Potential Energy Surface Research Articles

Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions.

Exploring potential energy surfaces (PES) is fundamental in computational chemistry, as it provides insights into the relationship between molecular energy, geometry, and chemical reactivity. We introduce Kick-MEP, a hybrid method for exploring the PES of atomic and molecular clusters, particularly those dominated by non-covalent interactions. Kick-MEP computes the Coulomb integral between the maximum and minimum electrostatic potential values on a 0.001 a.u. electron density isosurface for two interacting fragments. This approach efficiently estimates interaction energies and selects low-energy configurations at reduced computational cost. Kick-MEP was evaluated on silicon-lithium clusters, water clusters, and thymol encapsulated within Cucurbit[7]uril, consistently identifying the lowest energy structures, including global minima and relevant local minima. Kick-MEP generates an initial population of molecular structures using the stochastic Kick algorithm, which combines two molecular fragments (A and B). The molecular electrostatic potential (MEP) values on a 0.001 a.u. electron density isosurface for each fragment are used to compute the Coulomb integral between them. Structures with the lowest Coulomb integral are selected and refined through gradient-based optimization and DFT calculations at the PBE0-D3/Def2-TZVP level. Molecular docking simulations for the thymol-Cucurbit[7]uril complex using AutoDock Vina were performed for benchmarking. Kick-MEP was validated across different molecular systems, demonstrating its effectiveness in identifying the lowest energy structures, including global minima and relevant local minima, while maintaining a low computational cost.

Ortho-Para Conversion for H+ + H2 Collision in Low Temperature: A Fully Close-Coupled Time-Dependent Wave Packet Study.

The collision-induced rate coefficients of ortho-para conversion for the H+ + H2 reaction provide accurate information to probe the lifetime of cold environments in interstellar media. Rotationally resolved reaction probabilities are calculated at the low collision energy regime (0 < Ecol ≤ 0.3 eV) by employing the coupled three-dimensional (3D) time-dependent wave packet (TDWP) formalism in hyperspherical coordinates on a recently constructed ab initio ground adiabatic potential energy surface of H3+ [J. Chem. Phys. 2014, 141, 204306] for the process H+ + H2 (v = 0, j = 0-5) → H+ + H2 (v' = 0, j'). Cross-sections are then computed from the converged reaction probabilities as a function of total angular momentum (J) over the same energy regime and subsequently employed to obtain the rate constants for the ortho-to-para (O-P) and para-to-ortho (P-O) conversions and their ratio. The ratio of ortho-para conversion shows (a) appropriate convergence with the inclusion of a higher number of initial rotational states as well as a reasonable agreement with the results from a quantum statistical method and (b) a peak at lower temperature that could be due to the available collision energy for transitions involving lower rotational states (j = 0 → j' = 1).

On the Potential Energy Surface of the Pyrene Dimer

Knowledge of reliable geometries and associated intermolecular interaction energy () values at key fragments of the potential energy surface (PES) in the gas phase is indispensable for the modeling of various properties of the pyrene dimer (PYD) and other important aggregate systems of a comparatively large size (ca. 50 atoms). The performance of the domain-based local pair natural orbital (DLPNO) variant of the coupled-cluster theory with singles, doubles and perturbative triples in the complete basis set limit [CCSD(T)/CBS] method for highly accurate predictions of the at a variety of regions of the PES was established for a representative set of pi-stacked dimers, which also includes the PYD. For geometries with the distance between stacked monomers close to a value of such a distance in the minimum structure, an excellent agreement between the canonical CCSD(T)/CBS results and their DLPNO counterparts was found. This finding enabled us to accurately characterize the lowest-lying configurations of the PYD, and the physical origin of their stabilization was thoroughly analyzed. The proposed DLPNO-CCSD(T)/CBS procedure should be applied with the aim of safely locating a global minimum of the PES and firmly establishing the pertaining of even larger dimers in studies of packing motifs of organic electronic devices and other novel materials.

Response Matching for Generating Materials and Molecules.

Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration.

