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Intermolecular Forces: From Atoms and Molecules to Nanostructures

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 39345

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Special Issue Editors

Prof. Dr. Jorge M. C. Marques

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Centro de QuÍmica de Coimbra, Universidade de Coimbra, Coimbra, Portugal
Interests: development of efficient global optimization algorithms; physical chemistry; microsolvation; atomic and molecular clusters; colloidal systems; structure and intermolecular forces

Prof. Dr. Frederico Vasconcellos Prudente

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Instituto de Física, Universidade Federal da Bahia, 40170-115 Salvador-Bahia, Brazil
Interests: excitation, dissociation and ionization of molecules of biological interest in gas or condensed phase by interaction with photons, electrons, and atoms; confined quantum systems and information theory; atomic and molecular clusters: structural, electronic, and thermodynamic properties; intra- and intermolecular interactions

Prof. Dr. Fernando Pirani

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Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
Interests: nature, role, and modeling of intermolecular forces; weak hydrogen and halogen bond; atomic and molecular collisions; gas-phase molecular beam experiments, stereo-dynamics of chemi-ionization reactions

Special Issue Information

Dear Colleagues,

Intermolecular forces are at the core of the building up process of the formation of complex chemical structures. The aim of this Special Issue is to underline the relationship between intermolecular forces and other properties across different scales. The characterization of the different types of intermolecular forces is important in order to assess their role in the formation of simple gaseous adducts, clusters, and nanostructures. This constitutes a challenge for both experimentalists and theoreticians that will open new avenues in the study of increasingly complex systems.

This Special Issue aims to contribute to the awareness of the state-of-the-art research on intermolecular forces. Accordingly, it is expected to publish work that falls within the following lines of research and related topics:

- Theoretical methods and experimental techniques to evaluate molecular interactions;

- Potential models for describing intermolecular interactions;

- Fingerprints of hydrogen bonding and van der Waals interactions;

- Cooperative and selective processes involving inter- and intramolecular interactions;

- Intermolecular forces, microscopic and macroscopic properties;

- Microsolvation and the formation of clusters;

- Highlighting the role of intermolecular forces in molecular self-assembly to build nanostructures.

Prof. Dr. Jorge M. C. Marques
Prof. Dr. Frederico Vasconcellos Prudente
Prof. Dr. Fernando Pirani
Guest Editors

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Keywords

simple neutral and ionic aggregates
long-range interactions
potential energy functions
nanoclusters
spectroscopy
complex systems
solvation
thermodynamics
molecular assembly

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Published Papers (14 papers)

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Editorial

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3 pages, 190 KiB

Open AccessEditorial

Intermolecular Forces: From Atoms and Molecules to Nanostructures

by Jorge M. C. Marques, Frederico V. Prudente and Fernando Pirani

Molecules 2022, 27(10), 3072; https://doi.org/10.3390/molecules27103072 - 11 May 2022

Cited by 8 | Viewed by 2833

Abstract

Intermolecular forces, determined by the critical balance of interacting components having physical and chemical natures, control most of the static and dynamic properties of matter such as their existence in solid, liquid and gaseous phases, with their relative stability, and their chemical reactivity [...] Read more.

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

Research

Jump to: Editorial

15 pages, 7120 KiB

Open AccessArticle

Thermodynamic Signatures of Structural Transitions and Dissociation of Charged Colloidal Clusters: A Parallel Tempering Monte Carlo Study

by Frederico V. Prudente and Jorge M. C. Marques

Molecules 2022, 27(8), 2581; https://doi.org/10.3390/molecules27082581 - 16 Apr 2022

Cited by 2 | Viewed by 1872

Abstract

Computational simulation of colloidal systems make use of empirical interaction potentials that are founded in well-established theory. In this work, we have performed parallel tempering Monte Carlo (PTMC) simulations to calculate heat capacity and to assess structural transitions, which may occur in charged colloidal clusters whose effective interactions are described by a sum of pair potentials with attractive short-range and repulsive long-range components. Previous studies on these systems have shown that the global minimum structure varies from spherical-type shapes for small-size clusters to Bernal spiral and “beaded-necklace” shapes at intermediate and larger sizes, respectively. In order to study both structural transitions and dissociation, we have organized the structures appearing in the PTMC calculations by three sets according to their energy: (i) low-energy structures, including the global minimum; (ii) intermediate-energy “beaded-necklace” motifs; (iii) high-energy linear and branched structures that characterize the dissociative clusters. We observe that, depending on the cluster, either peaks or shoulders on the heat–capacity curve constitute thermodynamics signatures of dissociation and structural transitions. The dissociation occurs at

