1
|
Dasgupta S, Sen S, Sathe RY, Pophali S, Kadu A, Jain R, Bera S, Roy S, Misra R. Conformation Controlled Hydrogelation of Minimalistic α, γ Hybrid Peptide. Biomacromolecules 2024; 25:3715-3723. [PMID: 38723225 DOI: 10.1021/acs.biomac.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
A majority of short peptide (≤7 amino acids) hydrogels are primarily assembled via cross β-structure formation. In contrast to the natural trend, herein, we report the formation of supramolecular hydrogel from the ultrashort hybrid folded peptide composed of canonical α-amino acid and noncanonical γ-amino acid, Fmoc-γPhe-Phe-OH. The designed hybrid peptide hydrogel is composed of entangled fibers, has viscoelastic properties, exhibits proteolytic stability, and exhibits cytocompatibility with L929 fibroblast cells. Mutating the peptide sequence by altering the position of γPhe from the N-termini to C-termini transforms the self-assembly into crystalline aggregates. Combining FTIR, 2D NMR, and DFT calculations revealed that the hydrogel-forming peptide adopts a C9 H-bonded conformation, resembling the well-known γ-turn. However, the isomeric hybrid peptide adopts an extended structure. The present study highlights the importance of secondary structure in the higher order assembly of minimalist hybrid peptides and broadens the range of secondary structures to design short peptide-based hydrogels.
Collapse
Affiliation(s)
- Sneha Dasgupta
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Sourav Sen
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Rohit Y Sathe
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Mumbai, Maharashtra 400019, India
| | - Salil Pophali
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Archit Kadu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Santu Bera
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
| | - Sangita Roy
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Rajkumar Misra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| |
Collapse
|
2
|
Boukar O, Fifen JJ, Conradie J, Conradie MM. Solvation energies of the ferrous ion in water and in ammonia at various temperatures. J Mol Model 2024; 30:52. [PMID: 38285315 DOI: 10.1007/s00894-024-05839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
CONTEXT The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion. METHOD All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.
Collapse
Affiliation(s)
- Ousman Boukar
- Department of Physics, Faculty of Science, University of Maroua, P.O. Box 46, Maroua, Cameroon.
| | - Jean Jules Fifen
- Quantum Theory and Aplications Unit, Department of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | | |
Collapse
|
3
|
Anni D, Amika Mbema JC, Malloum A, Conradie J. Hydration of [Formula: see text]aminobenzoic acid: structures and non-covalent bondings of aminobenzoic acid-water clusters. J Mol Model 2024; 30:38. [PMID: 38214749 PMCID: PMC10786749 DOI: 10.1007/s00894-023-05810-2] [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: 10/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
CONTEXT Micro-hydration of the aminobenzoic acid is essential to understand its interaction with surrounding water molecules. Understanding the micro-hydration of the aminobenzoic acid is also essential to study its remediation from wastewater. Therefore, we explored the potential energy surfaces (PESs) of the para-aminobenzoic acid-water clusters, ABW[Formula: see text], [Formula: see text], to study the microsolvation of the aminobenzoic acid in water. In addition, we performed a quantum theory of atoms in molecules (QTAIM) analysis to identify the nature of non-covalent bondings in the aminobenzoic acid-water clusters. Furthermore, temperature effects on the stability of the located isomers have been examined. The located structures have been used to calculate the hydration free energy and the hydration enthalpy of the aminobenzoic acid using the cluster continuum solvation model. The hydration free energy and the hydration enthalpy of the aminobenzoic acid at room temperature are evaluated to be -7.0 kcal/mol and -18.1 kcal/mol, respectively. The hydration enthalpy is in perfect agreement with a previous experimental estimate. Besides, temperature effects on the calculated hydration enthalpy and free energy are reported. Finally, we calculated the gas phase binding energies of the most stable structures of the ABW[Formula: see text] clusters using twelve functionals of density functional theory (DFT), including empirical dispersion. The DFT functionals are benchmarked against the DLPNO-CCSD(T)/CBS. We have found that the three most suitable DFT functionals are classified in the following order: PW6B95D3 > MN15 > [Formula: see text]B97XD. Therefore, the PW6B95D3 functional is recommended for further study of the aminobenzoic acid-water clusters and similar systems. METHODS The exploration started with classical molecular dynamics simulations followed by complete optimization at the PW6B95D3/def2-TZVP level of theory. Optimizations are performed using Gaussian 16 suite of codes. QTAIM analysis is performed using the AIMAll program.