Ultracold charged atom-dimer collisions: State-selective charge exchange and three-body recombination

Based on an accurate determination of the potential energy surfaces of Rb3+ correlated to its first asymptotic limit Rb++Rb(5s)+Rb(5s), we identify the presence of intersections of a pair of singlet and triplet surfaces over all interparticle distances, leading to Jahn-Teller (JT) couplings. We elaborate scenarios for charge exchange between ultracold charged atom-dimer complex (Rb+Rb2+ or Rb++Rb2), predicting a strong selectivity on the preparation of the initial state of the dimer. We also demonstrate that the JT couplings must drive the three-body recombination (TBR) of Rb+, Rb, and Rb at ultracold energies. Using the current analysis, we provide a consistent picture of the TBR experiments performed in ion-atom hybrid Rb samples. We also demonstrate the presence of JT coupling as a general phenomenon in the singly charged homonuclear alkali triatomic systems. Published by the American Physical Society 2024

Δ-Machine Learning to Elevate DFT-Based Potentials and a Force Field to the CCSD(T) Level Illustrated for Ethanol.

Progress in machine learning has facilitated the development of potentials that offer both the accuracy of first-principles techniques and vast increases in the speed of evaluation. Recently, Δ-machine learning has been used to elevate the quality of a potential energy surface (PES) based on low-level, e.g., density functional theory (DFT) energies and gradients to close to the gold-standard coupled cluster level of accuracy. We have demonstrated the success of this approach for molecules, ranging in size from H3O+ to 15-atom acetyl-acetone and tropolone. These were all done using the B3LYP functional. Here, we investigate the generality of this approach for the PBE, M06, M06-2X, and PBE0 + MBD functionals, using ethanol as the example molecule. Linear regression with permutationally invariant polynomials is used to fit both low-level and correction PESs. These PESs are employed for standard RMSE analysis for training and test data sets, and then general fidelity tests such as energetics of stationary points, normal-mode frequencies, and torsional potentials are examined. We achieve similar improvements in all cases. Interestingly, we obtained significant improvement over DFT gradients where coupled cluster gradients were not used to correct the low-level PES. Finally, we present some results for correcting a recent molecular mechanics force field for ethanol and comment on the possible generality of this approach.

Exploring chemical reactivity through a combined conceptual DFT and ELF topology approach.

In a proof-of-concept study, we explore how a combined approach using the topology of the electron localization function (ELF) and the condensed dual descriptor (DD) function can guide the optimal orientation between reactants and mimic the potential energy surfaces of molecular systems at the beginning of the chemical pathway. The DD has been chosen for its ability to evaluate the regioselectivity of neutral and soft species and to potentially mimic the interaction energy obtained from the mutual interactions between nucleophilic and electrophilic regions of the building blocks under perturbative theory. Our method has been illustrated with examples in which the optimal orientation of several systems can be successfully identified. The limitations of the presented model in predicting chemical reactivity are outlined in particular the influence of the selected condensation scheme.

Dynamics of Lanthanide(III) complexes from crystallographic data and computational studies

In this study we take advantage of the large body of X-ray data reported for lanthanide complexes, as well as their similar coordination chemistry properties, to gain insight on the dynamic processes involving λ ↔ δ configurational changes leading to isomer interconversion. The analysis of X-ray data reveals that different donor groups are characterized by Gaussian distributions of the dihedral N–C–X–Y angles ϕ. In the case of ethylenediamine groups (X = C; Y = N) Gaussian distributions are very narrow, while acetates (X = C; Y = O) provide very broad distributions. The analysis of the potential energy surfaces (PESs) using DFT reveals that ethylenediamine groups are characterised by well-defined deep energy minima, while those of acetate groups are rather swallow. Other donor groups like acetamide, pyridine or phosphinate show intermediate Gaussian distributions with respect to ethylenediamine and acetates. The PESs were fitted to a potential incorporating quadratic, cubic and quartic terms. The quadratic force constants k11 obtained for the different donor types follow the trend of the full width at half maxima (FWHM) of Gaussian distributions obtained from X-ray data. The k11 values are very similar for a given donor group, while the anharmonic cubic (k111) and quartic (k1111) force constants vary significantly depending on the environment of the donor group. Overall, this work demonstrates that the analysis of X-ray crystallographic data in lanthanide complexes can provide very useful information on their coordination chemistry preferences and dynamic processes.

Extending the functional form of the methane PES in redundant coordinates for highly excited vibrational energy levels calculation

Potential energy surfaces (PES) of methanewhich are constructed using ten symmetrised combinations of four bond length and six interbond angles are referred to as (10S) PESs At high energy ranges, it was found that (10S) PESs permitted improving by factor of five the fit quality of ab initio electronic energies of methane versus standard nine symmetric coordinates (9S) PES representations both in internal, orthogonal or normal-mode coordinates. We extend predictions of vibrational band origins to spectral range above 10000 cm−1 to help future analyses of experimental spectra. Accuracy at high energies is increased without notable deterioration at low-E levels (rms deviation of 0.26 cm−1). Based on a comparison between various variants of (10S) PESs we expect that new theoretical band origins should have accuracy not worse than 1–3 cm−1 up to 13400 cm−1.