T = 0.20

for all studied clusters and it is characterized by the appearance of a significant number of linear structures, while the structural transitions corresponding to unrolling the Bernal spiral are quite dependent on the size of the colloidal system. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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19 pages, 4422 KiB

Open AccessFeature PaperArticle

The PM6-FGC Method: Improved Corrections for Amines and Amides

by Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago and Saulo A. Vázquez

Molecules 2022, 27(5), 1678; https://doi.org/10.3390/molecules27051678 - 3 Mar 2022

Cited by 2 | Viewed by 2204

Abstract

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH₂ group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH₃ molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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18 pages, 2662 KiB

Open AccessArticle

Unravelling the Interactions of Magnetic Ionic Liquids by Energy Decomposition Schemes: Towards a Transferable Polarizable Force Field

by Iván González-Veloso, Nádia M. Figueiredo and M. Natália D. S. Cordeiro

Molecules 2021, 26(18), 5526; https://doi.org/10.3390/molecules26185526 - 11 Sep 2021

Cited by 3 | Viewed by 2240

Abstract

This work aims at unravelling the interactions in magnetic ionic liquids (MILs) by applying Symmetry-Adapted Perturbation Theory (SAPT) calculations, as well as based on those to set-up a polarisable force field model for these liquids. The targeted MILs comprise two different cations, namely: 1-butyl-3-methylimidazolium ([Bmim]⁺) and 1-ethyl-3-methylimidazolium ([Emim]⁺), along with several metal halides anions such as [FeCl₄]⁻, [FeBr₄]⁻, [ZnCl₃]⁻ and [SnCl₄]²⁻ To begin with, DFT geometry optimisations of such MILs were performed, which in turn revealed that the metallic anions prefer to stay close to the region of the carbon atom between the nitrogen atoms in the imidazolium fragment. Then, a SAPT study was carried out to find the optimal separation of the monomers and the different contributions for their interaction energy. It was found that the main contribution to the interaction energy is the electrostatic interaction component, followed by the dispersion one in most of the cases. The SAPT results were compared with those obtained by employing the local energy decomposition scheme based on the DLPNO-CCSD(T) method, the latter showing slightly lower values for the interaction energy as well as an increase of the distance between the minima centres of mass. Finally, the calculated SAPT interaction energies were found to correlate well with the melting points experimentally measured for these MILs. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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12 pages, 923 KiB

Open AccessArticle

Adsorption Hysteresis in Open Slit-like Micropores

by Grygorii Dragan, Volodymyr Kutarov, Eva Schieferstein and Alexander Iorgov

Molecules 2021, 26(16), 5074; https://doi.org/10.3390/molecules26165074 - 21 Aug 2021

Cited by 15 | Viewed by 2829

Abstract

Adsorption hysteresis in the low-pressure range is only rarely described in the literature. To optimise, for example, heat storage technologies, a deeper understanding of the low-pressure hysteresis (LPH) process is necessary. Here, two thermodynamically based approaches are further developed for analysing the LPH within the framework of thermodynamically irreversible processes and fractal geometry. With both methods developed, it is possible to obtain the description of the adsorption and desorption branches with high accuracy. Within the framework of the two thermodynamic models of the hysteresis loop, generalised equations are obtained with the control parameter in the form of the degree of irreversibility. This is done by taking the adsorption of water on alumina as an example. It is shown that the fractal dimension of the adsorption process is larger than the fractal dimension of the desorption branch, meaning that the phase state of the adsorbate is more symmetric during the adsorption step than in the desorption process. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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12 pages, 3681 KiB

Open AccessArticle

Halogens in Acetophenones Direct the Hydrogen Bond Docking Preference of Phenol via Stacking Interactions

by Charlotte Zimmermann, Manuel Lange and Martin A. Suhm

Molecules 2021, 26(16), 4883; https://doi.org/10.3390/molecules26164883 - 12 Aug 2021

