Intermolecular Separation Research Articles

Collective Mid-Infrared Vibrations in Surface-Enhanced Raman Scattering.

Surface-enhanced Raman scattering (SERS) is typically assumed to occur at individual molecules neglecting intermolecular vibrational coupling. Here, we show instead how collective vibrations from infrared (IR) coupled dipoles are seen in SERS from molecular monolayers. Mixing IR-active molecules with IR-inactive spacer molecules controls the intermolecular separation. Intermolecular coupling leads to vibrational frequency upshifts up to 8 cm–1, tuning with the mixing fraction and IR dipole strength, in excellent agreement with microscopic models and density functional theory. These cooperative frequency shifts can be used as a ruler to measure intermolecular distance and disorder with angstrom resolution. We demonstrate this for photochemical reactions of 4-nitrothiophenol, which depletes the number of neighboring IR-active molecules and breaks the collective vibration, enabling direct tracking of the reaction. Collective molecular vibrations reshape SERS spectra and need to be considered in the analysis of vibrational spectra throughout analytical chemistry and sensing.

20 K H2 Physisorption on Metal–Organic Frameworks with Enhanced Dormancy Compared to Liquid Hydrogen Storage

Liquid hydrogen (LH2) is the best way of transporting hydrogen, as its high volumetric energy density translates into a significant reduction in hydrogen transportation and refueling operations expenses. However, the phase transformation from liquid to gaseous hydrogen, due to heat leakage of the LH2 vessel, causes a considerable volume change, results in boil-off losses, and makes long-term storage/transportation problematic. These boil-off losses are a severe drawback for continental transportation through truck tube trailers having evaporative losses of about 3–15% per day (depending on the volume). Herein, hydrogen storage by cryo-adsorption using metal–organic frameworks (MOFs) is proposed as an alternative to reduce boil-off losses and enhance dormancy during continental transportation. The stronger van der Waals interaction operating between adsorbate and adsorbent leads to superdense H2 adsorption, which compensates for the space occupied by the adsorbent skeleton and results in a volumetric storage capacity comparable to that of LH2 tanks (∼96%). Depending on the textural properties of MOFs, H2 desorption can start from 45 K, resulting in an extended dormancy time of the tank system. In addition, the observation of hindered rotational transition (J: 0 → 1) signal in neutron scattering analysis indicates that H2 are firmly attached and highly immobile on the adsorption sites. The hindered rotation by adsorption at 20 K on MOFs also suggests that the intermolecular separation is less than the bulk liquid (even solid) phase.

Unique O═N...O Pnicogen Interactions in Nitromethane Dimers: Evidence Using Matrix Isolation Infrared Spectroscopy and Computational Methodology.

Geometries of nitromethane homodimers have been revisited using ab initio and density functional methodologies, following their formation within cryogenic matrices, confirmed using infrared spectroscopy. In contrast to the claim that the intermolecular interactions are due to dispersion forces or very weak hydrogen bonds, in the present work, concrete evidence for the prevalence of O═N...O pnicogen bonding has been presented. The pnicogen bonds have been found to be primarily responsible for the characteristic geometry of a homodimer. The formation of a nitromethane dimer with pnicogen bonding stabilization is evidenced using matrix isolation infrared spectroscopy with Ne and Ar matrices and computations. The interactions within homodimers have been characterized using quantum theory of atoms in molecules, natural bond orbital, energy decomposition, electrostatic potential mapping, and noncovalent interaction analyses. The larger intermolecular separations in liquid nitromethane indicated by previous molecular dynamics-based studies alongside the supposed invariance of infrared spectra in the gas phase and liquid phase could have led to the assumption of a lack of intermolecular interactions. However, the prevalence of hydrogen and pnicogen bonds across these larger than usual separations is affirmed by the geometries presented here.

