for the first reaction step and 250 kJ/mol for the second. Finally, we discuss the influence of different aliphatic and aromatic substituents with varying electronic properties on chemical reactivity. Besides providing in-depth mechanistic insights, we believe that our findings pave the way for a greener route toward an important class of bioactive molecules.

Unveiling the Antifouling Potential of Stabilized Poly(phosphorus ylides).

Zwitterionic polymers have emerged as highly attractive building blocks for antifouling coatings in biomedical applications. Notably, these polymers offer effective alternatives to the widely used poly(ethylene glycol) (PEG), which has raised concerns regarding its immunotoxicity and the development of PEG-specific antibodies. Polymeric ylides, a largely overlooked class of zwitterionic polymers, have been reported as effective antifouling scaffolds. However, the reported subclasses, poly(sulfur ylides) and N-oxides, lack structural diversity and chemical variability. In this study, we present the synthesis and characterization of polymeric phosphorus ylides as an unexplored class of poly(ylides) with significantly increased structural diversity, which is of high value when designing future ylide-based antifouling materials. Our findings demonstrate that, owing to their low dipole moments and hydration layers, these polymeric phosphorus ylides significantly reduce bacterial attachment. Furthermore, we observe selective toxicity toward bacteria rather than mammalian cells. The bactericidal nature of poly(phosphorus ylides), coupled with their expanded chemical space, provides a distinct advantage over existing materials, including zwitterionic polymers from betaine scaffolds. We anticipate that these unexplored structures will broaden the scope of antifouling applications for poly(ylides).

Vibrational Circular Dichroism from DFT Molecular Dynamics: The AWV Method.

The paper illustrates the Activity Weighted Velocities (AWV) methodology to compute Vibrational Circular Dichroism (VCD) anharmonic spectra from Density Functional Theory (DFT) molecular dynamics. AWV calculates the spectra by the Fourier Transform of the time correlation functions of velocities, weighted by specific observables: the Atomic Polar Tensors (APTs) and the Atomic Axial Tensors (AATs). Indeed, AWV shows to correctly reproduce the experimental spectra for systems in the gas and liquid phases, both in the case of weakly and strongly interacting systems. The comparison with the experimental spectra is striking especially in the fingerprint region, as demonstrated by the three benchmark systems discussed: (1S)-Fenchone in the gas phase, (S)-(-)-Propylene oxide in the liquid phase, and (R)-(-)-2-butanol in the liquid phase. The time evolution of APTs and AATs can be adequately described by a linear combination of the tensors of a small set of appropriate reference structures, strongly reducing the computational cost without compromising accuracy. Additionally, AWV allows the partition of the spectral signal in its molecular components without any expensive postprocessing and any localization of the charge density or the wave function.

Chemically Accurate Vibrational Free Energies of Adsorption from Density Functional Theory Molecular Dynamics: Alkanes in Zeolites.

We present a methodology to compute, at reduced computational cost, Gibbs free energies, enthalpies, and entropies of adsorption from molecular dynamics. We calculate vibrational partition functions from vibrational energies, which we obtain from the vibrational density of states by projection on the normal modes. The use of a set of well-chosen reference structures along the trajectories accounts for the anharmonicities of the modes. For the adsorption of methane, ethane, and propane in the H-CHA zeolite, we limit our treatment to a set of vibrational modes localized at the adsorption site (zeolitic OH group) and the alkane molecule interacting with it. Only two short trajectories (1-20 ps) are required to reach convergence (<1 kJ/mol) for the thermodynamic functions. The mean absolute deviations from the experimentally measured values are 2.6, 2.8, and 4.7 kJ/mol for the Gibbs free energy, the enthalpy, and the entropy term (-TΔS), respectively. In particular, the entropy terms show a major improvement compared to the harmonic approximation and almost reach the accuracy of the previous use of anharmonic frequencies obtained with curvilinear distortions of individual modes. The thermodynamic functions so obtained follow the trend of the experimental values for methane, ethane, and propane, and the Gibbs free energy of adsorption at experimental conditions is correctly predicted to change from positive for methane (5.9 kJ/mol) to negative for ethane (-4.8 kJ/mol) and propane (-7.1 kJ/mol).

Molecular Fingerprints of Hydrophobicity at Aqueous Interfaces from Theory and Vibrational Spectroscopies.