Cited by 9 | Viewed by 3514

Abstract

Phenol is added to acetophenone (methyl phenyl ketone) and to six of its halogenated derivatives in a supersonic jet expansion to determine the hydrogen bonding preference of the cold and isolated 1:1 complexes by linear infrared spectroscopy. Halogenation is found to have a pronounced effect on the docking site in this intermolecular ketone balance experiment. The spectra unambiguously decide between competing variants of phenyl group stacking due to their differences in hydrogen bond strength. Structures where the phenyl group interaction strongly distorts the hydrogen bond are more difficult to quantify in the experiment. For unsubstituted acetophenone, phenol clearly prefers the methyl side despite a predicted sub-kJ/mol advantage that is nearly independent of zero-point vibrational energy, turning this complex into a challenging benchmark system for electronic structure methods, which include long range dispersion interactions in some way. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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9 pages, 2932 KiB

Open AccessArticle

The Effect of Cluster Size on the Intra-Cluster Ionic Polymerization Process

by Estefania Rossich Molina and Tamar Stein

Molecules 2021, 26(16), 4782; https://doi.org/10.3390/molecules26164782 - 7 Aug 2021

Cited by 2 | Viewed by 2341

Abstract

Polyaromatic hydrocarbons (PAHs) are widespread in the interstellar medium (ISM). The abundance and relevance of PAHs call for a clear understanding of their formation mechanisms, which, to date, have not been completely deciphered. Of particular interest is the formation of benzene, the basic building block of PAHs. It has been shown that the ionization of neutral clusters can lead to an intra-cluster ionic polymerization process that results in molecular growth. Ab-initio molecular dynamics (AIMD) studies in clusters consisting of 3–6 units of acetylene modeling ionization events under ISM conditions have shown maximum aggregation of three acetylene molecules forming bonded C₆H₆⁺ species; the larger the number of acetylene molecules, the higher the production of C₆H₆⁺. These results lead to the question of whether clusters larger than those studied thus far promote aggregation beyond three acetylene units and whether larger clusters can result in higher C₆H₆⁺ production. In this study, we report results from AIMD simulations modeling the ionization of 10 and 20 acetylene clusters. The simulations show aggregation of up to four acetylene units producing bonded C₈H₈⁺. Interestingly, C₈H₈⁺ bicyclic species were identified, setting a precedent for their astrochemical identification. Comparable reactivity rates were shown with 10 and 20 acetylene clusters. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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16 pages, 2185 KiB

Open AccessArticle

Concerning the Role of σ-Hole in Non-Covalent Interactions: Insights from the Study of the Complexes of ArBeO with Simple Ligands

by Stefano Borocci, Felice Grandinetti and Nico Sanna

Molecules 2021, 26(15), 4477; https://doi.org/10.3390/molecules26154477 - 24 Jul 2021

Cited by 2 | Viewed by 1715

Abstract

The structure, stability, and bonding character of some exemplary LAr and L-ArBeO (L = He, Ne, Ar, N₂, CO, F₂, Cl₂, ClF, HF, HCl, NH₃) were investigated by MP2 and coupled-cluster calculations, and by symmetry-adapted perturbation theory. The nature of the stabilizing interactions was also assayed by the method recently proposed by the authors to classify the chemical bonds in noble-gas compounds. The comparative analysis of the LAr and L-ArBeO unraveled geometric and bonding effects peculiarly related to the σ-hole at the Ar atom of ArBeO, including the major stabilizing/destabilizing role of the electrostatic interactionensuing from the negative/positive molecular electrostatic potential of L at the contact zone with ArBeO. The role of the inductive and dispersive components was also assayed, making it possible to discern the factors governing the transition from the (mainly) dispersive domain of the LAr, to the σ-hole domain of the L-ArBeO. Our conclusions could be valid for various types of non-covalent interactions, especially those involving σ-holes of respectable strength such as those occurring in ArBeO. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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14 pages, 281 KiB

Open AccessArticle

A Spectroscopic Validation of the Improved Lennard–Jones Model

by Rhuiago Mendes de Oliveira, Luiz Guilherme Machado de Macedo, Thiago Ferreira da Cunha, Fernando Pirani and Ricardo Gargano

Molecules 2021, 26(13), 3906; https://doi.org/10.3390/molecules26133906 - 26 Jun 2021

Cited by 10 | Viewed by 2216

Abstract

The Lennard–Jones (LJ) and Improved Lennard–Jones (ILJ) potential models have been deeply tested on the most accurate CCSD(T)/CBS electronic energies calculated for some weakly bound prototype systems. These results are important to plan the correct application of such models to systems at increasing complexity. CCSD(T)/CBS ground state electronic energies were determined for 21 diatomic systems composed by the combination of the noble gas atoms. These potentials were employed to calculate the rovibrational spectroscopic constants, and the results show that for 20 of the 21 pairs the ILJ predictions agree more effectively with the experimental data than those of the LJ model. The CCSD(T)/CBS energies were also used to determine the

