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At least 55 records · Page 3

Atomistic insight into the effects of electrostatic fields on hydrocarbon reaction kinetics

Reactive Molecular Dynamics (MD) and Density Functional Theory (DFT) computations are performed to provide insight into the effects of external electrostatic fields on hydrocarbon reaction kinetics. By comparing the results from MD and DFT, the suitability of the MD method in modeling electrodynamics is first assessed. Results show that the electric field-induced polarization predicted by the MD charge equilibration method is in good agreement with various DFT charge partitioning schemes. Then, the effects of oriented external electric fields on the transition pathways of non-redox reactions are investigated. Results on the minimum energy path suggest that electric fields can cause catalysis or inhibition of oxidation reactions, whereas pyrolysis reactions are not affected due to the weaker electronegativity of the hydrogen and carbon atoms. MD simulations of isolated reactions show that the reaction kinetics is also affected by applied external Lorentz forces and interatomic Coulomb forces since they can increase or decrease the energy of collision depending on the molecular conformation. In addition, electric fields can affect the kinetics of polar species and force them to align in the direction of field lines. These effects are attributed to energy transfer via intermolecular collisions and stabilization under the external Lorentz force. The kinetics of apolar species is not significantly affected mainly due to the weak induced dipole moment even under strong electric fields. The dynamics and reaction rates of species are studied by means of large-scale combustion simulations of n-dodecane and oxygen mixtures. Results show that under strong electric fields, the fuel, oxidizer, and most product molecules experience translational and rotational acceleration mainly due to close charge transfer along with a reduction in their vibrational energy due to stabilization. This study will serve as a basis to improve the current methods used in MD and to develop novel methodologies for the modeling of macroscale reacting flows under external electrostatic fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of intermolecular interactions on the infrared complex indices of refraction for binary liquid mixtures

This paper investigates the accuracy of deriving the composite optical constants of binary mixtures from only the complex indices of refraction of the neat materials. These optical constants enable the reflectance spectra of the binary mixtures to be modeled for multiple scenarios (e.g., different substrates, thicknesses, volume ratios), which is important for contact and standoff chemical detection. Using volume fractions, each mixture's complex index of refraction was approximated via three different mixing rules. To explore the impact of intermolecular interactions, these predictions are tested by experimental measurements for two representative sets of binary mixtures: (1) tributyl phosphate combined with n-dodecane, a non-polar medium, to represent mixtures which primarily interact via dispersion forces and (2) tributyl phosphate and 1-butanol to represent mixtures with polar functional groups that can also interact via dipole–dipole interactions, including hydrogen bonding. The residuals and the root-mean-square error between the experimental and calculated index values are computed and demonstrate that for miscible liquids in which the average geometry of the cross-interactions can be considered isotropic (e.g., dispersion), the refractive indices of the mixtures can be modeled using composite n and k values derived from volume fractions of the neat liquids. Conversely, in spectral regions where the geometry of the cross-interactions is more restricted and anisotropic (e.g., hydrogen bonding), the calculated n and k values vary from the measured values. The impact of these interactions on the reflectance spectra are then compared by modeling a thin film of the binary mixtures on an aluminum substrate using both the measured and the mathematically computed indices of refraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond

Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts

In this work, we present NENCI-2021, a benchmark database of ~8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation–π and anion–π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion–π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E int ) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent—these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)- based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation–π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E int values, and maximum errors of ±0.2–0.3 kcal/mol (i.e., ~±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Third-body stabilization of supercritical CO 2 in CO oxidation: development and application of a ReaxFF force field for the CO/O/CO 2 system

Supercritical CO 2 (scCO 2 ) plays a crucial role as a solvent in separation processes, advanced power cycles, and materials processing. Nonetheless, the atomistic comprehension of how the dense scCO 2 matrix influences the fundamental reaction of carbon monoxide (CO) is still insufficiently explored. Experimental studies and molecular dynamics (MD) simulations frequently fail to detect the highly reactive, transient intermediates, such as atomic oxygen (O), that drive these reactions. Here, to address this issue, we have developed a novel ReaxFF reactive force field for the CO 2 /CO/O system. The force field parameters were calibrated using density functional theory and second-order Møller-Plesset calculations to model CO 2 crystal properties, intermolecular interactions, bond dissociation curves, and reaction energy barriers. The force field reproduces the cohesive energy of the CO 2 crystal, the pressure characteristics of bulk scCO 2 , the equation-of-state behavior over a wide pressure–density range, the pressure dependence of the C–O bond length under compression, and the structural properties of liquid and scCO 2 , as documented by experiments, ab-initio MD, and prominent non-reactive models. The force field was subsequently applied to study the CO + O → CO 2 reaction. In a dilute environment, the reaction is inefficient as the newly formed CO 2 rapidly dissociates due to excess kinetic and potential energy acquired from the exothermic reaction. Conversely, in a dense scCO 2 environment, the surrounding matrix acts as an efficient third body, stabilizing the emerging CO2 product via molecular collisions. Statistical analysis confirms an average excess energy dissipation of 133.9 ± 3.6 kcal/mol over 112.4 ± 17.9 ps. Kinetic energy decomposition reveals that ∼ 92% of the excess kinetic energy is stored in internal (rotational and vibrational) degrees of freedom. This ReaxFF force field establishes a mechanistic foundation for third-body stabilization in dense reactive environments.