Hydrophobicity/hydrophilicity of aqueous interfaces at the molecular level results from a subtle balance in the water-water and water-surface interactions. This is characterized here via density functional theory-molecular dynamics (DFT-MD) coupled with vibrational sum frequency generation (SFG) and THz-IR absorption spectroscopies. We show that water at the interface with a series of weakly interacting materials is organized into a two-dimensional hydrogen-bonded network (2D-HB-network), which is also found above some macroscopically hydrophilic silica and alumina surfaces. These results are rationalized through a descriptor that measures the number of "vertical" and "horizontal" hydrogen bonds formed by interfacial water, quantifying the competition between water-surface and water-water interactions. The 2D-HB-network is directly revealed by THz-IR absorption spectroscopy, while the competition of water-water and water-surface interactions is quantified from SFG markers. The combination of SFG and THz-IR spectroscopies is thus found to be a compelling tool to characterize the finest details of molecular hydrophobicity at aqueous interfaces.

Deconvolution of BIL-SFG and DL-SFG spectroscopic signals reveals order/disorder of water at the elusive aqueous silica interface.

Through the prism of the rather controversial and elusive silica/water interface, ab initio DFT-based molecular dynamics simulations of the structure and non-linear SFG spectroscopy of the interface are analysed. Following our recent work [Phys. Chem. Chem. Phys., 2018, 20, 5190-5199], we show that once the interfacial water is decomposed into BIL (Binding Interfacial Layer) and DL (Diffuse Layer) interfacial regions, the SFG signals can be deconvolved and unambiguously interpreted, and a global microscopic understanding on silica/water interfaces can be obtained. By comparing crystalline quartz/water and amorphous (fused) silica/water interfaces, the dependence of interfacial structural and spectroscopic properties on the degree of surface crystallinity is established, while by adding KCl electrolytes at the quartz/water interface, the chaotropic effect of ions on the interfacial molecular arrangement is unveiled. The evolution of structure and SFG spectra of silica/water interfaces with respect to increasing surface deprotonation, i.e., with respect to pH conditions, is also evaluated. Spectroscopic BIL-SFG markers that experimentally allow one detect the water order/disorder in the BIL as a function of surface hydroxylation and ion concentration are revealed, while the pH-induced modulations in the experimentally recorded SFG spectra are rationalized in terms of changes in both BIL and DL SFG signatures.

Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment.

The combined approach of gas phase IR-UV ion dip spectroscopy experiments and DFT-based molecular dynamics simulations for theoretical spectroscopy reveals the 3D structures of (Ac-Phe-OMe)1,2 peptides using their far-IR/THz signatures. Both experimental and simulated IR spectra are well-resolved in the 100-800 cm-1 domain, allowing an unambiguous assignment of the conformers, that could not be achieved in other more congested spectral domains. We also present and make proofs-of-principles for our newly developed theoretical method for the assignment of (anharmonic) vibrational modes from MD simulations based on graph theory coupled to APT-weighted internal coordinates velocities DOS spectra. The principles of the method are reviewed, applications to the simple gas phase water and NMA (N-methyl-acetamide) molecules are presented, and application to the more complex (Ac-Phe-OMe)1,2 peptidic systems shows that the complexity in assigning vibrational modes from MD simulations is reduced with the graphs. Our newly developed graph-based methodology is furthermore shown to allow an easy comparison between the vibrational modes of isolated monomer(s) and their complexes, as illustrated by the (Ac-Phe-OMe)1,2 peptides.

DFT-MD of the (110)-Co3O4 cobalt oxide semiconductor in contact with liquid water, preliminary chemical and physical insights into the electrochemical environment.

Within the general context of the electrochemical oxygen evolution reaction of the water oxidation/electrolysis, we focus on one essential aspect of electrochemical interfaces, i.e., the comprehension of the interaction and organisation of liquid water at the (semiconductor) (110)-Co3O4 surface using density functional theory-molecular dynamics simulations. A detailed characterization of the chemical and physical properties of the aqueous interface is provided in terms of structure, dynamics, electric field, work function, and spectroscopy, as a preliminary step into the modelling of the (110)-Co3O4 aqueous surface in more relevant electrochemical conditions. The water at the aqueous B-termination is, in particular, shown more dynamical than that at the A-termination and more "undisciplined": the water is indeed mostly an HB-acceptor with the solid, with an orientation of their dipole moments found opposite the field generated by the negative surface charge. At both aqueous interfaces, the work function is twice lower than that at the bare (non-hydroxylated) surfaces. The SFG (Sum Frequency Generation) spectroscopy is shown dominated by the water in the diffuse layer, while the SFG signal from the binding interfacial layer reflects the single orientation of water at the aqueous A-termination and the two orientations of water at the aqueous B-termination.

Molecular hydrophobicity at a macroscopically hydrophilic surface.

