Pub Date : 2021-12-01DOI: 10.22036/PCR.2021.270358.1878
H. Miran, Zainab N. Jaf, Imad H. Khaleel, Abdulkareem A. Alkhafaji
In this contribution, density functional theory-based calculations have been carried out to assess the electronic, photocatalytic and optical properties of Ce1-xTixO2 system. Ti incorporation leads to a decrease of Ce 4f states and enhancement of Ti 3d states in the bottom of conduction band. Furthermore, it was found that doping ceria with Ti-like transition metals could evidently shift the absorption of pure CeO2 towards higher wavelength range. These findings can provide some new insights for designing CeO2-based photocatalysts with high photocatalytic performance. To the best of our knowledge, this investigation calculates Mullikan’s charge transfer of Ce1-xTixO2 system for the first time. Charge transfer reveals an ionic bond between Ce or Ti and O, and covalent bonds between Ce and Ti atoms in the studies systems.
{"title":"Photocatalytic and Optical Performances of CeO2 by Substitution of Titanium","authors":"H. Miran, Zainab N. Jaf, Imad H. Khaleel, Abdulkareem A. Alkhafaji","doi":"10.22036/PCR.2021.270358.1878","DOIUrl":"https://doi.org/10.22036/PCR.2021.270358.1878","url":null,"abstract":"In this contribution, density functional theory-based calculations have been carried out to assess the electronic, photocatalytic and optical properties of Ce1-xTixO2 system. Ti incorporation leads to a decrease of Ce 4f states and enhancement of Ti 3d states in the bottom of conduction band. Furthermore, it was found that doping ceria with Ti-like transition metals could evidently shift the absorption of pure CeO2 towards higher wavelength range. These findings can provide some new insights for designing CeO2-based photocatalysts with high photocatalytic performance. To the best of our knowledge, this investigation calculates Mullikan’s charge transfer of Ce1-xTixO2 system for the first time. Charge transfer reveals an ionic bond between Ce or Ti and O, and covalent bonds between Ce and Ti atoms in the studies systems.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"553-564"},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44111287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-12-01DOI: 10.22036/PCR.2021.270810.1880
N. Kolla, SRINIVASs Jaddu, Kavitha Ch, R. Dey
The viscosities of binary mixtures of 1,4-butanediol with o-cresol, m-cresol and p-cresol have been determined at 303.15, 308.15, 313.15 and 318.15 K over the entire mole fraction range. The deviation in viscosity,, and excess Gibbs energy of activation (G*E) of viscous flow have been examined in terms of structural changes and interactions. The deviations/excess values were fitted to the Redlich-Kister equation to determine the fitting parameters and the root-mean square deviations. The results obtained for viscosity of binary mixtures were used to test the semi-empirical relations of Bingham, Frenkel, Kendall, HindUbbelhode, Refutas, Sutherland Wassiljiewa, Gambill, McAllister, Hind, Grunberg, Wijk, McAllister 4 body, Tamura Kurata, Katti-Chaudhri and Nhaesi.
{"title":"Viscometric Properties of Binary Mixtures of 1,4-Butanediol + Cresols at Different Temperatures","authors":"N. Kolla, SRINIVASs Jaddu, Kavitha Ch, R. Dey","doi":"10.22036/PCR.2021.270810.1880","DOIUrl":"https://doi.org/10.22036/PCR.2021.270810.1880","url":null,"abstract":"The viscosities of binary mixtures of 1,4-butanediol with o-cresol, m-cresol and p-cresol have been determined at 303.15, 308.15, 313.15 and 318.15 K over the entire mole fraction range. The deviation in viscosity,, and excess Gibbs energy of activation (G*E) of viscous flow have been examined in terms of structural changes and interactions. The deviations/excess values were fitted to the Redlich-Kister equation to determine the fitting parameters and the root-mean square deviations. The results obtained for viscosity of binary mixtures were used to test the semi-empirical relations of Bingham, Frenkel, Kendall, HindUbbelhode, Refutas, Sutherland Wassiljiewa, Gambill, McAllister, Hind, Grunberg, Wijk, McAllister 4 body, Tamura Kurata, Katti-Chaudhri and Nhaesi.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"579-590"},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48162284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-12-01DOI: 10.22036/PCR.2021.278943.1901
H. Yazid, Y. Achour, A. Kassimi, I. Nadir, M. E. Himri, M. R. Laamari, M. Haddad
Adsorption experiments were carried out as part of the removal of Congo red (CR) as textile dye from aqueous solutions by using the powder of Cuttlefish bone (Sepia) as a new potential adsorbent. The prepared powder was characterized by FTIR, XRD, SEM, and elemental analysis. The effects of solution pH, adsorbent amount, CR concentration, temperature and contact time on the adsorption of CR studied were investigated. The experimental results showed that maximum pH was about 2 for efficient uptake of CR. The equilibrium was attained in 60 min. The adsorption of Congo red was exothermic in nature (ΔH° = 8.41 kJ/mol), while the positive value of entropy 20.85 J/mol.K indicated that the increasing randomness at the solid/liquid interface. The experimental data were analyzed using Langmuir and Freundlich isothermal models. The best fit was obtained by Langmuir model with a maximum monolayer adsorption capacity of 69.9 mg/g. adsorption kinetic data were properly fitted with the pseudo second-order kinetic model.