Chowdhury, Emdadul Haque [Pennsylvania State Univ.↗

Tautomerism induces bending and twisting of biogenic crystals

Understanding and exploiting material flexibility through phenomena such as the bending and twisting of molecular crystals has been a subject of increased interest owing to the number of applications that benefit from these properties, such as optoelectronics, mechanophotonics, soft robotics, and smart sensors. Here, we report the growth of spontaneously bent and twisted ammonium urate crystals induced by the keto–enol tautomerism of the urate molecule. The major tautomer is native to biogenic crystals, whereas the minor tautomer functions as an effective crystal growth modifier to induce naturally bent and twisted ammonium urate crystals. We show that the degree of curvature can be tailored based on the judicious selection of growth conditions. A combination of state-of-the-art microscopy and spectroscopy techniques are used to characterize the origin of bending. Spatially resolved nano-electron diffraction and high-resolution electron microscopy of naturally bent crystals show nearly single crystallinity with local lattice deformations generated by a combination of screw and edge dislocations. These observations are consistent with photoinduced force microscopy and contact resonance atomic force microscopy, which confirmed spatially resolved changes in the intermolecular interactions and the mechanical properties throughout the cross-sectional and axial regions of bent crystals. A mechanism of bending involving the generation of regionally specific dislocations is proposed as an alternative to more commonly reported models. These findings highlight a unique characteristic of tautomeric crystals that may have broader implications for other biogenic materials.

Science & Technology - Other Topics↗

How Accurate Are Simulations and Experiments for the Lattice Energies of Molecular Crystals?

Molecular crystals play a central role in a wide range of scientific fields, including pharmaceuticals and organic semiconductor devices. However, they are challenging systems to model accurately with computational approaches because of a delicate interplay of intermolecular interactions such as hydrogen bonding and Van der Waals dispersion forces. Here, by exploiting recent algorithmic developments, we report the first set of diffusion Monte Carlo lattice energies for all 23 molecular crystals in the popular and widely used X23 dataset. Comparisons with previous state-of-the-art lattice energy predictions (on a subset of the dataset) and a careful analysis of experimental sublimation enthalpies reveals that high-accuracy computational methods are now at least as reliable as (computationally derived) experiments for the lattice energies of molecular crystals. Overall, this work demonstrates the feasibility of high-level explicitly correlated electronic structure methods for broad benchmarking studies in complex condensed phase systems, and signposts a route towards closer agreement between experiment and simulation. Published by the American Physical Society 2024

Physics↗

The j and k dependencies of the line coupling and line mixing effects: Theoretical studies of the relaxation matrices of N 2 -broadened CH 3 D

Line coupling and line mixing effects in parallel and perpendicular bands of CH 3 D perturbed by N 2 have been studied. The work focuses on exhibiting the j and k dependencies of these two processes. The calculations were based on a previously reported anisotropic intermolecular potential including both the long-range multipole, induction, and dispersion forces and a short-range atom-atom model. Throughout this work, it is shown that components with L 1 = 3 of the atom-atom model are dominant contributions to the diffusion operator. As a consequence, in comparison with other molecular systems such as the CH 3 Cl-N 2 and CH 3 I-N 2 , theoretically predicted line coupling and line mixing effects exhibit completely new j and k dependencies. In general, the theoretically calculated halfwidths and intra-doublets’ off-diagonal elements of the relaxation matrix are in reasonable agreement with measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Observation of Twin van der Waals Molecular Chains

The van der Waals (vdW) assemblies are the most common structures of materials. However, directly mapping intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedently mapped the intermolecular electron cloud of the assembles of ethanol molecules via ethyl groups with noncontact atomic force microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from 2D vdW materials. In conclusion, these findings provide an "eye" to see the atomic world of vdW materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Emergent Above-Gap Photoluminescence in Molecularly Engineered Hybrid Bilayer Crystals