Interfaces between water and silicates are ubiquitous and relevant for, among others, geochemistry, atmospheric chemistry, and chromatography. The molecular-level details of water organization at silica surfaces are important for a fundamental understanding of this interface. While silica is hydrophilic, weakly hydrogen-bonded OH groups have been identified at the surface of silica, characterized by a high O-H stretch vibrational frequency. Here, through a combination of experimental and theoretical surface-selective vibrational spectroscopy, we demonstrate that these OH groups originate from very weakly hydrogen-bonded water molecules at the nominally hydrophilic silica interface. The properties of these OH groups are very similar to those typically observed at hydrophobic surfaces. Molecular dynamics simulations illustrate that these weakly hydrogen-bonded water OH groups are pointing with their hydrogen atom toward local hydrophobic sites consisting of oxygen bridges of the silica. An increased density of these molecular hydrophobic sites, evident from an increase in weakly hydrogen-bonded water OH groups, correlates with an increased macroscopic contact angle.

Influence of argon and D2 tagging on the hydrogen bond network in Cs+(H2O)3; kinetic trapping below 40 K.

The influence of enthalpic and entropic effects as well as of kinetic trapping processes on the structure of Ar/D2-tagged Cs+(H2O)3 clusters is studied by temperature-dependent infrared photodissociation spectroscopy combined with harmonic vibrational spectra calculations and anharmonic free energy profiles from finite temperature metadynamics molecular dynamics simulations. Each tag favors a different hydrogen bond network of water molecules, with Ar-tagging (vs. D2-tagging) of Cs+(H2O)3 leading to the lower energy conformation. The relative population of these conformers can be tuned over a temperature range of 12 to 21 K. The formation mechanisms of these tagged clusters can be deduced from the free energy profiles. This investigation demonstrates that a variety of factors, both thermodynamic and kinetic, play a role in the structure of flexible molecular species, even at cryogenic temperatures.

Structural definition of the BIL and DL: a new universal methodology to rationalize non-linear χ(2)(ω) SFG signals at charged interfaces, including χ(3)(ω) contributions.

This work provides unambiguous definitions from theoretical simulations of the two interfacial regions named the BIL (binding interfacial layer) and DL (diffuse layer) at charged solid/water and air/water interfaces. The BIL and DL nomenclature follows the pioneering work of Wen et al. [Phys. Rev. Lett. 2016, 116, 016101]. Our definitions are based on the intrinsic structural properties of water only. Knowing the BIL and DL interfacial regions, one is then able to deconvolve the χ(2)(ω) non-linear SFG (sum frequency generation) response into χ(ω) and χ(ω) contributions, thus providing a detailed molecular interpretation of these signals and of the measured total SFG. We furthermore show that the χ(ω) spectrum arises from the χ(3)(ω) non-linear third order contribution of bulk liquid water, here calculated for several charged interfaces and shown to be universal. The χ(ω) contribution therefore has the same origin in terms of molecular normal modes at any charged interface. The molecular interpretation of χ(ω) is hence at the heart of the unambiguous molecular comprehension and interpretation of the measured total SFG signal at any charged interface.

Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and Clusters.

Four models for the calculation of the IR spectrum of gas phase molecules and clusters from molecular dynamics simulations are presented with the aim to reduce the computational cost of the usual Fourier transform (FT) of the time correlation function of the dipole moment. These models are based on the VDOS, FT of time correlation function of velocities, and atomic polar tensors (APT). The models differ from each other by the number of APTs inserted into the velocities correlation function. Excellent accuracy is achieved by the model adopting a weighted linear combination of a few selected APTs adapted for the rotation of the molecule (model D). The achieved accuracy relates to band positions, band shapes, and band intensities. Depending on the degree of actual dynamics of the molecule, rotational motion, conformational isomerization, and large amplitude motions that can be seen during the finite temperature trajectory, one could also apply one of the other models (models A, B, or C), but with caution. Model D is therefore found simple and accurate, with appealing computational cost and should be systematically applied. Its generalization to condensed phase systems should be straightforward.

2D H-Bond Network as the Topmost Skin to the Air-Water Interface.

We provide a detailed description of the structure of water at the interface with the air (liquid-vapor LV interface) from state-of-the-art DFT-based molecular dynamics simulations. For the first time, a two-dimensional (2D) H-bond extended network has been identified and fully characterized, demonstrating that interfacial water is organized into a 2D sheet with H-bonds oriented parallel to the instantaneous surface and following its spatial and temporal oscillations. By analyzing the nonlinear vSFG (vibrational sum frequency generation) spectrum of the LV interface in terms of layer-by-layer signal, we demonstrate that the 2D water sheet is solely responsible for the spectral signatures, hence providing the interfacial 3.5 Å thickness effectively probed in nonlinear interfacial spectroscopy. The 2D H-bond network unraveled here is the essential key to rationalize macroscopic properties of water-air interfaces, as demonstrated here for spectroscopy and the surface potential.