Structure of a pathologic amyloid nucleus determined by rational genetic deconstruction of an intracellular nucleation barrier

A long‐standing goal of the study of amyloids has been to characterize the structural basis of the rate‐determining nucleating event. However, the ephemeral nature of that event has made it inaccessible to classical biochemistry, structural biology, and computational approaches. Here, we addressed that limitation by using Distributed Amphifluoric FRET to measure the dependence of amyloid formation on concentration and conformational templates in living cells, whose volumes are sufficiently small to resolve the outcomes of independent nucleation events. We characterized numerous rationally designed sequence variants of polyglutamine (polyQ), a polypeptide that precipitates Huntington’s and other amyloid‐associated neurodegenerative diseases when its length exceeds a characteristic threshold. This effort uncovered a pattern of approximately twelve Qs, only for polypeptides exceeding the clinical length threshold, that allow for amyloid nucleation to occur spontaneously within single polypeptides. Nucleation was inhibited by intermolecular phase separation. Using atomistic molecular dynamics simulations, we found that the pattern encodes a minimal steric zipper of interdigitated side chains. Lateral growth of the steric zipper competed with axial growth to produce “pre‐amyloid” oligomers. By illuminating the structural mechanism of polyQ amyloid formation in cells, our findings reveal a potential molecular etiology for polyQ diseases, and may provide a roadmap for the design of new therapies.

Contribution of the Induced-Dipole Interaction to Methane Aggregation in Water.

Apolar molecules in the gas phase have no dipole moments. However, when placed in an aqueous environment, they acquire a dipole moment induced by the electric fields of the surrounding water molecules. Could these induced dipole moments, not present in the gas phase but present in solution, play an important role in the hydrophobic interaction between two apolar molecules? In particular, for two methane molecules, our results show that the interaction between the induced-dipole moments only very weakly plays a role in the aggregation of a pair of methane molecules in water. The induced-dipole-induced-dipole interaction has a magnitude as large as 1 kcal/mol for certain mutual orientations of the induced dipole moments, which is larger than the magnitude of the free energy of aggregation of the methane solutes in water. However, when averaged over all physically occurring conformations for a fixed intersolute separation, this interaction averages to an insignificant value (magnitude less than 0.01 kcal/mol) except, possibly, for some very short intermolecular separation.

Appraisal of dispersion damping functions for the effective fragment potential method

The effective fragment potential (EFP) is a polarizable force field whose physically-motivated functional form is parameterized in an automated way from ab initio calculations, and whose dispersion potential has been suggested as a correction for Hartree-Fock or density functional theory calculations. However, the parameter-free dispersion damping potentials that are currently used in EFP do not follow from a rigorous derivation and do not satisfy simple limits for the dispersion energy. We introduce several new damping expressions that correct these deficiencies, then evaluate their performance alongside existing damping functions using a new database of ionic liquid constituents. This data set, which we call IL195×8, consists of complete-basis coupled-cluster interaction energies for 195 ion pairs at each of 8 different intermolecular separations. Ultimately, we recommend a new parameter-free dispersion damping function as a replacement for the one that is currently used in EFP.

Diffusion, viscosity, and Stokes-Einstein relation in dense supercritical methane

The new results on the diffusion in dense supercritical methane reported by Ranieri et al. [Nature Communications 12, 1958 (2021)] are examined from the freezing density scaling perspective. It is demonstrated that the high pressure behaviour of the self-diffusion coefficient is consistent with the freezing density scaling of dense Lennard-Jones and hard sphere fluids. It is also observed that the Stokes–Einstein relation of the form Dη(Δ/kBT)=αSE holds in a wide pressure and density regime, where it is expected to hold (here D and η are the diffusion and shear viscosity coefficients, Δ is the intermolecular separation and kBT is the temperature). Unexpected violation occurs at highest densities in the vicinity of the freezing point, where the coefficient αSE reaches values ≃10% higher than the upper theoretically expected limit.

Inclusion of More Physics Leads to Less Data: Learning the Interaction Energy as a Function of Electron Deformation Density with Limited Training Data.

Machine learning (ML) approaches to predicting quantum mechanical (QM) properties have made great strides toward achieving the computational chemist's holy grail of structure-based property prediction. In contrast to direct ML methods, which encode a molecule with only structural information, in this work, we show that QM descriptors improve ML predictions of dimer interaction energy, both in terms of accuracy and data efficiency, by incorporating electronic information into the descriptor. We present the electron deformation density interaction energy machine learning (EDDIE-ML) model, which predicts the interaction energy as a function of Hartree-Fock electron deformation density. We compare its performance with leading direct ML schemes and modern DFT methods for the prediction of interaction energies for dimers of varying charge type, size, and intermolecular separation. Under a low-data regime, EDDIE-ML outperforms other direct ML schemes and is the only model readily transferrable to larger, more complex systems including base pair trimers and porous cages. The underlying physical connection between the density and interaction energy enables EDDIE-ML to reach an accuracy comparable to modern DFT functionals in fewer training data points compared to other ML methods.