Bilayer crystals, built by stacking two-dimensional (2D) covalent monolayers, give rise to coupled excitonic states whose properties are constrained by fixed lattice symmetry and orientation. Replacing one covalent monolayer with a 2D molecular crystal––held together by non-covalent forces––overcomes this limitation, as molecular functional groups afford tunable in-plane lattice geometry, intermolecular spacing, and interlayer coupling, providing a powerful knob for exciton engineering. Here, in this study, we report four-atom-thick hybrid bilayer crystals (HBCs) synthesized by directly growing single-crystalline PDI molecular crystal atop WS 2 monolayers, which exhibit a robust photoluminescence (PL) peak 120 meV above the WS 2 optical band gap alongside a belowgap emission. Both peaks display strong polarization anisotropy—nearing unity for the above-gap emission—and maintain a perfectly linear power-law dependence up to an excitation density of ~10 7 mW/cm 2 , indicative of coexisting localized and delocalized excitonic states. Substituting PDI with a PTCDA monolayer on WS 2 fully quenches PL, demonstrating molecular control over excitonic emission. Lattice scale ab initio GW and GW-BSE calculations reveal a significantly hybridized bilayer band structure in PDI/WS 2 that supports interlayer excitonic species both above and below the WS 2 gap with strong polarization anisotropy, in excellent agreement with experiment. Our work introduces a molecule-based bilayer platform for the bottom-up design and control of excitonic phenomena in atomically thin optoelectronic and quantum materials.

2D materials↗

Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development

Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born–Oppenheimer potential energy surface. In particular, we focus on ab initio–based force fields that aim to explicitly reproduce many-body terms and are fitted to high-level electronic structure results. These force fields generally incorporate many-body effects through ( a) parameterization of distributed multipoles, ( b) explicit fitting of the MBE, ( c) inclusion of many-atom features in a neural network, and ( d) coarse-graining of many-body terms into an effective two-body term. We also discuss the emerging use of the MBE to improve the accuracy and speed of ab initio molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images

High resolution non-contact atomic force microscopy measurements characterize assemblies of trimesic acid molecules on Cu(111) and the link group interactions, providing the first fingerprints utilizing CO-based probes for this widely studied paradigm for hydrogen bond driven molecular self assembly. The enhanced submolecular resolution offered by this technique uniquely reveals key aspects of the competing interactions. Accurate comparison between full-density-based modeled images and experiment allows to identify key structural elements in the assembly in terms of the electron-withdrawing character of the carboxylic groups, interactions of those groups with Cu atoms in the surface, and the valence electron density in the intermolecular region of the hydrogen bonds. This study of trimesic acid assemblies on Cu(111) combining high resolution atomic force microscopy measurements with theory and simulation forges clear connections between fundamental chemical properties of molecules and key features imprinted in force images with submolecular resolution.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Modulating the Extent of Anisotropic Cuprophilicity via High Pressure with Piezochromic Luminescence Sensitization

We report metallophilicity has been widely studied as a fundamental supramolecular interaction. However, the extent and directionality thereof remain controversial. A major obstacle lies in the difficulty to separately control the geometry and chemical composition. Herein, we address this challenge by modulating metallophilicity with mechanical pressure. Using a multinuclear Cu(I) complex as model system, we report anomalous anisotropies of (supra)molecular structures, vibrations, and interaction energies upon isotropic compression as well as concomitant (essentially turn-on) piezochromic luminescence enhancement with ~10 3 modulation. The in situ characterizations indicate opposite behaviors of contact distances and cuprophilic interactions for intermolecular vs intramolecular Cu-Cu pairs under pressure. Theoretical calculations break down the attractive and repulsive forces associated with cuprophilicity, its spontaneous 4p-3d hybridization origin, and direction-dependent interaction strength. The use of isotropic mechanical force reveals the intrinsic anisotropy of metallophilicity in multinuclear systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiscale investigation of the mechanism of biomass deconstruction in the dimethyl isosorbide/water Co-solvent pretreatment system