{"title":"Removal of Congo Red from Aqueous Solution Using Cuttlefish Bone Powder","authors":"H. Yazid, Y. Achour, A. Kassimi, I. Nadir, M. E. Himri, M. R. Laamari, M. Haddad","doi":"10.22036/PCR.2021.278943.1901","DOIUrl":"https://doi.org/10.22036/PCR.2021.278943.1901","url":null,"abstract":"Adsorption experiments were carried out as part of the removal of Congo red (CR) as textile dye from aqueous solutions by using the powder of Cuttlefish bone (Sepia) as a new potential adsorbent. The prepared powder was characterized by FTIR, XRD, SEM, and elemental analysis. The effects of solution pH, adsorbent amount, CR concentration, temperature and contact time on the adsorption of CR studied were investigated. The experimental results showed that maximum pH was about 2 for efficient uptake of CR. The equilibrium was attained in 60 min. The adsorption of Congo red was exothermic in nature (ΔH° = 8.41 kJ/mol), while the positive value of entropy 20.85 J/mol.K indicated that the increasing randomness at the solid/liquid interface. The experimental data were analyzed using Langmuir and Freundlich isothermal models. The best fit was obtained by Langmuir model with a maximum monolayer adsorption capacity of 69.9 mg/g. adsorption kinetic data were properly fitted with the pseudo second-order kinetic model.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"565-577"},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48410557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-12-01DOI: 10.22036/PCR.2021.282662.1909
Benzir Ahmed, Bipul Bezbaruah, Ibrahim Ali, Pratyashee Barukial, M. J. Bezbaruah
Anticancer drugs bind with DNA nucleobase pairs (AT and GC) through different binding modes such as intercalation, groove binding, covalent binding etc. Quantum mechanical DFT method is quite useful for computing the interaction energy value for anticancer drug-DNA nucleobase complexes. In our study, we have taken some of the anticancer drugs to investigate the interaction energy for drug-DNA complexes. Among the different binding modes of anticancer drugs; minor and major groove binding in DNA base pair is also an important aspect for anticancer drugs; therefore some anticancer drugs may be minor groove specific and some may be major groove specific. Since, such sequence-specific experimental studies for drug-DNA nucleobase complexes are very complicated and hence this may be investigated by using quantum mechanical theoretical studies, using M062X basis set. Our studies reveal that the stacked models of anticancer drugs-DNA nucleobase (AT and GC) complexes always show negative interaction energy values and among all such complexes the most negative interaction energy value results the most stable and favoured stacked systems. The stacking interaction energies for anticancer drugs-DNA nucleobase (AT and GC) complexes can easily be reflected in the interaction of energy plots.