Three-body potential energy surface for para-hydrogen.

We present a 3D isotropic ab initio three-body (para-H2)3 interaction potential energy surface (PES). The electronic structure calculations are carried out at the correlated coupled-cluster theory level, with single, double, and perturbative triple excitations. The calculations use an augmented correlation-consistent triple zeta basis set and a supplementary midbond function. We construct the PES using the reproducing-kernel Hilbert space toolkit [O. T. Unke and M. Meuwly, J. Chem. Inf. Model. 57, 1923 (2017)] with phenomenological and empirical adjustments to account for short-range and long-range behaviors. The (para-H2)3 interaction energies deviate drastically from the Axilrod-Teller-Muto (ATM) potential at short intermolecular separations. We find that the configuration of three para-H2 molecules at the corners of an equilateral triangle is responsible for the majority of the (para-H2)3 interaction energy contribution in a hexagonal-close-packed lattice. In cases where two para-H2 molecules are close to one another while the third is far away, the (para-H2)3 interaction PES takes the form of a modified version of the ATM potential. We expect the combination of this PES together with a first-principles para-H2-para-H2 adiabatic hindered rotor potential to outperform a widely used effective pair potential for condensed many-body systems of para-H2.

The interaction of methylene with molecular hydrogen: potential energy surface and inelastic collisions

ABSTRACT The potential energy surface describing the interaction of methylene (CH) in its ground electronic state with molecular hydrogen has been calculated through explicitly correlated coupled cluster theory with inclusion of single, double, and (perturbatively) triple excitations [RCCSD(T)-F12a] and a correlation-consistent aug-cc-pVTZ basis. The calculated points for various geometries of the CH–H complex were fit to a functional form suitable for use in time-independent quantum scattering calculations of cross sections for collision-induced transitions between CH rotational levels. The well depth of the CH–H complex was found to equal 92.1 cm in a planar geometry and intermolecular separation . A representative set of cross sections is presented and compared with cross sections for the corresponding transitions in methylene induced by collisions with helium.

A path integral ground state approach for asymmetric top rotors with nuclear spin symmetry: Application to water chains

A path integral ground state (PIGS) approach for the simulation of asymmetric top rotors is presented. The method is based on Monte Carlo sampling of angular degrees of freedom. A symmetry-adapted rotational density matrix is used to account for nuclear spin statistics. To illustrate the method, ground-state properties of collections of para-water molecules confined to a one-dimensional lattice are computed. Those include energetic and structural observables. An advantage of the PIGS method is that expectation values can be obtained directly since the square of the wavefunction is sampled during a simulation. To benchmark the method, ground state energies and orientational distributions are computed using exact diagonalization for a single para-water molecule in an external field using a finite basis of symmetric top eigenfunctions. Benchmark results are also provided for N = 2 para-water molecules pinned to lattice sites at various distances to sample the crossover from hydrogen bonding to the dipole-dipole interaction regime. Excellent agreement between the PIGS results and the finite basis set calculations is observed. A thorough analysis of the convergence in terms of the imaginary time propagation length and systematic Trotter error is performed. The PIGS approach is then applied to a chain of N = 11 water molecules, and an equation of state is constructed in terms of the intermolecular separation. Ordering effects are also studied, and a transition between hydrogen bonding to dipole-dipole alignment is observed. The method is scalable and can also be applied in higher dimensions.

Breather Molecular Complexes in a Passively Mode‐Locked Fiber Laser

AbstractBreathing solitons are nonlinear waves in which the energy concentrates in a localized and oscillatory fashion. Similarly to stationary solitons, breathers in dissipative systems can form stable bound states displaying molecule‐like dynamics, which are frequently called breather molecules. So far, the experimental observation of optical breather molecules and the real‐time detection of their dynamics are limited to diatomic molecules, that is, bound states of only two breathers. In this work, the observation of different types of breather complexes in a mode‐locked fiber laser: multibreather molecules, and molecular complexes originating from the binding of two breather‐pair molecules or a breather pair molecule and a single breather is reported. The intermolecular temporal separation of the molecular complexes attains several hundreds of picoseconds, which is more than an order of magnitude larger than that of their stationary soliton counterparts and is a signature of long‐range interactions. Numerical simulations of the laser model support the experimental findings. Moreover, nonequilibrium dynamics of breathing solitons are also observed, including breather collisions and annihilation. This work opens the possibility of studying the dynamics of many‐body systems in which breathers are the elementary constituents.

