1,720,974 research outputs found
QTAIM analysis dataset for non-covalent interactions in curan clusters
Get PDFFuran clusters are very important to understand the dynam-
ics and properties of the furan solvent. They can be used
combined with quantum cluster equilibrium theory to theo-
retically determine the thermodynamics properties of the fu-
ran solvent. To understand the structures of the furan clus-
ters, one needs to understand the non-covalent interactions
that hold the furan molecules together. In this paper, we have
provided the data necessary to understand the non-covalent
interactions in furan clusters. Firstly, the structures of the
furan clusters have been generated using classical molecu-
lar dynamics as implemented in the ABCluster code. Sec-
ondly, the generated structures have been fully optimized at
the MP2/aug-cc-pVDZ level of theory. The optimized Carte-
sian coordinates of all the investigated structures are re-
ported in this work to enable further investigations of the
furan clusters. These Cartesian coordinates will save compu-
tational time for all further investigations involving the fu-
ran clusters. Thirdly, to understand the nature of the non-
covalent interactions in furan clusters, we have performed a
quantum theory of atoms in molecule (QTAIM) analysis using
AIMAll program. Using QTAIM, we have provided the critical
points, bond paths and their related properties for all the in-
vestigated structures. These data can be used to identify and
classify the non-covalent interactions in furan clusters
Adsorption free energy of phenol onto coronene: Solvent and temperature effects
Get PDFMolecular modeling can considerably speed up the discovery of materials with high adsorption capacity for wastewater treatment. Despite considerable efforts in computational studies, the molecular modeling of adsorption processes has several limitations in reproducing experimental conditions. Handling the environmental effects (solvent effects) and the temperature effects are part of the important limitations in the literature. In this work, we address these two limitations using the adsorption of phenol onto coronene as case study. In the proposed model, for the solvent effects, we used a hybrid solvation model, with
explicit water molecules and implicit solvation. We increasingly used
to
explicit water molecules. To account for the temperature effects, we evaluated the adsorption efficiency using the adsorption free energy for temperatures varying from 200 to 400 K. We generated initial configurations using classical molecular dynamics, before further optimisation at the
B97XD/aug-cc-pVDZ level of theory. Polarisable continuum solvation model (PCM) is used for the implicit solvation. The adsorption free energy is evaluated to be -1.3 kcal/mol at room temperature. It has been found that the adsorption free energy is more negative at low temperatures. Above 360 K, the adsorption free energy is found to be positive
Hydrogen bond networks of dimethylsulfoxide (DMSO) pentamer
Get PDFUnderstanding 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 500 K. It comes out that seven different kind of non-covalent bondings can be found in DMSO pentamers
Structures of DMSO clusters and quantum cluster equilibrium (QCE)
Get PDFDimethylsulfoxide (DMSO) clusters are crucial for understanding processes in liquid DMSO. Despite its importance, DMSO clusters have received negligible attention due to the complexity of their potential energy surfaces (PESs). In this work, we explored the PESs of the DMSO clusters from dimer to decamer, starting with classical molecular dynamics, followed by full optimizations at the PW6B95-D3/def2-TZVP level of theory. In addition, the binding energies, the binding enthalpy per DMSO, and the quantum theory of atoms in molecules (QTAIM) analysis of the most stable isomers are reported. Temperature effects on the stability of the isomers have also been assessed. After thoroughly exploring the PESs of the DMSO clusters, 159 configurations have been used to apply the quantum cluster equilibrium (QCE) theory to liquid DMSO. The quantum cluster equilibrium theory has been applied to determine the liquid properties of DMSO from DMSO clusters. Thus, using the QCE, the population of the liquid DMSO, its infrared spectrum, and some thermodynamic properties of the liquid DMSO are predicted. The QCE results show that the population of the liquid DMSO is mainly dominated by the DMSO dimer and decamer, with the contribution in trace of the DMSO monomer, trimer, tetramer, pentamer, and octamer. More interestingly, the predicted infrared spectrum of liquid DMSO is in qualitative agreement with the experiment
Data to Understand the Nature of Non-Covalent Interactions in the Thiophene Clusters
Get PDFWe have reported herein the data to understand the nature and number of non-covalent interactions that stabilize the structures of the thiophene clusters. In addition, we
have also provided the optimized Cartesian coordinates of
all the structures of the investigated thiophene clusters. Initially, the geometries have been generated using the ABCluster code which performs a global optimization to locate local and global minima structures of molecular clusters. The
located geometries have been optimized at the MP2/aug-ccpVDZ level of theory using Gaussian 16 suite of programs. To
understand the nature of non-covalent interactions, we have
performed a quantum theory of atoms in molecules (QTAIM)
analysis on all the structures of the thiophene dimer. Furthermore, the QTAIM analysis has been performed also on the
most stable structure of the thiophene trimer and tetramer.