{"title":"Quantum Mechanical Study of some Intercalating and Groove Binding Anticancer Drugs with AT and GC Base Pair of DNA Nucleobase","authors":"Benzir Ahmed, Bipul Bezbaruah, Ibrahim Ali, Pratyashee Barukial, M. J. Bezbaruah","doi":"10.22036/PCR.2021.282662.1909","DOIUrl":"https://doi.org/10.22036/PCR.2021.282662.1909","url":null,"abstract":"Anticancer drugs bind with DNA nucleobase pairs (AT and GC) through different binding modes such as intercalation, groove binding, covalent binding etc. Quantum mechanical DFT method is quite useful for computing the interaction energy value for anticancer drug-DNA nucleobase complexes. In our study, we have taken some of the anticancer drugs to investigate the interaction energy for drug-DNA complexes. Among the different binding modes of anticancer drugs; minor and major groove binding in DNA base pair is also an important aspect for anticancer drugs; therefore some anticancer drugs may be minor groove specific and some may be major groove specific. Since, such sequence-specific experimental studies for drug-DNA nucleobase complexes are very complicated and hence this may be investigated by using quantum mechanical theoretical studies, using M062X basis set. Our studies reveal that the stacked models of anticancer drugs-DNA nucleobase (AT and GC) complexes always show negative interaction energy values and among all such complexes the most negative interaction energy value results the most stable and favoured stacked systems. The stacking interaction energies for anticancer drugs-DNA nucleobase (AT and GC) complexes can easily be reflected in the interaction of energy plots.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"673-688"},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49018669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-12-01DOI: 10.22036/PCR.2021.272919.1886
Salma Dhifaoui, A. Azaid, M. Bourass, Laila Ben Haj Hassen, H. Nasri, M. Bouachrine
In this work, the Density Functional Theory (DFT) calculations, the Natural Bond Orbital (NBO) analysis, and the Hirschfeld surface analysis were carried out on the bis(4-cyanopyridine) [(meso-tetrakis(4-metoxyphenylporphyrinato)] iron (III) trifluoro-methane sulfonate chlorobenzene mono-solvate complex (I). The structure of the ferric porphyrin derivative (I) was optimized by using various quantum chemical methods: HF, B3PW91, BPV86, and B3LYP with three bases set 3-21, 6-31 G (d, p), and 6-311 G (d, p). The theoretical structural parameters of (I) are very close to those obtained by X-ray molecular structure. From the optimized structure, several parameters such as the HOMO-LUMO energies, the dipole moments, the molecular electrostatic potentials, the Mulliken electronegativity, the chemical hardness, and the electronic potential were calculated and discussed. On the other hand, the absorption properties of (I) were obtained and compared with those obtained with the experimental UV-visible spectrum. The reactivity of our [FeIII (TMPP) (4-CNpy)2] + ion complex using various descriptors such as local softness, electrophilicity, electronegativity, hardness, HOMO-LUMO gap, were calculated and the Hirschfeld data of the crystal packing of (I) were discussed.
本文通过密度泛函理论(DFT)计算、自然键轨道(NBO)分析和Hirschfeld表面分析对双(4-氰吡啶)[(中四基(4-甲氧基苯基卟啉)]铁(III)三氟甲烷磺酸氯苯单溶剂配合物(I)进行了研究，并利用各种量子化学方法对铁卟啉衍生物(I)的结构进行了优化:HF、B3PW91、BPV86和B3LYP分别具有3-21、6-31 G (d, p)和6-311 G (d, p)三个碱基。(I)的理论结构参数与x射线分子结构得到的参数非常接近。从优化后的结构出发，计算并讨论了HOMO-LUMO能、偶极矩、分子静电势、Mulliken电负性、化学硬度和电子势等参数。另一方面，得到了(I)的吸收特性，并与实验紫外可见光谱得到的吸收特性进行了比较。用局部柔软度、亲电性、电负性、硬度、HOMO-LUMO间隙等描述符计算了[FeIII (TMPP) (4-CNpy)2] +离子配合物的反应性，并讨论了(I)晶体填充物的Hirschfeld数据。
{"title":"DFT Studies on Molecular Structure, Absorption properties, NBO Analysis, and Hirshfeld Surface Analysis of Iron(III) Porphyrin Complex","authors":"Salma Dhifaoui, A. Azaid, M. Bourass, Laila Ben Haj Hassen, H. Nasri, M. Bouachrine","doi":"10.22036/PCR.2021.272919.1886","DOIUrl":"https://doi.org/10.22036/PCR.2021.272919.1886","url":null,"abstract":"In this work, the Density Functional Theory (DFT) calculations, the Natural Bond Orbital (NBO) analysis, and the Hirschfeld surface analysis were carried out on the bis(4-cyanopyridine) [(meso-tetrakis(4-metoxyphenylporphyrinato)] iron (III) trifluoro-methane sulfonate chlorobenzene mono-solvate complex (I). The structure of the ferric porphyrin derivative (I) was optimized by using various quantum chemical methods: HF, B3PW91, BPV86, and B3LYP with three bases set 3-21, 6-31 G (d, p), and 