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Matveychuk YV, Regel RL, Bartashevich EV. Noncovalent Interactions of Silatranes and Germatranes with the Surface of Stoichiometric and Hydroxylated 2D Silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:13227-13235. [PMID: 38870102 DOI: 10.1021/acs.langmuir.4c01367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Analysis of noncovalent interactions formed by the surface of a 2D silica bilayer and atrane molecules, as precursors of functional layers immobilized on a surface of silicatene, was performed. For this purpose, the systems of substituted silatranes and germatranes adsorbed on silicatene surfaces with different amounts of hydroxyl groups (0, 2, 4, and 30 per cell) were simulated by using quantum chemical modeling with periodic boundary conditions and full-electron basis sets. The observation results for interaction energy changes in the systems "atrane molecule-silicatene surface" with increasing silanol number of the silicatene surface can be used to predict the optimal degree of silicatene hydroxylation in order to control the effective progress of atrane deprotection on activated 2D silica materials. In addition to the typical hydrogen bonds, the ability of atranes to form noncovalent O···O and O···Hal interactions was discovered. In these bonds, the oxygen or halogen atoms of atranes act as electron-donor centers in relation to the silicatene oxygen atoms. The observed weakening of the Ge-O covalent bonds in germatranes, on which further deprotection reaction depends, is more manifested than for the Si-O bonds in adsorbed silatranes.
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Affiliation(s)
- Yury V Matveychuk
- MMMFM Research Laboratory, South Ural State University, Chelyabinsk 454080, Russia
| | - Roman L Regel
- MMMFM Research Laboratory, South Ural State University, Chelyabinsk 454080, Russia
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2
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Bubnov MP, Zolotukhin AA, Fukin GK, Rumyantcev RV, Bogomyakov AS. Valence tautomeric interconversion of bis-dioxolene cobalt complex with imino-pyridine functionalized by TEMPO moiety in solid solutions with isostructural nickel analogue: phase transitions and monocrystal destruction. Dalton Trans 2024; 53:9151-9160. [PMID: 38742270 DOI: 10.1039/d4dt00453a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Valence tautomeric complexes (VT) are promising systems for creating molecular devices. From this viewpoint, valence tautomeric complexes with a hysteresis loop on the magnetic curve are of special interest as potential memory elements. The hysteresis loop is a consequence of retarded structural rearrangements which investigation is an actual problem. Recently, we have described a new VT transition taking place in a bis-dioxolene cobalt complex with imino-pyridine having a TEMPO substituent (A. A. Zolotukhin, et al., Inorg. Chem., 2017, 56, 14751-14754). Valence tautomeric transformation occurs with a hysteresis loop and is accompanied by a phase transition. The phase transition taking place during cooling is accompanied by crystal destruction. This fact makes it impossible to monitor the structural changes responsible for the hysteresis loop. The current research attempts to resolve this problem. A nickel compound of the same composition (TEMPO-imino-pyridine)Ni(3,6-DBSQ)2 was synthesized and characterized. It was established to be isostructural with the cobalt complex. It was used as an inert matrix for the dilution of the VT cobalt complex. The number of solid solutions with Co/Ni ratios of 1 : 1, 1 : 2, 1 : 4, and 1 : 8 was obtained. Variable temperature magnetic susceptibility measurements show that VT transformation with a hysteresis loop takes place in all solid solutions. The hysteresis loop is shifted to low temperatures primarily due to the shifting of its low-temperature boundary with dilution. The hysteresis width does not change significantly with dilution. DSC detected that transformations are accompanied by phase transitions at different temperatures at cooling and heating. The phase transition at the first cooling occurs at slightly lower temperatures compared with subsequent cycles. These temperatures correspond to the transition temperatures detected from the magnetic curves. The phase transition during the first cooling is accompanied by crystal destruction. Physical destruction takes place in the crystals of all solid solutions. X-ray diffraction powder patterns confirm that phase transition is accompanied by considerable reorganization of the crystal structure typical for the first order transitions. The unit cell volume of solid solutions is larger than that of pure complexes. Especially calculated crystal invariom indicated that the "lattice energy" in a solid solution is the lowest compared with that in "pure" nickel and cobalt complexes.
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Affiliation(s)
- Michael P Bubnov
- G. A. Razuvaev Institute of Organometallic Chemistry of RAS, 49 Tropinina Str., GSP-445, 603950 Nizhny Novgorod, Russia.
| | - Alexey A Zolotukhin
- G. A. Razuvaev Institute of Organometallic Chemistry of RAS, 49 Tropinina Str., GSP-445, 603950 Nizhny Novgorod, Russia.
| | - Georgy K Fukin
- G. A. Razuvaev Institute of Organometallic Chemistry of RAS, 49 Tropinina Str., GSP-445, 603950 Nizhny Novgorod, Russia.
| | - Roman V Rumyantcev
- G. A. Razuvaev Institute of Organometallic Chemistry of RAS, 49 Tropinina Str., GSP-445, 603950 Nizhny Novgorod, Russia.
| | - Artem S Bogomyakov
- International Tomography Center of the SB of RAS, Institutskaya Str., 3a, Novosibirsk 630090, Russia.