Static vs dynamic DFT prediction of IR spectra of flexible molecules in the condensed phase: The (ClCF2CF(CF3)OCF2CH3) liquid as a test case.

First-principles molecular dynamics (FPMD) simulations in the framework of Density Functional Theory (DFT) are carried out for the prediction of the infrared spectrum of the fluorinated molecule ClCF2CF(CF3)OCF2CH3 in liquid and gas phase. This molecule is characterized by a flexible structure, allowing the co-existence of several stable conformers, that differ by values of the torsional angles. FPMD computed spectra are compared to the experimental ones, and to Boltzmann weighted IR spectra based on gas phase calculations.

Intermolecular modulation of IR intensities in the solid state. The role of weak interactions in polyethylene crystal: A computational DFT study.

Density functional theory calculations with periodic boundary conditions are exploited to study the infrared spectrum of crystalline polyethylene. Spectral changes lead by the intermolecular packing in the orthorhombic three-dimensional crystal are discussed by means of a careful comparison with calculations carried out for an isolated polymer chain in the all-trans conformation, described as an ideal one-dimensional crystal. The results are analyzed in the framework of the "oligomer approach" through the modelling of the IR spectrum of n-alkanes of different lengths. The study demonstrates that a relevant absorption intensity modulation of CH2 deformation transitions takes place in the solid state. This finding suggests a new interpretation for the experimental evidences collected in the past by means of IR intensity measurement during thermal treatment. Moreover, the comparison between calculations for 3-D crystal and for the isolated polyethylene chain (1-D crystal) allows to put in evidence the effect of the local electric field on the computed infrared intensities. This observation provides guidelines for the comparison between infrared absorption intensities predicted for an isolated unit and for a molecule belonging to a crystal, through the introduction of suitable correction factors based on the refraction index of the material and depending on the dimensionality of such units (0D-molecule; 1D-polymer; 2D-slab).

Crystal structure and vibrational spectra of poly(trimethylene terephthalate) from periodic density functional theory calculations.

The crystal structure and the IR spectrum of crystalline poly(trimethylene terephthalate), PTT, have been investigated by means of periodic density functional theory calculations including Grimme's correction for dispersion interactions. Both structural and spectroscopic results have been critically compared to the experimental data taken from the literature, showing very good agreement between theory and the experiments. The previous spectral assignments, based only on experimental investigations, have been revised, and further insights have been obtained. Furthermore, spectroscopic markers of crystallinity or regularity (i.e., of the regular conformation of the polymer chain) have been proposed. In addition to the analysis of the IR spectra, the effect of computational parameters on the crystal structure determination (basis sets and parameters for Grimme's correction) have been analyzed. This work demonstrates that state-of-the-art computational methods can provide an unambiguous description of the structural and vibrational properties of crystalline polymers on the basis of the peculiar intra- and intermolecular interactions occurring in different macromolecular materials.

Infrared intensities and charge mobility in hydrogen bonded complexes.

The analytical model for the study of charge mobility in the molecules presented by Galimberti et al. [J. Chem. Phys. 138, 164115 (2013)] is applied to hydrogen bonded planar dimers. Atomic charges and charge fluxes are obtained from density functional theory computed atomic polar tensors and related first derivatives, thus providing an interpretation of the IR intensity enhancement of the X-H stretching band observed upon aggregation. Our results show that both principal and non-principal charge fluxes have an important role for the rationalization of the spectral behavior; moreover, they demonstrate that the modulation of the charge distribution during vibrational motions of the -XH⋯Y- fragment is not localized exclusively on the atoms directly involved in hydrogen bonding. With these premises we made some correlations between IR intensities, interaction energies, and charge fluxes. The model was tested on small dimers and subsequently to the bigger one cytosine-guanine. Thus, the model can be applied to complex systems.

Charge mobility in molecules: charge fluxes from second derivatives of the molecular dipole.

On the basis of the analytical model previously suggested by Dinur, we discuss here a method for the calculation of vibrational charge fluxes in planar molecules, obtained as numerical second derivatives of the molecular dipole moment. This model is consistent with the partitioning of the atomic polar tensors into atomic charge and charge fluxes according to the Equilibrium Charges-Charge Fluxes model and it is directly related to experimentally measurable quantities such as IR intensities. On the basis of density functional theory calculations carried out for several small benchmark molecules, the complete set of charge fluxes is calculated for each molecule and compared with the approximated flux parameters previously derived and reported in the past literature. The degree of localization of charge fluxes is investigated and discussed; in addition, some approximations are analyzed in order to verify the applicability of the method to large and∕or non-planar molecules, aimed at obtaining a description of the electron charge mobility in different molecular environments.