β

parameter of the ILJ form, related to the softness/hardness of the interacting partners and controlling the shape of the potential well. This information supports the experimental finding that suggests the adoption of

β \approx 9

for most of the systems involving noble gas atoms. The He-Ne and He-Ar molecules have a lifetime of less than 1ps in the 200–500 K temperature range, indicating that they are not considered stable under thermal conditions of gaseous bulks. Furthermore, the controversy concerning the presence of a “virtual” or a “real” vibrational state in the He

_{2}

molecule is discussed. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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13 pages, 892 KiB

Open AccessArticle

Ca⁺ Ions Solvated in Helium Clusters

by Massimiliano Bartolomei, Paul Martini, Ricardo Pérez de Tudela, Tomás González-Lezana, Marta I. Hernández, José Campos-Martínez, Javier Hernández-Rojas, José Bretón and Paul Scheier

Molecules 2021, 26(12), 3642; https://doi.org/10.3390/molecules26123642 - 15 Jun 2021

Cited by 6 | Viewed by 2181

Abstract

We present a combined experimental and theoretical investigation on Ca

^{+}

ions in helium droplets, He

_{N}

^{+}

. The clusters have been formed in the laboratory by means of electron-impact ionization of Ca-doped helium nanodroplets. Energies and structures of such complexes [...] Read more.

We present a combined experimental and theoretical investigation on Ca

^{+}

ions in helium droplets, He

_{N}

^{+}

. The clusters have been formed in the laboratory by means of electron-impact ionization of Ca-doped helium nanodroplets. Energies and structures of such complexes have been computed using various approaches such as path integral Monte Carlo, diffusion Monte Carlo and basin-hopping methods. The potential energy functions employed in these calculations consist of analytical expressions following an improved Lennard-Jones formula whose parameters are fine-tuned by exploiting ab initio estimations. Ion yields of He

_{N}

^{+}

-obtained via high-resolution mass spectrometry- generally decrease with N with a more pronounced drop between

N = 17

and

N = 25

, the computed quantum He

_{N}

^{+}

evaporation energies resembling this behavior. The analysis of the energies and structures reveals that covering Ca

^{+}

with 17 He atoms leads to a cluster with one of the smallest energies per atom. As new atoms are added, they continue to fill the first shell at the expense of reducing its stability, until

N = 25

, which corresponds to the maximum number of atoms in that shell. Behavior of the evaporation energies and radial densities suggests liquid-like cluster structures. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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14 pages, 3149 KiB

Open AccessArticle

From Oligo(Phenyleneethynylene) Monomers to Supramolecular Helices: The Role of Intermolecular Interactions in Aggregation

by Berta Fernández, Zulema Fernández, Emilio Quiñoá and Félix Freire

Molecules 2021, 26(12), 3530; https://doi.org/10.3390/molecules26123530 - 9 Jun 2021

Cited by 2 | Viewed by 2263

Abstract

Supramolecular helices that arise from the self-assembly of small organic molecules via non-covalent interactions play an important role in the structure and properties of the corresponding materials. Here we study the supramolecular helical aggregation of oligo(phenyleneethynylene) monomers from a theoretical point of view, always guiding the studies with experimentally available data. In this way, by systematically increasing the number of monomer units, optimized n-mer geometries are obtained along with the corresponding absorption and circular dichroism spectra. For the geometry optimizations we use density functional theory together with the B3LYP-D3 functional and the 6–31G** basis set. For obtaining the spectra we resort to time-dependent density functional theory using the CAM-B3LYP functional and the 3–21G basis set. These combinations of density functional and basis set were selected after systematic convergence studies. The theoretical results are analyzed and compared to the experimentally available spectra, observing a good agreement. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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21 pages, 5178 KiB

Open AccessArticle

Competition of Intra- and Intermolecular Forces in Anthraquinone and Its Selected Derivatives

by Kamil Raczyński, Andrzej Pihut, Jarosław J. Panek and Aneta Jezierska

Molecules 2021, 26(11), 3448; https://doi.org/10.3390/molecules26113448 - 6 Jun 2021