6-311 G (d, p). The theoretical structural parameters of (I) are very close to those obtained by X-ray molecular structure. From the optimized structure, several parameters such as the HOMO-LUMO energies, the dipole moments, the molecular electrostatic potentials, the Mulliken electronegativity, the chemical hardness, and the electronic potential were calculated and discussed. On the other hand, the absorption properties of (I) were obtained and compared with those obtained with the experimental UV-visible spectrum. The reactivity of our [FeIII (TMPP) (4-CNpy)2] + ion complex using various descriptors such as local softness, electrophilicity, electronegativity, hardness, HOMO-LUMO gap, were calculated and the Hirschfeld data of the crystal packing of (I) were discussed.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"701-713"},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44746234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-01DOI: 10.22036/PCR.2021.247363.1829
Mohaddeseh Bahramian-Nasab, Fatemeh S. Mohseni‐Shahri
The binding of ciprofloxacin (CIP) to bovine serum albumin (BSA) in the existence and absence of 6-shogaol was investigated by multiple techniques. Fluorescence spectroscopy results indicated that CIP was able to be quenching of BSA without and with 6-shogaol by way of a static mechanism. The CIP and 6-shogaol binding to BSA leads to the increase of the binding constant (Ka) value of CIP to BSA. In accordance with the minus amounts of ΔH0 and ΔS0, the functions of hydrogen bond and van der Waals forces are very important all over this special binding. In addition, the minus amounts of ΔH0 and ΔS0 for BSA-CIP in the existence of 6-shogaol have been larger than those of the absence of 6-shogaol, which illustrates the higher importance of hydrogen bonding and van der Waals forces. As indicated by the synchronized fluorescence spectroscopy at Δλ = 60 nm, the location of CIP with mixed BSA in binary and trinary systems has been nearer to Tyr residues.
{"title":"The Influence of 6-Shogaol, a Therapeutic Agent of Zingiber Officinale, on the Interaction of Ciprofloxacin with Bovine Serum Albumin","authors":"Mohaddeseh Bahramian-Nasab, Fatemeh S. Mohseni‐Shahri","doi":"10.22036/PCR.2021.247363.1829","DOIUrl":"https://doi.org/10.22036/PCR.2021.247363.1829","url":null,"abstract":"The binding of ciprofloxacin (CIP) to bovine serum albumin (BSA) in the existence and absence of 6-shogaol was investigated by multiple techniques. Fluorescence spectroscopy results indicated that CIP was able to be quenching of BSA without and with 6-shogaol by way of a static mechanism. The CIP and 6-shogaol binding to BSA leads to the increase of the binding constant (Ka) value of CIP to BSA. In accordance with the minus amounts of ΔH0 and ΔS0, the functions of hydrogen bond and van der Waals forces are very important all over this special binding. In addition, the minus amounts of ΔH0 and ΔS0 for BSA-CIP in the existence of 6-shogaol have been larger than those of the absence of 6-shogaol, which illustrates the higher importance of hydrogen bonding and van der Waals forces. As indicated by the synchronized fluorescence spectroscopy at Δλ = 60 nm, the location of CIP with mixed BSA in binary and trinary systems has been nearer to Tyr residues.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"525-538"},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41534421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-01DOI: 10.22036/PCR.2021.257894.1856
Safia Bouhara, D. Hammoutène
Detecting glyphosate is of great importance as it has been classified as a probable carcinogen. In literature, many nanotubes have been used to detect Glyp among them CNT. However, we did not found any study that used BNNT to detect it. So, in this work, we focus on performing a comparative study of the Glyp adsorption on CNT (5.5) and BNNT (5.5) using B3LYP, M06-2X, and B97X-D/6-31G(d) by first-principles calculations in the framework of Density Functional Theory. From our results, we conclude that the adsorption energies of BNNT (5.5)/Glyp are slightly higher than those calculated by CNT (5.5)/ Glyp and are in very close agreement with the NCI analyses. The thermodynamics parameters also showed that the two nanotubes could detect glyphosate with a physisorption process that was exothermic and thermodynamically favourable. Besides that, TDOS and QTAIM analyses revealed the non-covalent interaction between glyphosate and the two nanotubes.