Luminescent Mannich bases: Synthesis, crystal structures, and photophysical properties

Three Mannich bases have been obtained starting from 5-bromo-salicylaldehyde: 5-bromo-3-(((2-(dimethylamino)ethyl)(methyl)amino)methyl)-2-hydroxybenzaldehyde (TMEN), 5-bromo-3-((benzyl(methyl)amino)methyl)-2-hydroxybenzal-dehyde (MBA), 5-bromo-3-(ethyl(methyl)amino)methyl)-2-hydroxybenzaldehyde (EMA). The crystal structure of MBA has been solved. The UV-Vis absorption and emission spectra were investigated in different solvents, revealing the presence of several species, the neutral forms, the zwitterionic, the anionic and the cationic (the protonated nitrogen) ones. In order to characterize the last two species, further experiments were performed in the presence of hydrogen extracting and hydrogen donating compounds, sodium fluoride (NaF) and tetra butyl ammonium hydroxide (TBOH) to evidence the anion, and trichloroacetic acid (TCA) for the protonated cation. The experimental results were rationalized by DFT calculations of the potential energy surfaces (PES) of the S0 and S1 states and of the absorption and emission maxima.

Hunting for Sulfur-containing Molecules in Space: A Spectroscopic Characterization of Cyclopropenethione Based on High-level Ab Initio Calculations

Cyclopropenethione falls into the class of complex organic molecules but has not yet been observed in the interstellar medium or any circumstellar disks. However, its existence is very likely, and thus this study provides high-level ab initio predictions, which may serve as reference data for future observations or experimental work. Rovibrational configuration interaction theory based on multidimensional potential energy surfaces being obtained from explicitly correlated coupled-cluster calculations has been used to predict the fundamental vibrational modes, the microwave spectrum, and low-lying rovibrational transitions. Rotational constants as well as quartic and sextic centrifugal distortion constants were obtained from vibrational perturbation theory.

Two P, Ten P, White P, Red P: Mechanistic Exploration of the Oligomerization of Red Phosphorus from Diphosphorus with the Ab Initio Nanoreactor.

Phosphorus is critical to humans on many fronts, yet we do not have a mechanistic understanding of some of its most basic transformations and reactions─namely the oligomerization of white phosphorus to red. With heat or under ultraviolet (UV) exposure, it has been experimentally demonstrated that white phosphorus dissociates into diphosphorus units which readily form red phosphorus. However, the mechanism of this process is unknown. The ab initio nanoreactor approach was used to explore the potential energy surface of phosphorus clusters. Density functional theory and metadynamics simulations were used to characterize potential reaction pathways. A mechanism for oligomerization is proposed to take place via diphosphorus additions at π-bonds and weak σ-bonds through three membered ring intermediates. Downhill paths through P6 and P8 clusters eventually result in P10 clusters that can oligomerize into red phosphorus chains. The initial, rate limiting step for this process has an energy barrier of 24.2 kcal/mol.

Coarse-grained modeling of high-enthalpy air flows based on the updated vibrational state-to-state kinetics

The state-to-state (StS) model can accurately describe high-temperature thermochemical nonequilibrium flows. For the five-species air gas mixture, we develop a comprehensive database for the state-specific rate coefficients for temperatures 300–25 000 K in this paper. The database incorporates recent molecular dynamics simulations (based on the ab initio potential energy surfaces) in the literature, and theoretical methods, including the forced harmonic oscillator model and the Marrone–Treanor model, are employed to complement the rate coefficients that are unavailable from molecular dynamics calculations. The post-shock StS simulations using the present database agree with the experimental NO infrared radiation. Based on this updated StS kinetics database, we investigate the post-shock high-enthalpy air flows by employing both the StS and coarse-grained models (CGM). The CGM, which lumps molecular vibrational states into groups, shows results that align with the StS model, even utilizing only two groups for each molecule. However, the CGM-1G model, with only one group per molecule and belonging to the multi-temperature model (but uses StS kinetics), fails to reproduce the StS results. Analysis of vibrational energy source terms for different kinetic processes and fractions of vibrational groups reveals that the deficiency of the CGM-1G model stems from the overestimation of high-lying vibrational states, leading to higher dissociation rates and increased consumption of vibrational energy in dissociation. Furthermore, the presence of the Zeldovich-exchange processes indirectly facilitates energy transfer in N2 and O2, a phenomenon not observed in binary gas systems. These findings have important implications for developing the reduced-order model based on coarse-grained treatment.

