Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11- Flux-Ional Cluster

Coordination of Mercury(II) in Water Promoted over Hydrolysis in Solvated Clusters [Hg(H2O)1-6](aq)2+: Insights from Relativistic Effects and Free Energy Analysis

Understanding the nature of the interaction between mercury(II) ions, Hg2+, and water molecules is crucial to describe the stability and chemical behavior of structures formed during solvation, as well as the conditions that favor the Hg2+ coordination or inducing water hydrolysis. In our study, we explored exhaustively the potential energy surface of Hg2+ with up to six water molecules. We analyzed electronic and Gibbs free energies, binding, and nuclear magnetic resonance parameters. We used the zeroth-order regular approximation Hamiltonian, including scalar and spin-orbit relativistic corrections for free energy calculations and geometry optimizations to explore the interplay between electron correlation and relativistic effects. We analyzed intermolecular interactions with energy decomposition analysis, quantum theory of atoms in molecules, and natural bond orbital. Additionally, we used the four-component Dirac Hamiltonian to compute solvent effect on the magnetic shielding and J-coupling constants. Our results revealed that the water hydrolysis by Hg2+ requires a minimum of three water molecules. We found that the interaction between Hg2+ and water molecules is an orbital interaction due to relativistic effects and the most stable structures are opened-shape clusters, reducing the number of oxygen-mercury contacts and maximizing the formation of hydrogen bonds among water molecules. In these types of clusters, Hg2+ promotes the water hydrolysis over coordination with oxygen atoms. However, when we considered the change associated with the transfer of a cluster from the ideal gas to a solvated system, our solvation free energy analysis revealed that closed-shape clusters are more favorable, maximizing the number of oxygen-mercury contacts and reducing the formation of hydrogen bonds among water molecules. This finding suggests that, under room conditions, the coordination of Hg2+ is more favorable than hydrolysis. Our results have significant implications for understanding Hg2+ behavior in water, helping to develop targeted strategies for mercury remediation and management, and contributing to advancements in the broader field of environmental chemistry.

Insights into structural, spectroscopic, and hydrogen bonding interaction patterns of nicotinamide-oxalic acid (form I) salt by using experimental and theoretical approaches

In the present work, nicotinamide-oxalic acid (NIC-OXA, form I) salt was crystallized by slow evaporation of an aqueous solution. To understand the molecular structure and spectroscopic properties of NIC after co-crystallization with OXA, experimental infrared (IR), Raman spectroscopic signatures, X-ray powder diffraction (XRPD), and differential scanning calorimetry (DSC) techniques were used to characterize and validate the salt. The density functional theory (DFT) methodology was adopted to perform all theoretical calculations by using the B3LYP/6-311++G (d, p) functional/basis set. The experimental geometrical parameters were matched in good correlation with the theoretical parameters of the dimer than the monomer, due to the fact of covering the nearest hydrogen bonding interactions present in the crystal structure of the salt. The IR and Raman spectra of the dimer showed the red (downward) shifting and broadening of bands among (N15-H16), (N38-H39), and (C13=O14) bonds of NIC and (C26=O24), (C3=O1), and (C26=O25) groups of OXA, hence involved in the formation of NIC-OXA salt. The atoms in molecules (AIM) analysis revealed that (N8-H9···O24) is the strongest (conventional) intermolecular hydrogen bonding interaction in the dimer model of salt with the maximum value of interaction energy -12.1 kcal mol-1. Furthermore, the natural bond orbital (NBO) analysis of the Fock matrix showed that in the dimer model, the (N8-H9···O24) bond is responsible for the stabilization of the salt with an energy value of 13.44 kcal mol-1. The frontier molecular orbitals (FMOs) analysis showed that NIC-OXA (form I) salt is more reactive and less stable than NIC, as the energy gap of NIC-OXA (form I) salt is less than that of NIC. The global and local reactivity descriptor parameters were calculated for the monomer and dimer models of the salt. The electrophilic, nucleophilic, and neutral reactive sites of NIC, OXA, monomer, and dimer models of salt were visualized by plotting the molecular electrostatic potential (MESP) surface. The study provides valuable insights into combining both experimental and theoretical results that could define the physicochemical properties of molecules.