{"title":"Comparative Study of Glyphosate Adsorption on Armchair CNT(5.5) and BNNT(5.5): A DFT Study","authors":"Safia Bouhara, D. Hammoutène","doi":"10.22036/PCR.2021.257894.1856","DOIUrl":"https://doi.org/10.22036/PCR.2021.257894.1856","url":null,"abstract":"Detecting glyphosate is of great importance as it has been classified as a probable carcinogen. In literature, many nanotubes have been used to detect Glyp among them CNT. However, we did not found any study that used BNNT to detect it. So, in this work, we focus on performing a comparative study of the Glyp adsorption on CNT (5.5) and BNNT (5.5) using B3LYP, M06-2X, and B97X-D/6-31G(d) by first-principles calculations in the framework of Density Functional Theory. From our results, we conclude that the adsorption energies of BNNT (5.5)/Glyp are slightly higher than those calculated by CNT (5.5)/ Glyp and are in very close agreement with the NCI analyses. The thermodynamics parameters also showed that the two nanotubes could detect glyphosate with a physisorption process that was exothermic and thermodynamically favourable. Besides that, TDOS and QTAIM analyses revealed the non-covalent interaction between glyphosate and the two nanotubes.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"373-384"},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42312018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-01DOI: 10.22036/PCR.2021.264541.1869
J. Maowa, Hosen, A. Alam, K. M. Rana, Y. Fujii, Y. Ozeki, S. Kawsar
In this investigation, we have optimized uridine and its acylated derivatives employing density functional theory (DFT). All designed derivatives were optimized at the B3LYP/3-21G level of theory. Charge distribution, polarizability, and thermodynamic properties such as free energy, heat capacity, and entropy of modified derivatives were explored in the subsequent analysis to evaluate how certain groups impact the drug properties. To understand the mode of binding and molecular interaction, molecular docking calculation was carried out to point out the potential inhibitors of the SARS-CoV-2 main protease (PDB: 6Y84 and 6LU7) by screening a total of fourteen derivatives which exhibited significant antibacterial and antifungal activities. It was observed that all derivatives were thermodynamically more stable and some of them were more chemically reactive than others. Most of the compounds, studied out here could bind near the crucial catalytic residues, HIS41, and CYS145 of the main protease, and the compounds were surrounded by other active site residues like GLY143, MET49, MET165, GLY143, HIS163, PRO168, GLU166, GLN189, and SER144. Finally, all the modified uridine derivatives were analyzed in silico ADMET and drug-like properties. Our patulous computational and statistical analysis showed that these selected uridine derivatives may use as potential inhibitors against the SARS-CoV-2 Mpro.