Oscillatory self-organization dynamics between soliton molecules induced by gain fluctuation.

In passively mode-locked fiber lasers (PMLFLs), the dissipative solitons (DSs) can self-organize to form complex structures through delicate interactions. However, it is still elusive to control these soliton structures by external influences. We here find that at a certain critical power, the location between two soliton molecules can be controlled by a slow modulated pump power. After applying the pump power with periodic fluctuation, two soliton molecules oscillate from the state of soliton molecular complex to stable distribution with maximum inter-molecular separation. During this process, the internal structure of each soliton molecule keeps steady. The slow gain depletion and recovery mechanism which plays a dominant role affects the motion of soliton molecules. These results could further expand the molecular analogy of spectroscopy and stimulate the development of optical information storage and processing.

Visualizing Interfacial Jamming Using an Aggregation‐Induced‐Emission Molecular Reporter

AbstractWith the interfacial jamming of nanoparticles (NPs), a load‐bearing network of NPs forms as the areal density of NPs increases, converting the assembly from a liquid‐like into a solid‐like assembly. Unlike vitrification, the lineal packing of the NPs in the network is denser, while the remaining NPs can remain in a liquid‐like state. It is a challenge to determine the point at which the assemblies jam, since both jamming and vitrification lead to a solid‐like behavior of the assemblies. Herein, we show a real‐time fluorescence imaging method to probe the evolution of the interfacial dynamics of NP surfactants at the water/oil interface using aggregation‐induced emission (AIE) as a reporter for the transition of the assemblies into the jammed state. The AIEgens show typical fluorescence behavior at densities at which they can move and rotate. However, when aggregation of these fluorophores occurs, the smaller intermolecular separation distance arrests rotation, and a significant enhancement in the fluorescence intensity occurs.

Visualizing Interfacial Jamming Using an Aggregation-Induced-Emission Molecular Reporter.

With the interfacial jamming of nanoparticles (NPs), a load-bearing network of NPs forms as the areal density of NPs increases, converting the assembly from a liquid-like into a solid-like assembly. Unlike vitrification, the lineal packing of the NPs in the network is denser, while the remaining NPs can remain in a liquid-like state. It is a challenge to determine the point at which the assemblies jam, since both jamming and vitrification lead to a solid-like behavior of the assemblies. Herein, we show a real-time fluorescence imaging method to probe the evolution of the interfacial dynamics of NP surfactants at the water/oil interface using aggregation-induced emission (AIE) as a reporter for the transition of the assemblies into the jammed state. The AIEgens show typical fluorescence behavior at densities at which they can move and rotate. However, when aggregation of these fluorophores occurs, the smaller intermolecular separation distance arrests rotation, and a significant enhancement in the fluorescence intensity occurs.

Collisional excitation of interstellar PN by H2: New interaction potential and scattering calculations.

Rotational excitation of interstellar PN molecules induced by collisions with H2 is investigated. We present the first ab initio four-dimensional potential energy surface (PES) for the PN-H2 van der Waals system. The PES was obtained using an explicitly correlated coupled cluster approach with single, double, and perturbative triple excitations [CCSD(T)-F12b]. The method of interpolating moving least squares was used to construct an analytical PES from these data. The equilibrium structure of the complex was found to be linear, with H2 aligned at the N end of the PN molecule, at an intermolecular separation of 4.2 Å. The corresponding well-depth is 224.3 cm-1. The dissociation energies were found to be 40.19 cm-1 and 75.05 cm-1 for complexes of PN with ortho-H2 and para-H2, respectively. Integral cross sections for rotational excitation in PN-H2 collisions were calculated using the new PES and were found to be strongly dependent on the rotational level of the H2 molecule. These new collisional data will be crucial to improve the estimation of PN abundance in the interstellar medium from observational spectra.

Long-range light-modulated charge transport across the molecular heterostructure doped protein biopolymers.

