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1.
Environ Pollut ; 357: 124407, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38908679

ABSTRACT

Polychlorinated naphthalenes (PCNs) were included in the banned list of the Stockholm Convention due to their potential to provoke a wide range of adverse effects on living organisms and the environment. Many reviews have been written to clarify the state of knowledge and identify the research needs of this pollutant class. However, studies have yet to analyse the scientometric complexities of PCN literature. In this study, we used bibliometric R and vosviewer programs as a scientometric tool to fill this gap by focusing on articles indexed on Web of Science and Scopus databases and those published between 1973 and 2022. A total of 707 articles were published within this period with a publication/author, author/publication, and co-authors/publication ratios of 0.45, 2.19, and 4.86, respectively. Developed countries dominated most scientometric indices (number of publications, citations, and collaboration networks) in the survey period. Lotka's inverse square rule of author productivity showed that Lotka's laws do not fit PCN literature. An annual percentage growth rate of 7.46% and a Kolmogorov-Smirnoff goodness-of-fit of 0.88 suggests that more output on PCNs is likely in years to come. More research is needed from scholars from developing countries to measure the supremacy of the developed nations and to effectively comply with the Stockholm Convention agreement.

3.
J Comput Chem ; 45(15): 1279-1288, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38353541

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.

4.
J Mol Model ; 30(2): 38, 2024 Jan 12.
Article in English | MEDLINE | ID: mdl-38214749

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.

5.
Environ Res ; 243: 117870, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38072111

ABSTRACT

The class of insecticides known as neonicotinoid insecticides has gained extensive application worldwide. Two characteristics of neonicotinoid pesticides are excellent insecticidal activity and a wide insecticidal spectrum for problematic insects. Neonicotinoid pesticides can also successfully manage pest insects that have developed resistance to other insecticide classes. Due to its powerful insecticidal properties and rapid plant absorption and translocation, dinotefuran, the most recent generation of neonicotinoid insecticides, has been widely used against biting and sucking insects. Dinotefuran has a wide range of potential applications and is often used globally. However, there is growing evidence that they negatively impact the biodiversity of organisms in agricultural settings as well as non-target organisms. The objective of this review is to present an updated summary of current understanding regarding the non-target effects of dinotefuran; we also enumerated nano- and bio-based mitigation and management strategies to reduce the impact of dinotefuran on non-target organisms and to pinpoint knowledge gaps. Finally, future study directions are suggested based on the limitations of the existing studies, with the goal of providing a scientific basis for risk assessment and the prudent use of these insecticides.


Subject(s)
Guanidines , Insecticides , Animals , Insecticides/toxicity , Ecosystem , Neonicotinoids/toxicity , Nitro Compounds/toxicity , Insecta
6.
J Mol Graph Model ; 126: 108661, 2024 01.
Article in English | MEDLINE | ID: mdl-37913567

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.


Subject(s)
Dimethyl Sulfoxide , Molecular Dynamics Simulation , Thermodynamics , Isomerism , Quantum Theory , Polymers
7.
Heliyon ; 9(12): e22187, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38076079

ABSTRACT

Amodiaquine (AQ) was synthesized by a condensation reaction and characterized by experimental FT-IR, 1H and 13C nuclear magnetic resonance (NMR) and UV spectroscopies. In the present work, Density Functional Theory (DFT) calculations. The structural and spectroscopic (FT-IR, 1H and 13C NMR and UV) data of amodiaquine molecule in ground state have been investigated by using Density Functional Theory (DFT). The calculations have been performed at the using B3LYP method with 6-311++G(d,p) and 6-311++G(2d, p) basis sets theory level were performed, first, to confirm its structure, then to explain its reactive nature through its molecular properties such as natural charges, local and global reactivity descriptors or natural bond orbital (NBO). Afterwards, the calculated properties were compared with experimental results. The 1H and 13C NMR chemical shifts were calculated by using the gauge-independent atomic orbital (GIAO) method, while the electronic UV-Vis spectrum is predicted using the time-dependent density functional theory (TD-DFT). Globally, the computerized results showed good agreement close similarity with the experimental values. The molecular properties such as natural charges, local and global reactivity descriptors, molecular electrostatic potential (MEP), natural bond orbital (NBO) of title molecule were calculated insights into the stability, reactivity and reactive sites on the molecule. The calculated energy band gap (ELUMO-EHOMO) value of AQ was found to be 4.09 eV suggesting that it could be considered as a hard molecule with high stability, supported by global reactivity descriptors. Molecular electrostatic potential (MEP) analysis revealed heteroatoms (oxygen and nitrogen) as the most putative nucleophilic sites when hydrogen atoms to which they are linked appear as electrophilic sites. The potential use of amodiaquine as non-linear optical (NLO) material and its thermodynamic indicators have also been assessed.