Quantum mechanical modeling of interstellar molecules on cosmic dusts: H2O, NH3, and CO2

Since the first detection of CH molecule in interstellar medium (ISM), more than 270 molecules have been identified in various astronomical sources in ISM. These molecules include big complex ones, such as fullerene (C60) and polycyclic aromatic hydrocarbons (PAHs), which are the main components of carbonaceous dust. Dust surface chemistry plays an important role in explaining the formation of interstellar molecules. However, many of the dust surface chemical parameters, such as the adsorption energies, are still of uncertainty. Here we present a study of the adsorption of water (H2O), ammonia (NH3), and carbon dioxide (CO2) on graphene-like substrate within the framework of density functional theory (DFT). We used Gaussian 16 software and adopted the corrected generalized gradient approximation (GGA) with the Perdew–Burke–Ernzerhof (PBE) functions. We determined the optimal accretion position of the studied molecules on the graphene-like surface and calculated the adsorption energies. Furthermore, according to the density of states and molecular orbitals of the adsorbed states, we analyzed the charge transfer between the molecules and the graphene-like surface. These results can provide more accurate parameters for calculating the chemical reaction rates on the dust surface, thus contributing to the understanding of dust-surface reactions in ISM.

Why an integrated approach between search algorithms and chemical intuition is necessary?

Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C₁₂O₂Mg₂ system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol^-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.

Relative Populations and IR Spectra of Cu38 Cluster at Finite Temperature Based on DFT and Statistical Thermodynamics Calculations

The relative populations of Cu₃₈ isomers depend to a great extent on the temperature. Density functional theory and nanothermodynamics can be combined to compute the geometrical optimization of isomers and their spectroscopic properties in an approximate manner. In this article, we investigate entropy-driven isomer distributions of Cu₃₈ clusters and the effect of temperature on their IR spectra. An extensive, systematic global search is performed on the potential and free energy surfaces of Cu₃₈ using a two-stage strategy to identify the lowest-energy structure and its low-energy neighbors. The effects of temperature on the populations and IR spectra are considered via Boltzmann factors. The computed IR spectrum of each isomer is multiplied by its corresponding Boltzmann weight at finite temperature. Then, they are summed together to produce a final temperature-dependent, Boltzmann-weighted spectrum. Our results show that the disordered structure dominates at high temperatures and the overall Boltzmann-weighted spectrum is composed of a mixture of spectra from several individual isomers.

Ground and Electronically Excited States of Main-Group-Metal-Doped B20 Double Rings

Ab initio coupled-cluster, electron propagator, and Møller-Plesset second-order perturbation theory calculations are utilized to analyze the low-lying electronic states of several metal-doped B₂₀. In the ground state, the presently focused AB₂₀/EB₂₀ (A = Li, Na, and K; E = Mg and Ca) consist of charge-separated A⁺B₂₀^-/E²⁺B₂₀^2- frameworks. The excited electronic states of AB₂₀ and EB₂₀⁺ were analyzed by computing the vertical electron attachment energies (VEAEs) of AB₂₀⁺ and EB₂₀²⁺. In several excited states, the radical electron is predominantly localized on the B₂₀ frames, which are counterparts of the low-lying states of bare B₂₀^-. A variety of basis sets were tested on obtaining VEAEs, and the aug-cc-pVDZ/_A,E d-aug-cc-pVDZ/_B combination provided the best accuracy-efficiency compromise on them. Furthermore, this work analyzes the Rydberg-like excited states of AB₂₀ and EB₂₀⁺ and will serve as a guide for future studies on similar metal-doped boron systems.

Effects of Temperature on Enantiomerization Energy and Distribution of Isomers in the Chiral Cu13 Cluster

In this study, we report the lowest energy structure of bare Cu₁₃ nanoclusters as a pair of enantiomers at room temperature. Moreover, we compute the enantiomerization energy for the interconversion from minus to plus structures in the chiral putative global minimum for temperatures ranging from 20 to 1300 K. Additionally, employing nanothermodynamics, we compute the probabilities of occurrence for each particular isomer as a function of temperature. To achieve that, we explore the free energy surface of the Cu₁₃ cluster, employing a genetic algorithm coupled with density functional theory. Moreover, we discuss the energetic ordering of isomers computed with various density functionals. Based on the computed thermal population, our results show that the chiral putative global minimum strongly dominates at room temperature.

Theoretical Prediction of Structures, Vibrational Circular Dichroism, and Infrared Spectra of Chiral Be4B8 Cluster at Different Temperatures

Lowest-energy structures, the distribution of isomers, and their molecular properties depend significantly on geometry and temperature. Total energy computations using DFT methodology are typically carried out at a temperature of zero K; thereby, entropic contributions to the total energy are neglected, even though functional materials work at finite temperatures. In the present study, the probability of the occurrence of one particular Be4B8 isomer at temperature T is estimated by employing Gibbs free energy computed within the framework of quantum statistical mechanics and nanothermodynamics. To identify a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surfaces is carried out using a multi-level multistep global genetic algorithm search coupled with DFT. In addition, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The total VCD/IR spectra as a function of temperature are computed using each isomer's probability of occurrence in a Boltzmann-weighted superposition of each isomer's spectrum. Additionally, we present chemical bonding analysis using the adaptive natural density partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.