We have used the AIMAll program to perform the QTAIM
analysis. The data reported in this paper contains the critical points, the bonds paths and their related properties, for
each investigated structures. Besides, the data contains the
optimized Cartesian coordinates of all the investigated structures of the thiophene clusters. This can be use for any further investigations involving thiophene clusters. For further
information and analysis, the reader is referred to the original related research article (Malloum and Conradie, 2022)
QTAIM analysis dataset for non-covalent interactions in furan clusters
No full textFuran clusters are very important to understand the dynam- ics and properties of the furan solvent. They can be used combined with quantum cluster equilibrium theory to theo- retically determine the thermodynamics properties of the fu- ran solvent. To understand the structures of the furan clus- ters, one needs to understand the non-covalent interactions that hold the furan molecules together. In this paper, we have provided the data necessary to understand the non-covalent interactions in furan clusters. Firstly, the structures of the furan clusters have been generated using classical molecu- lar dynamics as implemented in the ABCluster code. Sec- ondly, the generated structures have been fully optimized at the MP2/aug-cc-pVDZ level of theory. The optimized Carte- sian coordinates of all the investigated structures are re- ported in this work to enable further investigations of the furan clusters. These Cartesian coordinates will save compu- tational time for all further investigations involving the fu- ran clusters. Thirdly, to understand the nature of the non- covalent interactions in furan clusters, we have performed a quantum theory of atoms in molecule (QTAIM) analysis using AIMAll program. Using QTAIM, we have provided the critical points, bond paths and their related properties for all the in- vestigated structures. These data can be used to identify and classify the non-covalent interactions in furan clusters.Publisher's versio
Free energy and enthalpy data of neutral and protonated clusters in the solvent phase
No full textStructures of neutral and protonated acetonitrile in the sol- vent phase are important to describe proton behavior and to calculate thermodynamic quantities related to the solva- tion of ions or molecules in acetonitrile. In this work, we provide data related to the calculation of the solvation free energy and enthalpy of the proton in acetonitrile. We have thoroughly explored the potential energy surfaces (PESs) of neutral and protonated acetonitrile clusters from dimer to heptamer in the solvent phase at both MN15/6–31 ++ G (d,p) and MP2/aug-cc-pVDZ levels of theory. We report the struc- tures and relative stability of neutral and protonated acetoni- trile clusters in the solvent phase at the MN15/6–31 ++ G (d,p) level of theory. In addition, enthalpies and free energies of neutral and protonated acetonitrile are also reported at the MP2/aug-cc-pVDZ and MP2/CBS levels of theory. Further- more, Cartesian coordinates of the clusters in the solvent phase as optimized at the MP2/aug-cc-pVDZ level of theory are provided as supplementary file. The data provided in this work will be useful for further investigations that would in- volve neutral and protonated acetonitrile clusters. The free energies and enthalpies of the investigated clusters in the solvent phase have been used to compute the solvation free energy and enthalpy of the proton in acetonitrile. For more insights on the solvation free energy and enthalpy of the pro- ton in acetonitrile, see the related main research paper.Published versio
Microsolvation of phenol in water: structures, hydration free energy and enthalpy
Get PDFIn this work, we have studied the microsolvation of phenol in water. We started by identifying initial configurations of phenol-water clusters using classical molecular dynamics. The configurations are optimised at the ωB97XD/aug-cc-pVDZ level of theory. To understand the interaction between phenol and the solvating water molecules, we performed a quantum theory of atoms in molecules (QTAIM) analysis. The results show that the structures of phenol-water clusters are similar to those of neutral water clusters. The QTAIM analysis shows that the structures of phenol-water clusters are stabilised by strong OH··· O hydrogen bondings, weak CH··· O hydrogen bondings, and OH⋯π
bonding interactions. The located structures of phenol-water clusters have been used to calculate the absolute hydration free energy and enthalpy of phenol for temperatures between 20 and 400 K. The hydration energies are calculated using the cluster continuum solvation model. It has been found that the explicit solvation has negligible effects on the hydration free energy and enthalpy of phenol. Furthermore, the hydration free energy of phenol is found to be linearly varying with increasing temperature, while the hydration enthalpy is found to be temperature independent. The estimated hydration free energy of phenol is slightly underestimated as compared to a previously reported experimental estimate
Data to understand the nature of non-covalent interactions in the thiophene clusters
No full textWe have reported herein the data to understand the nature and number of non-covalent interactions that stabilize the structures of the thiophene clusters. In addition, we have also provided the optimized Cartesian coordinates of all the structures of the investigated thiophene clusters. Initially, the geometries have been generated using the ABCluster code which performs a global optimization to locate local and global minima structures of molecular clusters. The located geometries have been optimized at the MP2/aug-cc-pVDZ level of theory using Gaussian 16 suite of programs. To understand the nature of non-covalent interactions, we have performed a quantum theory of atoms in molecules (QTAIM) analysis on all the structures of the thiophene dimer. Furthermore, the QTAIM analysis has been performed also on the most stable structure of the thiophene trimer and tetramer. We have used the AIMAll program to perform the QTAIM analysis. The data reported in this paper contains the critical points, the bonds paths and their related properties, for each investigated structures. Besides, the data contains the optimized Cartesian coordinates of all the investigated structures of the thiophene clusters. This can be use for any further investigations involving thiophene clusters. For further information and analysis, the reader is referred to the original related research article (Malloum and Conradie, 2022).Publisher's versio
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