8.
J Mol Model ; 29(12): 380, 2023 Nov 18.
Article in English | MEDLINE | ID: mdl-37979000

ABSTRACT

CONTEXT: The search for highly efficient adsorbent materials remains a significant requirement in the field of adsorption for wastewater treatment. Computational study can highly contribute to the identification of efficient material. In this work, we propose a computational approach to study the adsorption of four cationic basic dyes, basic blue 26 (BB26), basic green 1 (BG1), basic yellow 2 (BY2), and basic red 1 (BR1), onto two models of graphene oxide as adsorbents. The main objectives of this study are the assessment of the adsorption capacity of the graphene oxide towards basic dyes and the evaluation of the environmental and temperature effects on the adsorption capacity. Quantum theory of atoms in molecules (QTAIM) analysis has been used to understand the interactions between the dyes and graphene oxides. In addition, adsorption free energies of the dyes onto graphene oxides are calculated in gas and solvent phases for temperatures varying from 200 to 400 K. As a result, the adsorption free energy varies linearly depending on the temperature, highlighting the importance of temperature effects in the adsorption processes. Furthermore, the results indicate that the environment (through the solvation) considerably affects the calculated adsorption free energies. Overall, the results show that the two models of graphene oxide used in this work are efficient for removing dyes from wastewater. METHODS: We have optimized the complexes formed by the interaction of dyes with graphene oxides at the PW6B95-D3/def2-SVP level of theory. The SMD solvation model realizes the implicit solvation, and water is used as the solvent. Calculations are performed using the Gaussian 16 suite of program. QTAIM analysis is performed using the AIMAll program. Gibbs free energies as function of temperature are calculated using the TEMPO program.

9.
J Phys Chem A ; 127(5): 1103-1111, 2023 Feb 09.
Article in English | MEDLINE | ID: mdl-36716408

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.

10.
J Mol Graph Model ; 118: 108363, 2023 01.
Article in English | MEDLINE | ID: mdl-36308947

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.


Subject(s)
Dimethyl Sulfoxide , Quantum Theory , Hydrogen Bonding , Dimethyl Sulfoxide/chemistry , Water/chemistry , Molecular Dynamics Simulation
11.
J Mol Graph Model ; 118: 108375, 2023 01.
Article in English | MEDLINE | ID: mdl-36423517

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.


Subject(s)
Phenol , Phenols , Solvents , Temperature , Water
12.
J Mol Model ; 29(1): 1, 2022 Dec 05.
Article in English | MEDLINE | ID: mdl-36469138

ABSTRACT

Optoelectrical, electronic, and thermodynamic properties of {6}cycloparaphenylene ({6}CPP) and its derivative, N,N-dimethyl-diaza{6}cycloparaphenylene (DMDA{6}CPP), are theoretically investigated in this work. Using the density functional theory (DFT) and time-dependent DFT (TD-DFT) supported by the APFD and B3LYP-D3 functionals and the 6-311++G (d,p) basis set, the new compound, DMDA{6}CPP, revealed an optical band gap [Formula: see text] eV. With the lowest energy transition excited state recorded at [Formula: see text] and associated light-harvesting efficiency (LHE)[Formula: see text], this derivative demonstrates good characteristics as absorber material in organic solar cell (OSC) devices. The analysis of its charge transport abilities exhibits a ratio of hole/electron reorganization energies [Formula: see text], providing very consistent information on good hole transport abilities. Moreover, this derivative of {6}CPP registered amazing linear and NLO properties with polarizability and first-order hyperpolarizability [Formula: see text] a.u and [Formula: see text] a.u, respectively. These values are far higher than those of both para-nitro aniline (p-NA) and urea commonly used as reference molecules in linear and nonlinear optics, positioning this molecule as a perfect candidate for NLO applications and optoelectronics. Molecular atomization energy calculation, spectra analysis, and thermodynamic descriptor calculations have also revealed a very stable structure.

13.
J Mol Graph Model ; 117: 108287, 2022 12.
Article in English | MEDLINE | ID: mdl-35969938

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.


Subject(s)
Environmental Pollutants , Wastewater , Aniline Compounds , Solvents , Thermodynamics , Water
14.
Data Brief ; 42: 108024, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35313495

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 ω B97XD/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].