Collapse
Affiliation(s)
- Diane Anni
- Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon
| | - Jean Claude Amika Mbema
- Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon
| | - Alhadji Malloum
- Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa.
| | - 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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Da-yang TE, Lai CH. Potential energy surfaces of the Cu2+(NH3)n=1−10 clusters in solvent phase: A DFT study. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
6
|
Malloum A, Conradie J. Solvation of Manganese(III) Ion in Water and in Ammonia. J Phys Chem A 2023; 127:1103-1111. [PMID: 36716408 DOI: 10.1021/acs.jpca.2c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this work, we have studied the solvation of manganese(III) ion in water and in ammonia using three levels of theory: MP2, MN15, and ωB97XD associated with the aug-cc-pVDZ basis set. The studied systems are constituted of Mn3+(H2O)6 and Mn3+(NH3)6 in gas and solvent phases as well as Mn3+(H2O)18 and Mn3+(NH3)18 in the gas phase. Four aspects of the solvation of manganese(III) ion have been examined for the aforementioned systems at the three levels of theory. First, we started by locating the Jahn-Teller elongated and compressed configuration in Mn3+(H2O)6 and Mn3+(NH3)6. Second, we calculated the spin state energies and the spin state free energies for temperatures ranging from 50 to 400 K to look at possible spin crossover in the studied systems. Third, we carried out a quantum theory of atoms in molecules (QTAIM) analysis, and we determined the ionic radii of manganese(III) ion in water and in ammonia. Fourth, we calculated the solvation free energies and the solvation enthalpies of manganese(III) ion in water and in ammonia using the cluster continuum solvation model. For these four aspects of the solvation of manganese(III) ion, most of the reported properties are provided in this work for the first time. We particularly found that the calculated solvation enthalpy of the manganese(III) ion in water is in good agreement with an experimental estimate.
Collapse
Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein9300, South Africa.,Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein9300, South Africa.,Department of Chemistry, UiT - The Arctic University of Norway, N-9037Tromsø, Norway
| |
Collapse
|
7
|
Zhao H, Wang S, Sun J, Zhang Y, Tang Y. OH-initiated degradation of 1,2,3-trimethylbenzene in the atmosphere and wastewater: Mechanisms, kinetics, and ecotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159534. [PMID: 36272473 DOI: 10.1016/j.scitotenv.2022.159534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
1,2,3-Trimethylbenzene (1,2,3-TMB) is an important volatile organic compound (VOC) present in petroleum wastewater and the atmosphere. This compound can be degraded by OH radicals via abstraction, addition and substitution mechanisms. Results show that the addition mechanism is dominant and H-abstraction is subdominant, while methyl abstraction and substitution mechanisms are negligible in the gas and aqueous phases. Moreover, H-abstraction products undergo further reactions with O2, NO, NO2, H2O, and OH radicals in the atmosphere. Time-dependent density functional theory (TDDFT) calculations show that the degraded products, including 2,3,4-trimethylphenyl-nitroperoxoite, 1,2,3-trimethyl-4-nitrobenzene, 1,2,3-trimethyl-5-nitrobenzene, 2,6-dimethylbenzyl nitroperoxoite, 2,3-dimethylphenyl nitroperoxoite, 2,6-dimethylbenzaldehyde, and 2,3-dimethylbenzaldehyde, can photolyze under the sunlight. Kinetically, the calculated total rate constant is 5.57 × 10-11 cm3 molecule-1·s-1 at 1 atm and 298 K, which is consistent with available experimental values measured in the atmosphere. In addition, the calculated total reaction rate constant in water is close to that in the gas phase. In terms of ecotoxicity, all degradation products are less toxic than the initial reactant to fish, green algae and daphnia. For mammals represented by rats, 1,2,3-TMB and its products are moderately toxic, except for 2,3-dimethylphenol and 2,6-dimethylphenol, which are slightly toxic.