In the context of promoting a circular bioeconomy, the development of green and efficient lignocellulosic biomass pretreatment technologies so as to realize high value-added biomass utilization is of intense interest. We demonstrated the potential of the bio-based green solvent dimethyl isosorbide (DMI) for the fractionation of Eucalyptus biomass with excellent performance. Here, to investigate the mechanisms involved in biomass fractionation, microimaging and microspectroscopic techniques were employed together with molecular dynamics (MD) simulation and COSMO-RS quantum chemical calculations to derive multiscale information. Both the microstructure and regional chemistry of the cell wall vary significantly with the volume ratio of DMI/H 2 O. The strongest effects were found at DMI/H 2 O = 9:1 and showed visible cell wall tearing cracks and cell wall deformation and collapse as well as the lowest values of cell wall thickness and circularity. From the MD simulations, lignin exhibits collapsed-like structure in pure H 2 O with low solvent accessibility surface area (SASA) and radius of gyration (R g ). In contrast, lignin in DMI/H 2 O shows extended structure with high SASA and solvent interactions dominated by van der Waals forces, with maximal contact in the 9:1 (v/v) system. Further, the COSMO-RS calculated sigma (σ-) potential suggests the intermolecular interactions in DMI and DMI/H 2 O co-solvent are weak, leading to stronger interaction with lignin and correspondingly higher lignin dissolution. The radial distribution functions and σ-potential all show that again DMI/H 2 O at 9:1 is an optimal volume ratio for high lignin dissolution. Finally, this study provides a solvent-ratio dependent mechanism for the action of polar aprotic solvents in the deconstruction of biomass.

09 BIOMASS FUELS↗

Predicting and Understanding Non-Covalent Interactions Using Novel Forms of Symmetry-Adapted Perturbation Theory

Although sometimes derided as “weak” interactions, non-covalent forces play a critical role in ligand binding and crystal packing and in determining the conformational landscape of flexible molecules. Symmetry-adapted perturbation theory (SAPT) provides a framework for accurate ab initio calculation of intermolecular interactions and furnishes a natural decomposition of the interaction energy into physically meaningful components: semiclassical electrostatics (rigorously obtained from monomer charge densities), Pauli or steric repulsion, induction (including both polarization and charge transfer), and dispersion. This decomposition helps to foster deeper understanding of non-covalent interactions and can be used to construct transferable, physics-based force fields. Separability of the SAPT interaction energy also provides the flexibility to construct composite methods, a feature that we exploit to improve the description of dispersion interactions. Furthermore, these are challenging to describe accurately because they arise from nonlocal electron correlation effects that appear for the first time at second order in perturbation theory but are not quantitatively described at that level.

74 ATOMIC AND MOLECULAR PHYSICS↗

Molecular dynamics simulation studies of 1,3-dimethyl imidazolium nitrate ionic liquid with water

The fundamental understanding of intermolecular interactions of ionic liquids (ILs) with water is essential in predicting IL–water thermodynamic properties. In this study, intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium [DMIM]+ cation and nitrate [NO 3 ] – anion with water, employing quantum mechanics and molecular dynamics simulations. Molecular dynamics simulations were performed using a revised multipolar polarizable force field. The effect of water on ionic liquids was evaluated in terms of thermodynamic and dynamic properties. Thermodynamic properties included liquid densities ρ, excess molar volumes ΔV E , and liquid structures g(r)⁠. Dynamic properties included self-diffusion coefficients D of mixture constituents as a function of water concentration. The density of ionic liquid–water mixtures monotonically decrease with increasing concentration of water. A negative excess volume was obtained for low and high water concentrations, demonstrating strong intermolecular interactions of water with ionic liquid components. Liquid structures of ionic liquid–water mixtures revealed a tendency for anions to interact with cations at shorter intermolecular distances when the water concentration is increased. Diffusion rates were found to increase for all mixture components with increase in the fraction of water. A significant change in the diffusion rate was found at ~0.3 weight fraction of water. However, the water self-diffusion coefficient was dominant at all concentrations. Furthermore, the ratio of water/anion and anion/cation self-diffusion coefficients was found to decrease linearly with increasing concentration of water molecules.

36 MATERIALS SCIENCE↗

Influence of Long-Range Forces on the Transition States and Dynamics of NaCl Ion-Pair Dissociation in Water

We study NaCl ion-pair dissociation in a dilute aqueous solution using computer simulations both for the full system with long-range Coulomb interactions and for a well-chosen reference system with short-range intermolecular interactions. Analyzing results using concepts from Local Molecular Field (LMF) theory and the recently proposed AI-based analysis tool “State predictive information bottleneck” (SPIB), we show that the system with short-range interactions can accurately reproduce the transition rate for the dissociation process, the dynamics for moving between the underlying metastable states, and the transition state ensemble. Contributions from long-range interactions can be largely neglected for these processes because long-range forces from the direct interionic Coulomb interactions are almost completely canceled (>90%) by those from solvent interactions over the length scale where the transition takes place. Thus, for this important monovalent ion-pair system, short-range forces alone are able to capture detailed consequences of the collective solvent motion, allowing the use of physically suggestive and computationally efficient short-range models for the dissociation event. Here, we believe that the framework here should be applicable to disentangling mechanisms for more complex processes such as multivalent ion disassociation, where previous work has suggested that long-range contributions may be more important.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Science & Technology - Other Topics↗