Selenium Adsorption on the (111), (100), (110) and (211) Surfaces of Face‐Centered‐Cubic Metals: Density Functional Calculations of the Potential Energy Surfaces

AbstractIn this study, we expand the computational investigation of selenium, which has previously been limited to metals such as Cu, Fe, Pd, Au, and Pt. Utilizing density functional theory calculations, we explore the adsorption and diffusion of selenium at a low‐coverage regime of 0.25 ML on a broader range of metal surfaces, including Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au. Our results reveal that selenium exhibits a distinct preference for three‐fold or four‐fold high‐coordination sites on most studied surfaces. We further analyze the minimum energy diffusion pathways, demonstrating that the energy barrier for selenium's surface diffusion varies significantly based on the orientation and nature of the metal surfaces. Specifically, on (100) surfaces, selenium exhibits the highest diffusion energy, ranging from 0.60 eV in Au(100) to 1.12 eV in Pd(100). The diffusion behavior on (110) and (211) surfaces is also elaborated, emphasizing the unique trends observed compared to previously studied elements like sulfur. Importantly, this study is a new reference for future computational analyses, filling existing gaps by providing comprehensive data on selenium adsorption on various face‐centered cubic metal surfaces not previously reported.

Theoretical and modeling studies on the kinetics of diethylamine dehydrogenation and subsequent isomerization and decomposition reactions

Small-molecule nitrogen-containing contaminants can be produced by the pyrolysis of diethylamine (DEA) alone or in conjunction with other molecules. To investigate the theoretical chemistry of the combustion of DEA, the CBS method determines the potential energy surface and the rate constants are calculated based on a combination of RRKM and TST theories. The H-abstraction reactions by H radicals are more kinetically advantageous. Site α has the most difficult H-abstraction procedure, but site γ has the competitive capacity to form subsequent products. The H-abstraction by NO2 radical produces trans-HONO, cis-HONO, and HNO2. For the reaction channels of DEA radicals, decomposition reactions have more kinetic advantages than isomerization. Kinetic parameters were obtained and the model was modified based on the fitted rate constants. The modified model has better predictive ability at low temperatures. This work provides extensive data to improve the modeling of DEA combustion at low and medium temperatures.

Bioinspired surface modification of mussel shells and their application as a biogenic filler in polypropylene composites

This study explores the potential of mussel shells (MS) as biogenic fillers in polymer composites. The chemical composition and crystal structures of MS were characterised. To improve MS filler dispersion and adhesion within a polypropylene (PP) matrix, three surface modification methods were evaluated: polydopamine (PDA) coating, maleic anhydride-grafted polypropylene (MAPP) modification, and PDA/MAPP co-modification. The PDA coating, inspired by the adhesive properties of mussel foot proteins, successfully functionalized the MS surface, as confirmed by X-ray photoelectron spectroscopy (XPS). Thermodynamic analysis, based on contact angle measurements, revealed that MAPP and PDA/MAPP modifications reduced surface energies and potential energy differences. These changes enhanced filler dispersion and interfacial bonding by increasing hydrophobicity and reducing agglomeration in the PP matrix. Consequently, PP composites with 20% PDA/MAPP-modified MS fillers exhibited a 2.9% increase in tensile strength and a 7.5% increase in flexural strength compared to neat PP. Scanning electron microscopy (SEM) also showed reduced filler-matrix debonding and fewer voids. The proposed mechanism attributes these macroscopic property enhancements to the ability of the PDA coating to facilitate chemical and hydrogen bonding between MS fillers and MAPP.

Machine-learned coarse-grained potentials for particles with anisotropic shapes and interactions

Computational investigations of biological and soft-matter systems governed by strongly anisotropic interactions typically require resource-demanding methods such as atomistic simulations. However, these techniques frequently prove to be prohibitively expensive for accessing the long-time and large-length scales inherent to such systems. Conversely, coarse-grained models offer a computationally efficient alternative. Nonetheless, models of this type have seldom been developed to accurately represent anisotropic or directional interactions. In this work, we introduce a straightforward bottom-up, data-driven approach for constructing single-site coarse-grained potentials suitable for particles with arbitrary shapes and highly directional interactions. Our method for constructing these coarse-grained potentials relies on particle-centered descriptors of local structure that effectively encode dependencies on rotational degrees of freedom in the interactions. By using these descriptors as regressors in a linear model and employing a simple feature selection scheme, we construct single-site coarse-grained potentials for particles with anisotropic interactions, including surface-patterned particles and colloidal superballs in the presence of non-adsorbing polymers. We validate the efficacy of our models by accurately capturing the intricacies of the potential-energy surfaces from the underlying fine-grained models. Additionally, we demonstrate that this simple approach can accurately represent the contact function (shape) of non-spherical particles, which may be leveraged to construct continuous potentials suitable for large-scale simulations.