Biological electron transfer (ET) across proteins is ubiquitous, such as the notable photosynthesis example, where light-induced charge separation takes place within the reaction center, followed by sequential ET via intramolecular cofactors within the protein. Far from biology, carbon dots (C-Dots) with their unique optoelectronic properties can be considered as game-changers for next-generation advanced technologies. Here, we use C-Dots for making heterostructure (HS) configurations by conjugating them to a natural ET mediator, the hemin molecule, thus making an electron donor–acceptor system. We show by transient absorption and emission spectroscopy that the rapid intramolecular charge separation happens following light excitation, which can be ascribed to an ultrafast electron and hole transfer (HT) from the C-Dot donor to the hemin acceptor. Upon integrating the HS into a protein matrix, we show that this HT within the HS configuration is 3.3 times faster compared to the same process in solution, indicating the active role of the protein in supporting the rapid light-induced long-range intermolecular charge separation. We further use impedance, electrochemical, and transient photocurrent measurements to show that the light-induced transient charge separation results in an enhanced ET and HT efficiency across the protein biopolymer. The charge conduction across our protein biopolymers, reaching nearly 0.01 S cm−1, along with the simplicity and low-cost of their formation promotes their use in a variety of optoelectronic devices, such as artificial photosynthesis, photo-responsive protonic–electronic transistors, and photodetectors.

Nonrotational Mechanism of Polarization in Alcohols.

Chemical polarity governs various mechanical, chemical, and thermodynamic properties of dielectrics. Polar liquids have been amply studied, yet the basic mechanisms underpinning their dielectric properties remain not fully understood, as standard models following Debye's phenomenological approach do not account for quantum effects and cannot aptly reproduce the full dc-up-to-THz spectral range. Here, using the illustrative case of monohydric alcohols, we show that deep tunneling and the consequent intermolecular separation of excess protons and "proton-holes" in the polar liquids govern their static and dynamic dielectric properties on the same footing. We performed systematic ultrabroadband (0-10 THz) spectroscopy experiments with monohydric alcohols of different (0.4-1.6 nm) molecular lengths and show that the finite lifetime of molecular species and the proton-hole correlation length are the two principle parameters responsible for the dielectric response of all the studied alcohols across the entire frequency range. Our results demonstrate that a quantum nonrotational intermolecular mechanism drives the polarization in alcohols while the rotational mechanism of molecular polarization plays a secondary role, manifesting itself in the sub-terahertz region only.

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170-175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536; Nguyen & Volkov (2019). Acta Cryst. A75, 448-464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283-4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10-5 kJ mol-1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28-64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

Studying the change in organic light-emitting diode performance at various vacuum-deposition rates of hole and electron transport layers

The electroluminescence (EL) of classic and thermally activated delayed fluorescence (TADF) organic light-emitting diodes (OLEDs) at various vacuum-deposition rates of hole and electron transport layer (HTL and ETL) has been studied. The external quantum efficiency (EQE) measurements showed that the best performance devices were those with a high charge carrier balance inside the emitting layer, which was engineered using hole and electron current manipulation as a result of vacuum-deposition rate control. Changing the vacuum-deposition rate of HTL and ETL leads to a change in the maximum EQE ( $$ {\text{EQE}}_{ {\mathrm{max}} } $$ ) of the classic and TADF OLEDs without obvious changes in EQE roll-off ratio at high current density. We used a simple analytical model to clarify that the enhanced hole current in HTL at high deposition rates is dominated by high hole mobility attributed to the increased hole hopping rate due to the reduction of the intermolecular separation between horizontally oriented N,N′-diphenyl-N,N′-bis(1-naphthyl)-1,1′-biphenyl-4,4′-diamine (α-NPD) molecules. The increase in the electron current of tris-(8-hydroxyquinoline) aluminium (Alq3) ETL at low deposition rate was ascribed to high electron injection from cathode into ETL by the fabrication and comparison of J–V characteristic of two electron-only devices with a difference at deposition rate of ETL near cathode interface. Finally, we introduced an OLED with novel gradient and barrier structures for the emitting layer in which high injected charge carriers recombined inside added recombination zone to raise radiative recombination and efficiency of the device. Our results demonstrated that EL efficiency of an OLED can be changed by controlling the vacuum-deposition rate of organic layers.