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Maya J, Malloum A, Fifen JJ, Dhaouadi Z, Fouda HPE, Conradie J. Quantum cluster equilibrium theory applied to liquid ammonia. J Comput Chem 2024; 45:1279-1288. [PMID: 38353541 DOI: 10.1002/jcc.27327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 04/19/2024]
Abstract
Through this paper, the authors propose using the quantum cluster equilibrium (QCE) theory to reinvestigate ammonia clusters in the liquid phase. The ammonia clusters from size monomer to hexadecamer were considered to simulate the liquid ammonia in this approach. The clusterset used to model the liquid ammonia is an ensemble of different structures of ammonia clusters. After studious research of the representative configurations of ammonia clusters through the cluster research program ABCluster, the configurations have been optimized at the MN15/6-31++G(d,p) level of theory. These optimizations lead to geometries and frequencies as inputs for the Peacemaker code. The QCE study of this molecular system permits us to get the liquid phase populations in a temperature range of 190-260 K, covering the temperatures from the melting point to the boiling point. The results show that the population of liquid ammonia comprises mainly the ammonia hexadecamer followed by pentadecamer, tetradecamer, and tridecamer. We noted that the small-sized ammonia clusters do not contribute to the population of liquid ammonia. In addition, the thermodynamic properties, such as heat of vaporization, heat capacity, entropy, enthalpy, and free energies, obtained by the QCE theory have been compared to the experiment given some relatively good agreements in the gas phase and show considerable discrepancies in liquid phase except the density. Finally, based on the predicted population, we calculated the infrared spectrum of liquid ammonia at 215 K temperature. It comes out that the calculated infrared spectrum qualitatively agrees with the experiment.
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Affiliation(s)
- Josué Maya
- Department of Physics, Faculty of Science, University of Ngaoundere, Ngaoundere, Cameroon
- National Radiation Protection Agency, Yaounde, Cameroon
| | - Alhadji Malloum
- Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science, University of Ngaoundere, Ngaoundere, Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Application, Université de Tunis El Manar, Tunis, Tunisie
| | | | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
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Malloum A, Conradie J. Structures of DMSO clusters and quantum cluster equilibrium (QCE). J Mol Graph Model 2024; 126:108661. [PMID: 37913567 DOI: 10.1016/j.jmgm.2023.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
Dimethylsulfoxide (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.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa; Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa; Department of Chemistry, UiT - The Arctic University of Norway, N-9037 Tromsø, Norway
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Sohail U, Ullah F, Binti Zainal Arfan NH, Abdul Hamid MHS, Mahmood T, Sheikh NS, Ayub K. Transition Metal Sensing with Nitrogenated Holey Graphene: A First-Principles Investigation. Molecules 2023; 28:molecules28104060. [PMID: 37241800 DOI: 10.3390/molecules28104060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The toxicity of transition metals, including copper(II), manganese(II), iron(II), zinc(II), hexavalent chromium, and cobalt(II), at elevated concentrations presents a significant threat to living organisms. Thus, the development of efficient sensors capable of detecting these metals is of utmost importance. This study explores the utilization of two-dimensional nitrogenated holey graphene (C2N) nanosheet as a sensor for toxic transition metals. The C2N nanosheet's periodic shape and standard pore size render it well suited for adsorbing transition metals. The interaction energies between transition metals and C2N nanosheets were calculated in both gas and solvent phases and were found to primarily result from physisorption, except for manganese and iron which exhibited chemisorption. To assess the interactions, we employed NCI, SAPT0, and QTAIM analyses, as well as FMO and NBO analysis, to examine the electronic properties of the TM@C2N system. Our results indicated that the adsorption of copper and chromium significantly reduced the HOMO-LUMO energy gap of C2N and significantly increased its electrical conductivity, confirming the high sensitivity of C2N towards copper and chromium. The sensitivity test further confirmed the superior sensitivity and selectivity of C2N towards copper. These findings offer valuable insight into the design and development of sensors for the detection of toxic transition metals.