{"title":"Pharmacokinetics and Molecular Docking Studies of Uridine Derivatives as SARS-COV-2 Mpro Inhibitors","authors":"J. Maowa, Hosen, A. Alam, K. M. Rana, Y. Fujii, Y. Ozeki, S. Kawsar","doi":"10.22036/PCR.2021.264541.1869","DOIUrl":"https://doi.org/10.22036/PCR.2021.264541.1869","url":null,"abstract":"In this investigation, we have optimized uridine and its acylated derivatives employing density functional theory (DFT). All designed derivatives were optimized at the B3LYP/3-21G level of theory. Charge distribution, polarizability, and thermodynamic properties such as free energy, heat capacity, and entropy of modified derivatives were explored in the subsequent analysis to evaluate how certain groups impact the drug properties. To understand the mode of binding and molecular interaction, molecular docking calculation was carried out to point out the potential inhibitors of the SARS-CoV-2 main protease (PDB: 6Y84 and 6LU7) by screening a total of fourteen derivatives which exhibited significant antibacterial and antifungal activities. It was observed that all derivatives were thermodynamically more stable and some of them were more chemically reactive than others. Most of the compounds, studied out here could bind near the crucial catalytic residues, HIS41, and CYS145 of the main protease, and the compounds were surrounded by other active site residues like GLY143, MET49, MET165, GLY143, HIS163, PRO168, GLU166, GLN189, and SER144. Finally, all the modified uridine derivatives were analyzed in silico ADMET and drug-like properties. Our patulous computational and statistical analysis showed that these selected uridine derivatives may use as potential inhibitors against the SARS-CoV-2 Mpro.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"385-412"},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42021899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-01DOI: 10.22036/PCR.2021.241166.1798
Homa Moghadam, B. Ghalami-Choobar, Mojgan Shafaghat-Lonbar
In this study, phosphorus trichloride (PCl3) and phosphorus triiodide (PI3) as the condensed inorganic materials were investigated based on the molecular dynamics simulation. To this purpose, molecular dynamics simulations were performed by applying force field parameters derived from the quantum chemistry approach. The potential energy data were computed at the B3LYP/6-31+G (d) and B3LYP/dgdzvpd levels of theory for different configurations of PCl3 and PI3, respectively. To determine force field parameters, a four-site all-atom force field model was used to correlate the potential energy data. Therefore, the force field parameters were applied to perform the molecular dynamics simulations. The MD simulations were performed to obtain the atomic number density, enthalpy, heat capacity, and radial distribution function in the NPT and NVT ensembles for PCl3 and PI3 dimers. There is a good consistency between the experimental data and simulation results over a wide range of experimental conditions.
{"title":"Molecular Dynamics Simulation of Phosphorus Trichloride (PCl3) and Phosphorus Triiodide (PI3) Liquids by Using the Force-fields Derived from a Quantum Chemical Approach","authors":"Homa Moghadam, B. Ghalami-Choobar, Mojgan Shafaghat-Lonbar","doi":"10.22036/PCR.2021.241166.1798","DOIUrl":"https://doi.org/10.22036/PCR.2021.241166.1798","url":null,"abstract":"In this study, phosphorus trichloride (PCl3) and phosphorus triiodide (PI3) as the condensed inorganic materials were investigated based on the molecular dynamics simulation. To this purpose, molecular dynamics simulations were performed by applying force field parameters derived from the quantum chemistry approach. The potential energy data were computed at the B3LYP/6-31+G (d) and B3LYP/dgdzvpd levels of theory for different configurations of PCl3 and PI3, respectively. To determine force field parameters, a four-site all-atom force field model was used to correlate the potential energy data. Therefore, the force field parameters were applied to perform the molecular dynamics simulations. The MD simulations were performed to obtain the atomic number density, enthalpy, heat capacity, and radial distribution function in the NPT and NVT ensembles for PCl3 and PI3 dimers. There is a good consistency between the experimental data and simulation results over a wide range of experimental conditions.","PeriodicalId":20084,"journal":{"name":"Physical Chemistry Research","volume":"9 1","pages":"509-523"},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44857188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-01DOI: 10.22036/PCR.2021.276552.1902
Hossein Malekhossini, K. Mahanpoor
ZnFe2O4/Copper slag (CS) which is an environmentally friendly and cost-effective catalyst was produced by co-precipitation methods and a thermal process. The synthesized catalyst was characterized by XRD, SEM, EDX and BET surface area analysis. The X-rays diffraction pattern confirmed that the crystal structure of ZnFe2O4 after stabilization on CS zeolite has not changed. The SEM images showed that, despite their varying sizes, the particles all have the same shape. Photocatalytic activity of the catalyst was tested for the degradation of ethylbenzene (EB) in water by UV + H2O2 method in the reverse-flow packed bed photo reactor. The process optimization and modeling were performed using the full factorial method. The initial concentration of EB = 30 ppm, pH = 9 and initial H2O2 concentration = 15 ppm were the best conditions. Under ideal process conditions, the removal efficiency of EB was greater than 99.5%. The validity of the Langmuir-Hinshelwood kinetics model was confirmed using EB photocatalytic degradation experimental results. The values of 〖∆H〗^⫲and 〖∆S〗^⫲ for the photocatalytic degradation of EB by ZnFe2O4/CS catalyst in the UV+H2O2 process were calculated based on the transition state theory and gave 1.67 kJ mol-1 and -263.057 J K-1 mol-1 respectively.
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