Collapse
Affiliation(s)
- Hui Zhao
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Fushun Road 11, Qingdao, Shandong 266033, PR China
| | - Shuangjun Wang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Fushun Road 11, Qingdao, Shandong 266033, PR China
| | - Jingyu Sun
- College of Chemistry and Environmental Engineering, Hubei Normal University, Cihu Road 11, Huangshi, Hubei 435002, PR China
| | - Yunju Zhang
- College of Chemistry and Chemical Engineering, Mianyang Normal University, Mianyang 621000, PR China
| | - Yizhen Tang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Fushun Road 11, Qingdao, Shandong 266033, PR China.
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
Malloum A, Conradie J. Hydrogen bond networks of dimethylsulfoxide (DMSO) pentamer. J Mol Graph Model 2023; 118:108363. [PMID: 36308947 DOI: 10.1016/j.jmgm.2022.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022]
Abstract
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.
Collapse
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
| |
Collapse
|
10
|
Malloum A, Conradie J. Adsorption free energy of phenol onto coronene: Solvent and temperature effects. J Mol Graph Model 2023; 118:108375. [PMID: 36423517 DOI: 10.1016/j.jmgm.2022.108375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Molecular 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 n explicit water molecules and implicit solvation. We increasingly used n=1 to n=12 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 400K. We generated initial configurations using classical molecular dynamics, before further optimisation at the ωB97XD/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 -1.3kcal/mol at room temperature. It has been found that the adsorption free energy is more negative at low temperatures. Above 360K, the adsorption free energy is found to be positive.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Hu Q, Zhao H, Ouyang S, Liang Y, Yang H, Zhu X. The water structure around chloride ion investigated from D2O ↔ H2O substitution effect. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
13
|
Falyouna O, Maamoun I, Ghosh S, Malloum A, Othmani A, Eljamal O, Amen TW, Oroke A, Bornman C, Ahmadi S, Hadi Dehghani M, Hossein Mahvi A, Nasseri S, Tyagi I, Suhas, Reddy Koduru J. Sustainable Technologies for the Removal of Chloramphenicol from Pharmaceutical Industries Effluent: A critical review. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
14
|
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
| |
Collapse
|
15
|
Otlyotov AA, Minenkov Y. Conformational energies of microsolvated Na + clusters with protic and aprotic solvents from GFNn-xTB methods. J Comput Chem 2022; 43:1856-1863. [PMID: 36053781 DOI: 10.1002/jcc.26988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022]
Abstract
Performance of contemporary tight-binding semiempirical GFNn-xTB methods for the conformational energies of singly charged sodium clusters Na+ (S)n (n = 4-8) with 3 protic and 8 aprotic solvents is examined against the reference RI-MP2/CBS method. The median Pearson correlation coefficients of ρ = 0.84 (GFN2-xTB) and ρ = 0.82 (GFN1-xTB) do not give the clear preference to any tested approach. GFN1-xTB method demonstrates more stable performance than its GFN2-xTB successor with the average mean absolute errors (MAEs)/mean signed errors (MSEs) of 1.2/0.2 and 2.3/1.6 kcal mol-1 , respectively. Conformational energies produced by the computationally efficient DFT functional PBE and double-ζ basis set complemented with -D3(BJ) dispersion correction are suitable for the preliminary sampling (median ρ = 0.93), but should be used with a caution for the calculations of the average ensemble properties (MAE/MSE = 1.7/1.1 kcal mol-1 ). Higher-ranking PBE0-D3(BJ) and ωB97M-V with triple-ζ basis sets yield significantly lower MAEs/MSEs of 0.55/0.20 and 0.51/0.23 kcal mol-1 , respectively.
