Structural Characterization of the (Methanol)4 Potential Energy Surface

Hydrogen bond networks of dimethylsulfoxide (DMSO) pentamer

Understanding of clusters of dimethylsulfoxide (DMSO) is important in several applications in Chemistry. Despite its importance, very few studies of DMSO clusters, (DMSO)_n, have been reported in comparison to systems such as water clusters or methanol clusters. In order to provide further understanding of DMSO clusters, we investigated the structures and non-covalent interactions of the (DMSO)_n, n=5. Therefore, the potential energy surface (PES) of the DMSO pentamer has been examined using classical molecular dynamics. The structures generated using classical molecular dynamics are further optimized at the PW6B95D3/aug-cc-pVDZ level of theory. To comprehend the non-covalent bondings in the DMSO pentamer, we carried out a quantum theory of atoms in molecule (QTAIM) analysis. In addition, the effects of temperature on the structural stability is investigated between 20 and 500K. It comes out that seven different kind of non-covalent bondings can be found in DMSO pentamers.

An efficient and robust procedure to calculate absorption spectra of aqueous charged species applied to NO2. Phys Chem Chem Phys 2021;23:14857-14872. [PMID: 34223573 DOI: 10.1039/d1cp00652e]

Accurate calculation of absorption spectra of aqueous NO2- requires rigorously sampling the quantum potential energy surfaces for microsolvation of NO2- with at least five explicit water molecules and embedding the resulting clusters in a continuum solvent accounting for the statistical weighted contributions of individual isomers. This method, which we address as ASCEC + PCM, introduces several desired features when compared against MD simulations derived QM/MM spectra: comparatively fewer explicit solvent molecules to be treated with expensive QM methods, the identification of equilibrium structures in the quantum PES to be used in further vibrational spectroscopy, and the unequivocal identification of cluster orbitals undergoing electronic transitions and charge transfer that originate the spectral bands.

A molecular twist on hydrophobicity

A thorough exploration of the molecular basis for hydrophobicity with a comprehensive set of theoretical tools and an extensive set of organic solvent S/water binary systems is discussed in this work. Without a single exception, regardless of the nature or structure of S, all quantum descriptors of bonding yield stabilizing S⋯water interactions, therefore, there is no evidence of repulsion and thus no reason for etymological hydrophobicity at the molecular level. Our results provide molecular insight behind the exclusion of S molecules by water, customarily invoked to explain phase separation and the formation of interfaces, in favor of a complex interplay between entropic, enthalpic, and dynamic factors. S⋯water interfaces are not just thin films separating the two phases; instead, they are non-isotropic regions with density gradients for each component whose macroscopic stability is provided by a large number of very weak dihydrogen contacts. We offer a definition of interface as the region in which the density of the components in the A/B binary system is not constant. At a fundamental level, our results contribute to better current understanding of hydrophobicity.

Notwithstanding the very weak nature of individual contacts, it is the cumulative effect of a large number of interactions (green NCI surfaces) which provides macroscopic stability to the interfaces.

Size of the hydrogen bond network in liquid methanol: a quantum cluster equilibrium model with extensive structure search

Studies have debated what is a favorable cluster size in liquid methanol. Applications of the quantum cluster equilibrium (QCE) model on a limited set of cluster structures have demonstrated the dominance of cyclic hexamers in liquid methanol. In this study, we examined the aforementioned question by integrating our implementation of QCE with a molecular-dynamics-based structural searching scheme. QCE simulations were performed using a database comprising extensively searched stable conformers of (MeOH)n for n = 2-14, which were optimized by B3LYP/6-31+G(d,p) with and without the dispersion correction. Our analysis indicated that an octamer structure can contribute significantly to cluster probability. By reoptimizing selected conformers with high probability at the MP2 level, we found that the aforementioned octamer became the dominant species due to favorable vibrational free energy, which was attributed to modes of intermolecular vibration.