Formation of acetonitrile (CH3CN) under cold interstellar, tropospheric and combustion mediums

The knowledge of the formation of gas-phase carcinogenic acetonitrile (CH3CN) is limited in interstellar, troposphere, and combustion mediums; thus, its formation and fate are of great importance for all these gas-phase environments when accessing its toxicity and its wide range of applications. In this work, we propose a mechanism for the formation of CH3CN from the reaction of OH/O2 on ethanimine (CH3CH=NH) using ab initio/Density Functional Theory (DFT) potential energy surface in combination with microcanonical variational transition state theory (µVTST) and Ramsperger–Kassel–Marcus (RRKM)/master equation (ME) simulation to predict the rate constants and branching fraction in the temperature range of 100 K to 1000 K and pressure range of 0.0001 bar to 100 bar. The reaction starts with cis (Z) and trans (E) CH3CH=NH isomer with OH radical followed by spontaneous formation via pre-reactive complex, forming the carbon and nitrogen-centered radicals. The O2 radical then attacks the carbon and nitrogen-centered radicals to form acetonitrile (CH3CN) and HO2 radicals. The results show that N–H and C–H dominate the H-atoms abstraction by OH radicals is similar to its isoelectronic analogous reaction system, i.e., CH3CHO + OH/O2 and CH3CHCH2 + OH/O2 and similar to methanimine (CH2NH) systems. The calculated rate constants for OH-initiated oxidation of CH3CH=NH are in the range of ~ 10–11 cm3 molecule−1 s−1 (at 300 K) and are in very good agreement with previous experimental values of its isoelectronic reaction system. The atmospheric lifetime due to the loss of CH3CHNH by OH radical (10 to 11 h) is in very good agreement with the similar pollutants in the troposphere temperature range between 200 and 320 K. The results indicate that its contribution to global warming is negligible. However, the formation of products such as CH3CN may interact with other atmospheric species, which could lead to the production of potentially hazardous compounds such as cyanogen (N2C2) and hydrogen cyanide (HCN).

Data-efficient fine-tuning of foundational models for first-principles quality sublimation enthalpies.

Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy - even with the aid of machine learning potentials - is a challenge that requires sub-kJ mol-1 accuracy in the potential energy surface and finite-temperature sampling. We present an accurate and data-efficient protocol for training machine learning interatomic potentials by fine-tuning the foundational MACE-MP-0 model and showcase its capabilities on sublimation enthalpies and physical properties of ice polymorphs. Our approach requires only a few tens of training structures to achieve sub-kJ mol-1 accuracy in the sublimation enthalpies and sub-1% error in densities at finite temperature and pressure. Exploiting this data efficiency, we perform preliminary NPT simulations of hexagonal ice at the random phase approximation level and demonstrate a good agreement with experiments. Our results show promise for finite-temperature modelling of molecular crystals with the accuracy of correlated electronic structure theory methods.

Ballistic and delayed photodissociation channels in the B̃ 2A11 state of water studied with resonant inelastic x-ray scattering

Photodissociation is one of the most important photoinduced chemical reactions. It occurs when the potential energy curve along a chemical bond is repulsive in an excited state. Typically, “ballistic” ultrafast dissociation leads to the broadening of absorption resonances and the smearing out of vibrational fine-structure. We report on the photodissociation of H2O in the B̃ 2A11 electronic state, characterized by a |3a1−14a11〉 configuration, which can be reached via resonant inelastic x-ray scattering or direct ultraviolet absorption. In both cases the spectra show narrow vibrational resonances, in spite of the dissociative character of the state. We find that “delayed” dissociation pathways, caused by reflection of the nuclear wave packet, are responsible for this effect. In spite of the analogous topology of the potential energy surfaces of the core- and valence-excited states, the reflection of the wave packet takes place only in the latter. The two-dimensional wave packet of the O-H stretching coordinates becomes trapped in a “cavity” near the Franck-Condon region, resulting from a mismatch between the OH vibrational frequency in the cavity and the one at the dissociation limit. Published by the American Physical Society 2024