Collapse
Affiliation(s)
- Arseniy A Otlyotov
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russian Federation
| | - Yury Minenkov
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russian Federation.,Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
16
|
Malloum A, Conradie J. Non-covalent interactions in dimethylsulfoxide (DMSO) clusters and DFT benchmarking. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Malloum A, Conradie J. Dimethylsulfoxide (DMSO) Clusters Dataset: DFT Relative Energies, Non-Covalent Interactions, and Cartesian Coordinates. Data Brief 2022; 42:108024. [PMID: 35313495 PMCID: PMC8933536 DOI: 10.1016/j.dib.2022.108024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/05/2022] Open
Abstract
Theoretical understanding of dimethylsulfoxide (DMSO) liquid depends on the understanding of the DMSO clusters. In this work, we provide the structures and the energetics of the DMSO clusters. The structures have been generated using ABCluster and further optimized at the MP2/aug-cc-pVDZ level of theory. The final structures have been optimized at two different levels of theory: PW6B95D3/aug-cc-pVDZ and ωB97XD/aug-cc-pVDZ. The Cartesian coordinates of the structures optimized at the MP2/aug-cc-pVDZ level of theory are also reported. The relative energies of the structures can be used to locate the most favorable structures of the DMSO clusters. The Cartesian coordinates of the structures can be used for further investigations on DMSO clusters. In addition, we report the data related to the quantum theory of atoms in molecule (QTAIM) analysis of the investigated clusters. The QTAIM data reported in this work can be used to understand and determine the nature of non-covalent interactions in DMSO clusters. For further reading and discussion on the data reported here, please report to the original manuscript Malloum and Conradie (2022) [1].
Collapse
|
18
|
Malloum A, Conradie J. Data to understand the nature of non-covalent interactions in the thiophene clusters. Data Brief 2022; 40:107818. [PMID: 35071711 PMCID: PMC8762079 DOI: 10.1016/j.dib.2022.107818] [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: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022] Open
Abstract
We 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).
Collapse
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, Tromsø N-9037, Norway
| |
Collapse
|
19
|
|
20
|
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].
Collapse
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
| |
Collapse
|
21
|
|
22
|
Malloum A, Conradie J. Structures, binding energies and non-covalent interactions of furan clusters. J Mol Graph Model 2021; 111:108102. [PMID: 34915345 DOI: 10.1016/j.jmgm.2021.108102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022]
Abstract
Understanding of the furan solvent is subjected to the knowledge of the structures of the furan clusters and interactions taking place therein. Although, furan clusters can be very important to determine the dynamics and the properties of the furan solvent, there has been only a few investigations reported on furan dimer. In this work, we have explored the potential energy surfaces (PESs) of the furan clusters using two incremental levels of theory. Structures have been initially generated using classical molecular dynamics followed by full optimization at the MP2/aug-cc-pVDZ level of theory. The results show that the most stable structure of the furan dimer has a stacking configuration while that of the trimer has a cyclic configuration. We have noted that the structures of the furan tetramer have no definite configurations. In addition, we have performed a quantum theory of atoms in molecule (QTAIM) analysis to identify all possible non-covalent interactions of the furan clusters. The results show that six different types of non-covalent interactions can be identified in furan clusters. We have noted that the CH⋯C and CH⋯O hydrogen bondings are the strongest non-covalent interactions while the H⋯H bonding interaction is found to be the weakest. Furthermore, we have assessed the performance of ten DFT functionals in calculating the binding energies of the furan clusters. The ten DFT functionals (M05, M05-2X, M06, M06-2X, M08HX, PBE0, ωB97XD, PW6B95D3, APFD and MN15) have been benchmarked to DLPNO-CCSD(T)/CBS. The functionals M05-2X and M06 are recommended for further affordable investigations of the furan clusters.
Collapse
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
| |
Collapse
|
23
|
Malloum A, Conradie J. Hydrogen bond networks of ammonia clusters: What we know and what we don’t know. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
24
|
|