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Affiliation(s)
- Uroosa Sohail
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Faizan Ullah
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | | | | | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Isa Town 32038, Bahrain
| | - Nadeem S Sheikh
- Chemical Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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Malloum A, Conradie J. Microsolvation of phenol in water: structures, hydration free energy and enthalpy. MOLECULAR SIMULATION 2023. [DOI: 10.1080/08927022.2022.2163674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- Department of Chemistry, UiT – The Arctic University of Norway, Tromsø, Norway
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Malloum A, Conradie J. Molecular simulations of the adsorption of aniline from waste-water. J Mol Graph Model 2022; 117:108287. [PMID: 35969938 DOI: 10.1016/j.jmgm.2022.108287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/14/2023]
Abstract
Molecular simulations of adsorption processes have received considerable attention. Despite the attention, exploration of the literature shows serious limitations, among which solvent and temperature effects are the most important. In this work, we propose a computational approach to study the adsorption of aniline (as an example of pollutant) from wastewater using coronene as adsorbent. We identified all possible adsorption sites using classical molecular dynamics for further optimization at the ωB97XD/aug-cc-pVDZ level of theory. Three different solvation schemes have been explored: implicit solvation of aniline + coronene, explicit solvation of aniline + coronene, and implicit-explicit solvation of aniline + coronene. For the explicit solvation, we used six water molecules, while the implicit solvation is performed using the PCM (polarizable continuum medium) solvation model. For each of the four cases (gas phase and the three solvation schemes), the adsorption free energy is evaluated as function of temperature from 200 K to 400 K. The results show that solvation has a considerable effects on the adsorption free energy. Furthermore, we noted that the adsorption free energy varies from -39.5 kJ mol-1 at 200 K to 27.7 kJ mol-1 at 400 K using the implicit-explicit solvation of aniline + coronene. This result highlights the importance of considering temperature effects in molecular simulations study of adsorption processes.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa; Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa; Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
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Malloum A, Conradie J. Dimethylformamide clusters: non-covalent bondings, structures and temperature-dependence. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2118188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- Department of Chemistry, UiT – The Arctic University of Norway, Tromsø, Norway
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Yang T, Wang L, Wang Z, Xu Y, Feng G. Noncovalent Interactions between Aromatic Heterocycles and Carboxylic Acids: Rotational Spectroscopy of the Furan-Formic Acid and Thiophene-Formic Acid Complexes. J Phys Chem A 2022; 126:4608-4616. [PMID: 35796534 DOI: 10.1021/acs.jpca.2c03770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binary molecular complexes formed between the aromatic heterocycles furan and thiophene with formic acid were investigated using pulsed-jet Fourier transform microwave spectroscopy and quantum chemical computations. For both of the complexes, rotational spectra of the lowest energy isomer were detected and assigned. Rotational spectroscopic results and density functional theory calculations support that the preferred conformation of the furan-formic acid complex is characterized by a relatively strong O-H···O and a weak C-H···O hydrogen bonds while the O-H···π and C-H···O hydrogen bonds stabilize the thiophene-formic acid complex. Natural bond orbital analysis further proves the experimental observation, suggesting that the strength of the O-H···O(furan) interaction is about two times stronger than that of O-H···π(thiophene). The symmetry adapted perturbation theory analysis reveals that electrostatic interaction is dominant in stabilizing the two complexes and that dispersion becomes significant in the thiophene-formic acid complex compared to furan-formic acid.
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Affiliation(s)
- Tingting Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Road 55, 401331 Chongqing, China
| | - Liuting Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Road 55, 401331 Chongqing, China
| | - Zhen Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Road 55, 401331 Chongqing, China
| | - Yugao Xu
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Road 55, 401331 Chongqing, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Road 55, 401331 Chongqing, China
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Malloum A, Conradie J. QTAIM analysis dataset for non-covalent interactions in furan clusters. Data Brief 2022; 40:107766. [PMID: 35005152 PMCID: PMC8718740 DOI: 10.1016/j.dib.2021.107766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 11/29/2022] Open
Abstract
Furan clusters are very important to understand the dynamics and properties of the furan solvent. They can be used combined with quantum cluster equilibrium theory to theoretically determine the thermodynamics properties of the furan solvent. To understand the structures of the furan clusters, 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 molecular dynamics as implemented in the ABCluster code. Secondly, the generated structures have been fully optimized at the MP2/aug-cc-pVDZ level of theory. The optimized Cartesian coordinates of all the investigated structures are reported in this work to enable further investigations of the furan clusters. These Cartesian coordinates will save computational time for all further investigations involving the furan 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 investigated structures. These data can be used to identify and classify the non-covalent interactions in furan clusters. The reader can refer to the original article for further information and discussion of the data provided herein Malloum and Conradie (2022) [1].
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa.,Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa.,Department of Chemistry, UiT - The Arctic University of Norway, N-9037 Tromsø, Norway
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