Structural Assessment of Hydrogen Bonds on Methylpentynol-Azide Clusters To Achieve Regiochemical Outcome of 1,3-Dipolar Cycloaddition Reactions Using Density Functional Theory

This study was focused on the geometries and properties of the structural isomers obtained from a random walk of methylpentynol-HN₃ clusters. The theoretical aspects of hydrogen bonding effects on the discussed 1,3-dipolar cycloaddition (1,3-DC) reactions [between methylpentynol (a) as a dipolarophile and azide (b) as a 1,3-dipole] have shown regioselective output concepts. The dipolarophile methylpentynol (a) was applied for the treatment of insomnia. Both methylpentynol (a) and azide (b) can be H-bond acceptor and H-bond donor agents. Because of this trait of them, structures of H-bonding arrays (c-f) and methylpentynol-azide clusters (g-m) can be probable. In this work, regioselectivity of the 1,3-DC reaction [between methylpentynol (a) as a dipolarophile and azide (b) as a 1,3-dipole] was determined based on these structures (c-m) using density functional theory (DFT). The energy levels of the reactants (a and b) and the structures of H-bonding arrays (c-f), methylpentynol-azide clusters (g-m), transition states, and products (1 and 2) were studied, and also, the free energies of the reaction (Δ_r G and ΔG ^#, in kcal mol^-1) and rate constants were determined using Eyring's equation (k). Structural data were calculated and obtained by the DFT/B3LYP method. Seven different basis sets have been used to obtain the most appropriate results from comparison of data.

Exploration of the potential energy surfaces of small ethanol clusters

The potential energy surfaces of small ethanol clusters, from dimer to pentamer, have been thoroughly explored using two different levels of theory. There is a clear relative energy gap between cyclic, linear and branched cyclic structures.

Fe3+chelating quinoline–hydrazone hybrids with proven cytotoxicity, leishmanicidal, and trypanocidal activities

Neglected tropical diseases cause great concern in developing countries where there are millions of reported infected humans. Our calculations support a direct relationship between biological activity and the Fe³⁺chelating ability of the shown set of quinoline–hydrazone hybrids.

Solvation energies of the proton in methanol revisited and temperature effects

Various functionals assessing solvation free energies and enthalpies of the proton in methanol.

A global optimization perspective on molecular clusters

Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca²⁺ ions with various types of solvents.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Exploration of hydrogen bond networks and potential energy surfaces of methanol clusters using a two-stage clustering algorithm

A two-stage algorithm based both on the similarity in shape and hydrogen bond network is developed to explore the potential energy surface of methanol clusters.

Microsolvation of NO3−: structural exploration and bonding analysis

A rich and complex structural diversity is uncovered in the microsolvation of the nitrate anion.

Microsolvation of methylmercury: structures, energies, bonding and NMR constants (199Hg,13C and17O)

Hartree–Fock (HF) and second order perturbation theory (MP2) calculations within the scalar and full relativistic frames were carried out in order to determine the equilibrium geometries and interaction energies between cationic methylmercury (CH₃Hg⁺) and up to three water molecules.

Theoretical tools to distinguish O-ylides from O-ylidic complexes in carbene–solvent interactions

Orbital interactions and bond indices are among the theoretical tools suitable to distinguishO-ylides fromO-ylidic carbene–solvent complexes.

Determination of size of molecular clusters of ethanol by means of NMR diffusometry and hydrodynamic calculations

The microscopic structure of ethanol in the liquid state is characterized as a dynamic equilibrium of hydrogen-bonded clusters of different sizes and topologies. We have developed a novel method for determination of the average size of the clusters that combines the measurement of diffusion coefficient by means of NMR diffusometry technique and hydrodynamic simulations. The approach includes the use of HydroNMR [J. Garcı̀a de la Torre, M. L. Huertas, and B. Carrasco, J. Magn. Reson. 147, 2000, 138] for small molecules, which is attained here by the calibration procedure using a dilute solution of tetramethylsilane. It is thus possible to correlate the experimentally determined diffusion coefficient of ethanol with calculated diffusion coefficients of the modeled clusters of different sizes. We found that average size of the clusters in 0.16 M solution of ethanol in n-hexane corresponds to the monomer above 300 K and to the pentamer/hexamer below 240 K. The clusters in the case of 0.44 M solution are generally slightly larger, from the average size corresponding to the dimer at 320 K and the hexamer at 210 K.

Potential energy surfaces of WC6 clusters in different spin states

Stochastic explorations of the structural possibilities of neutral WC6 clusters in several spin states lead to very rich and complex potential energy surfaces, with geometries quite different from those of pure carbon clusters at the PBE0/def2-TZVP level. The global minimum is predicted to be a triplet-state semicyclic C6 conformation having every carbon in direct coordination to the W atom. Interaction energies are comparable to those of C7 clusters, revealing very strong W-C bonding. Our results suggest that C-C interactions in the clusters should be considered as intermediate between single and double bonds.