Cited by 7 | Viewed by 3142

Abstract

Intra- and intermolecular forces competition was investigated in the 9,10-anthraquinone (1) and its derivatives both in vacuo and in the crystalline phase. The 1,8-dihydroxy-9,10-anthraquinone (2) and 1,8-dinitro-4,5-dihydroxy-anthraquinone (3) contain Resonance-Assisted Hydrogen Bonds (RAHBs). The intramolecular hydrogen bonds properties were studied in the electronic ground and excited states employing Møller-Plesset second-order perturbation theory (MP2), Density Functional Theory (DFT) method in its classical formulation as well as its time-dependent extension (TD-DFT). The proton potential functions were obtained via scanning the OH distance and the dihedral angle related to the OH group rotation. The topological analysis was carried out on the basis of theories of Atoms in Molecules (AIM—molecular topology, properties of critical points, AIM charges) and Electron Localization Function (ELF—2D maps showing bonding patterns, calculation of electron populations in the hydrogen bonds). The Symmetry-Adapted Perturbation Theory (SAPT) was applied for the energy decomposition in the dimers. Finally, Car–Parrinello molecular dynamics (CPMD) simulations were performed to shed light onto bridge protons dynamics upon environmental influence. The vibrational features of the OH stretching were revealed using Fourier transformation of the autocorrelation function of atomic velocity. It was found that the presence of OH and NO

_{2}

substituents influenced the geometric and electronic structure of the anthraquinone moiety. The AIM and ELF analyses showed that the quantitative differences between hydrogen bonds properties could be neglected. The bridged protons are localized on the donor side in the electronic ground state, but the Excited-State Intramolecular Proton Transfer (ESIPT) was noticed as a result of the TD-DFT calculations. The hierarchy of interactions determined by SAPT method indicated that weak hydrogen bonds play modifying role in the organization of these crystal structures, but primary ordering factor is dispersion. The CPMD crystalline phase results indicated bridged proton-sharing in the compound 2. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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14 pages, 1934 KiB

Open AccessArticle

Modeling of Solute-Solvent Interactions Using an External Electric Field—From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides

by Ilya G. Shenderovich and Gleb S. Denisov

Molecules 2021, 26(5), 1283; https://doi.org/10.3390/molecules26051283 - 26 Feb 2021

Cited by 10 | Viewed by 3497

Abstract

An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute–solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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19 pages, 2504 KiB

Open AccessArticle

Quasi-Classical Trajectory Study of the CN + NH₃ Reaction Based on a Global Potential Energy Surface

by Joaquin Espinosa-Garcia, Cipriano Rangel, Moises Garcia-Chamorro and Jose C. Corchado

Molecules 2021, 26(4), 994; https://doi.org/10.3390/molecules26040994 - 13 Feb 2021

Cited by 6 | Viewed by 3080

Abstract

Based on a combination of valence-bond and molecular mechanics functions which were fitted to high-level ab initio calculations, we constructed an analytical full-dimensional potential energy surface, named PES-2020, for the hydrogen abstraction title reaction for the first time. This surface is symmetrical with respect to the permutation of the three hydrogens in ammonia, it presents numerical gradients and it improves the description presented by previous theoretical studies. In order to analyze its quality and accuracy, stringent tests were performed, exhaustive kinetics and dynamics studies were carried out using quasi-classical trajectory calculations, and the results were compared with the available experimental evidence. Firstly, the properties (geometry, vibrational frequency and energy) of all stationary points were found to reasonably reproduce the ab initio information used as input; due to the complicated topology with deep wells in the entrance and exit channels and a “submerged” transition state, the description of the intermediate complexes was poorer, although it was adequate to reasonably simulate the kinetics and dynamics of the title reaction. Secondly, in the kinetics study, the rate constants simulated the experimental data in the wide temperature range of 25–700 K, improving the description presented by previous theoretical studies. In addition, while previous studies failed in the description of the kinetic isotope effects, our results reproduced the experimental information. Finally, in the dynamics study, we analyzed the role of the vibrational and rotational excitation of the CN(v,j) reactant and product angular scattering distribution. We found that vibrational excitation by one quantum slightly increased reactivity, thus reproducing the only experimental measurement, while rotational excitation strongly decreased reactivity. The scattering distribution presented a forward-backward shape, associated with the presence of deep wells along the reaction path. These last two findings await experimental confirmation. Full article

(This article belongs to the Special Issue Intermolecular Forces: From Atoms and Molecules to Nanostructures)

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