15.
Data Brief ; 41: 107840, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35146081

ABSTRACT

We have established a design to increase the absorption capacity, optoelectronic, linear and nonlinear optical properties of the graphene oxide nanosheet (GON) based on the coronene molecule [C24H12] with the help of doping, using the aluminum atom. The attachment of functional groups to the coronene surface was defined according to the Lerf-Klinowski model, based on experimental predictions [1]. Two GON structures (GON1 and GON2 with formula (C24H11)(O)(OH)COOH)) have been proposed for this purpose, and it should be noted that each of them is distinguished by a different distribution of functional groups within their honeycomb lattice. A series of substitutions of the carbon atoms of the two isomers considered GON1 and GON2 were performed with the aluminum atom, resulting in the abbreviated derivative systems GON1-Alx and GON2-Alx (x = 1-6), respectively to each of the GON1 and GON2 units. In this work, we provide data carried out in the gas phase, from density functional theory (DFT) methods that allowed us to understand the effects of aluminum atom doping on the circular graphene oxide nanosheets. First, we report the wavenumber data related to the IR spectrum peak characteristics computed at the B3LYP, B3LYP-D3 and ωB97XD/6-31+G(d,p) levels of theory, that allowed us to validate the designs of both proposed graphene oxide models. Then, we provide electronic, reactivity, optoelectronic, linear and nonlinear optical data parameters of both graphene oxide nanosheets and their aluminum-doped derivatives computed at the B3LYP, B3LYP-D3 and /6-31+G(d,p) levels of theory. Finally the UV-vis spectra of the investigated compounds evaluated from time-dependent (TD) B3LYP and B3LYP-D3/6-31+G(d,p) levels of theory and the HOMO & LUMO orbitals of the derivatives of graphene oxide isomers computed at the B3LYP/6-31+G(d,p) level of theory are provided. In addition, the raw data of UV-vis spectra, optoelectronic parameters, Cartesian coordinates of all studied compounds and also those of IR spectra of both studied graphene oxide models are provided as supplementary file. The data reported in this work are useful to expose some specific positions of aluminum within circular model of graphene oxide nanosheet that improve its electronic, reactive, optoelectronic, linear and nonlinear optical characteristics. All the formulas and details of calculation performed to obtain the data reported in this work are provided in our previous work (Foadin et al., 2020) and summarized in the experimental section of this paper. To learn more about the ideal doping positions of the aluminum atom within both proposed graphene oxide designs that increase their electronic, reactivity, optoelectronic, linear optical and nonlinear optical properties, respectively, please see the corresponding main research paper (Foadin et al., 2022).

16.
J Mol Graph Model ; 113: 108141, 2022 06.
Article in English | MEDLINE | ID: mdl-35180573

ABSTRACT

We have theoretically conducted a comprehensive investigation on the cyclocondensation reaction between ciprofloxacin and thiosemicarbazide at the MN15/6-311++G(d,p) level of approximation. In order to revisit and understand the sequence of electronic flow rearrangement, as described in terms of electron pair distribution, within the framework of Bonding Evolution Theory (BET) approach as provided by the application of Thom's elementary Catastrophe Theory (CT) to the changes, along the intrinsic reaction coordinate, of the gradient vector field of the electron localization function (ELF). This reaction has two channels (a and b) and each one takes place via three steps. The CDFT results show that ciprofloxacin and thiosemicarbazide have an electrophilic and nucleophilic characters respectively and therefore allowing this reaction to have a polar character. All the transition state (TS) of all reaction steps have been localized and characterized. In addition, the analysis of activation energy predicts the formation of ciprofloxacin thiosemicarbazone 3a (channels a) as a main product in good agreement with experimental outcomes. The BET analysis results along channel a reveal that the mechanism for each reaction step is divided into four structural stability domains. During the first step, a new N2-C2 bond occurs at the SSD-II, followed by a rupture of the H1-N2 single bond (SSD-III) illustrating the restoration of lone pairs of the N2 nitrogen atom, and finally, the formation of a new H1-O1 single bond. For the second step, the process involves the breaking of O1-C2 and N2-H3 bonds at the SSD-II and SSD-III, respectively, followed by the formation of O1-H3 bond at the SSD-IV. For the last step, it is noted the formation of C4-N8 bond at the SSD-II, followed by the breaking of N8-H9 and C4-O6 bonds simultaneously at the SSD-III with water elimination at the last domain (SSD-IV).


Subject(s)
Ciprofloxacin , Electrons , Semicarbazides
17.
Data Brief ; 40: 107766, 2022 Feb.
Article in English | MEDLINE | ID: mdl-35005152

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].

18.
Data Brief ; 40: 107818, 2022 Feb.
Article in English | MEDLINE | ID: mdl-35071711

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).

19.
J Mol Graph Model ; 111: 108102, 2022 03.
Article in English | MEDLINE | ID: mdl-34915345

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.


Subject(s)
Furans , Quantum Theory , Hydrogen Bonding
20.
J Mol Graph Model ; 111: 108075, 2022 03.
Article in English | MEDLINE | ID: mdl-34894437

ABSTRACT

We studied the absorption capacity, optoelectronic and non-linear optical (NLO) properties of graphene oxide nanosheet (GON) and its doped derivatives with aluminum (-Al) atoms. The investigations have been performed using three functionals (B3LYP, B3LYP-D3 and ωB97XD) of the density functional theory (DFT) associated to the basis set 6-31+G(d,p). Aluminum atoms were incorporated into GON at different sites in order to search for suitable candidates that could lead to the enhancement of NLO properties and decrease the band gap value of pristine graphene oxide. As per our molecular investigations, several doped molecular design schemes based on push-pull models of GON were proposed. The best electronic and NLO configurations responses highlight the doped derivatives which were obtained by replacement of carbon atoms which support the functional groups present on the honeycomb lattice of GON with -Al atoms.


Subject(s)
Graphite , Electronics , Models, Molecular
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