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

Hsu, Po-Jen; Ho, Kun-Lin; Lin, S. H.; Kuo, Jer‐Lai

doi:10.1039/c6cp07120a

Cited by 44 publications

(33 citation statements)

References 46 publications

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“…Because of the presence of methyl groups, the structures of neutral acetonitrile clusters exhibit part of the behavior of neutral methanol clusters 32,45‐51 and neutral ethanol clusters, 52‐54 which are stabilized by both hydrogen bonds and CH⋯O interactions. Besides, the dipole–dipole interactions guide the structures of acetonitrile clusters in similar arrangements as those of the carbon dioxide clusters 55‐57 and the nitrous oxide clusters 58‐60 .…”

Section: Resultsmentioning

confidence: 99%

Binding energies and isomer distribution of neutral acetonitrile clusters

Malloum

Fifen

Conradie

2020

Int J of Quantum Chemistry

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Structures and relative stabilities of neutral acetonitrile clusters up to decamer have been investigated. We used the ABCluster code to thoroughly explore the potential energy surfaces (PESs) of the acetonitrile clusters and to generate initial geometries, which are further fully optimized at the MN15/6-31++G(d,p) level of theory. Our exploration yielded several new local and global minima structures of the acetonitrile clusters. We located new global minimum structures of the acetonitrile pentamer to decamer. The results show that the PESs of the acetonitrile clusters are very flat, yielding several isoenergetic structures. Our investigations also revealed that the stability of the acetonitrile clusters is due both to CHÁ Á ÁN and dipole-dipole interactions. Structures stabilized by the latter are found to be more stable than those stabilized by the former at low temperatures. Furthermore, we examined the effect of temperature on the stability of the structures of the acetonitrile clusters for temperatures in the range 20 to 400 K. We found that several structures contribute to the population of the clusters at high temperatures, and also that a significant contribution to the population comes from isomers that lie within 2.0 kcal/mol from the most stable one. In addition, we used the most stable structures to compute the binding energies of the acetonitrile clusters and to assess the performance of some DFT functionals (MN15, ωB97XD, PW6B95D3, and B2PLYP) in comparison with the MP2 method associated to the aug-cc-pVTZ basis set in calculating the binding energies. We found that the MN15 functional performs better than ωB97XD and PW6B95D3, and that MN15 is less sensitive to the basis set change. We also used an extrapolation scheme to calculate the binding energies of the acetonitrile clusters at the highly accurate W1BD, CBS-QB3, and G4MP2 levels of theory. The resulting binding energies are recommended for future benchmarking of the acetonitrile clusters. K E Y W O R D S acetonitrile clusters, binding energy, DFT functionals, molecular clusters, relative energy, temperature effects, ABCluster code

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Section: Resultsmentioning

confidence: 99%

Binding energies and isomer distribution of neutral acetonitrile clusters

Malloum

Fifen

Conradie

2020

Int J of Quantum Chemistry

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“…These optimized structures served as the initial structures. Next, structural screening of the DFTB geometrically optimized structures was performed by using the shape recognition and screening method, , in which highly similar structures were classified into groups, and only the structure with the lowest energy in each group was selected for next step. Then the sodium ion was replaced with a lithium ion before applying density functional theory (DFT)/B3LYP for geometry optimization.…”

Section: Methodsmentioning

confidence: 99%

Identification of Anomericity and Linkage of Arabinose and Ribose through Collision-Induced Dissociation

Tsai

Nguan

2021

J. Phys. Chem. A

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Arabinose and ribose are two common pentoses that exist in both furanose and pyranose forms in plant and bacteria oligosaccharides. In this study, each pentose isomer, namely α-furanose, β-furanose, α-pyranose, and β-pyranose, was first separated through high-performance liquid chromatography followed by an investigation of collision-induced dissociation in an ion trap mass spectrometer. The major dissociation channels, dehydration and cross-ring dissociation, were analyzed by using high-level quantum chemistry calculations and transition state theory. The branching ratio of major dissociation channels was governed by two geometrical features: one being the cis or trans configuration of O1 and O2 atoms determining dehydration preferability and the other being the number of hydroxyl groups on the same side of the ring as the O1 atom determining the preferability of cross-ring dissociation. The relative branching ratios of the major channels were used to identify anomericity and the linkages of arabinose and ribose. Arabinose in the β-configuration and ribose in the α-configuration are predicted to have larger relative dehydration branching ratios than arabinose in the α-configuration and ribose in the β-configuration, respectively. Arabinose and ribose at the reducing end of oligosaccharides with 1 → 2 (pyranose and furanose), 1 → 3 (pyranose and furanose), 1 → 4 (pyranose only), and 1 → 5 (furanose only) linkages are predicted to undergo 0,2 X, 0,3 X, 0,2 A, and 0,2 A/ 0,3 A cross-ring dissociation, respectively. Application of the dissociation mechanism to the disaccharide linkage determination is demonstrated.

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“…27 The normal mode analysis was carried out to ensure that the true local minima were found. This multistage optimization scheme efficiently obtains a set of well-converged structures at a higher level of theory and has been successfully applied to hydrogenbonded 28,29 and π-stacked complexes. 30,31 To understand the dissociation of HCl embedded in DMSO solvent clusters, the electric field calculations were carried out.…”

Section: ■ Methodologymentioning

confidence: 99%

“…The normal mode analysis was carried out to ensure that the true local minima were found. This multistage optimization scheme efficiently obtains a set of well-converged structures at a higher level of theory and has been successfully applied to hydrogen-bonded , and π-stacked complexes. , …”

Section: Methodsmentioning

confidence: 99%

Is Dissociation of HCl in DMSO Clusters Bistable?

et al. 2021

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The dissociation of HCl embedded in DMSO clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. A large number of distinct structures (about 1500) consisting of up to five DMSO molecules were considered in the present work for statistical reliability. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm -1 along the H-Cl bond. However, a large number of exceptions wherein the electric field values much higher than the critical electric field of 137 MV cm -1 did not result in dissociation of HCl in addition to several cases wherein the HCl dissociates with an electric field less than the critical electric field. On the other hand, the MP2 level calculations reveal that the critical electric field for the HCl dissociation is about 181 MV cm -1 with almost no exceptions. The B3LYP-D3 calculations suggest that the dissociation of HCl embedded in DMSO clusters is bistable, which is an artefact, suggesting care must be exercised in interpreting processes proton transfer. The answer to the question raised as the title of this paper is NO.

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

Cited by 44 publications

References 46 publications

Binding energies and isomer distribution of neutral acetonitrile clusters

Binding energies and isomer distribution of neutral acetonitrile clusters

Identification of Anomericity and Linkage of Arabinose and Ribose through Collision-Induced Dissociation

Is Dissociation of HCl in DMSO Clusters Bistable?

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