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El Bakri Y, Ahmad B, Saravanan K, Ahmad I, Bakhite EA, Younis O, Al-Waleedy SAH, Ibrahim OF, Nafady A, Mague JT, Mohamed SK. Insight into crystal structures and identification of potential styrylthieno[2,3- b]pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach. J Biomol Struct Dyn 2024; 42:4325-4343. [PMID: 37318002 DOI: 10.1080/07391102.2023.2220799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Basharat Ahmad
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Etify A Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Osama Younis
- Chemistry Department, Faculty of Science, the New Valley University, El-Kharja, Egypt
| | | | - Omaima F Ibrahim
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Ayman Nafady
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, England
- Chemistry Department, Faculty of Science, Minia University, El-Minia, Egypt
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Hannachi A, El Bakri Y, Saravanan K, Gómez-García CJ, Abuelizz HA, Al-Salahi R, Smirani W. Metamagnetism and canted antiferromagnetic ordering in two monomeric Co II complexes with 1-(2-pyrimidyl)piperazine. Hirshfeld surface analysis and theoretical studies. RSC Adv 2024; 14:11557-11569. [PMID: 38601708 PMCID: PMC11004733 DOI: 10.1039/d4ra00716f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Here we present the magnetic properties of two cobalt complexes formulated as: [Co(SCN)2(L)2] (1) and (H2L)2[Co(SCN)4]·H2O (2) (L = 1-(2-pyrimidyl)piperazine). The two compounds contain isolated tetrahedral CoII complexes with important intermolecular interactions that lead to the presence of a canted antiferromagnetic order below 11.5 and 10.0 K, with coercive fields at 2 K of 38 and 68 mT, respectively. Theoretical calculations have been used to explain this behaviour. Hirshfeld surface analysis shows the presence of strong intermolecular interactions in both compounds. The crystal geometries were used for geometry optimization using the DFT method. From the topological properties, electrostatic potential maps and molecular orbital analysis, information about the noncovalent interaction and chemical reactivity was obtained.
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Affiliation(s)
- Anissa Hannachi
- Laboratory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage 7021 Zarzouna Bizerte Tunisia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University Lenin Prospect 76 Chelyabinsk 454080 Russian Federation
| | | | - Carlos J Gómez-García
- Departamento de Química Inorgánica, Universidad de Valencia C/Dr Moliner 50, 46100 Burjasot Valencia Spain
| | - Hatem A Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
| | - Wajda Smirani
- Laboratory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage 7021 Zarzouna Bizerte Tunisia
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Karthikeyan S, Sundaramoorthy A, Kandasamy S, Bharanidharan G, Aruna P, Suganya R, Mangaiyarkarasi R, Ganesan S, Pandian GN, Ramamoorthi A, Chinnathambi S. A biophysical approach of tyrphostin AG879 binding information in: bovine serum albumin, human ErbB2, c-RAF1 kinase, SARS-CoV-2 main protease and angiotensin-converting enzyme 2. J Biomol Struct Dyn 2024; 42:1455-1468. [PMID: 37114656 DOI: 10.1080/07391102.2023.2204368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/01/2023] [Indexed: 04/29/2023]
Abstract
Viral infections cause significant health problems all over the world, and it is critical to develop treatments for these problems. Antivirals that target viral genome-encoded proteins frequently cause the virus to become more resistant to treatment. Because viruses rely on several cellular proteins and phosphorylation processes that are essential to their life cycle, drugs targeting host-based targets could be a viable treatment option. To reduce costs and improve efficiency, existing kinase inhibitors could be repurposed as antiviral medications; however, this method rarely works, and specific biophysical approaches are required in the field. Because of the widespread use of FDA-approved kinase inhibitors, it is now possible to better understand how host kinases contribute to viral infection. The purpose of this article is to investigate the tyrphostin AG879 (Tyrosine kinase inhibitor) binding information in Bovine Serum Albumin (BSA), human ErbB2 (HER2), C-RAF1 Kinase (c-RAF), SARS-CoV-2 main protease (COVID 19), and Angiotensin-converting enzyme 2 (ACE-2).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subramani Karthikeyan
- Division of Physics, School of Advanced Sciences, Vellore Institute of Technology University, Chennai, India
| | | | | | | | | | | | | | | | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
| | | | - Shanmugavel Chinnathambi
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan
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6
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Mookkan M, Kandasamy S, Al-Odayni AB, Abduh NAY, Srinivasan S, Revannasidappa BC, Kumar V, Chinnasamy K, Aravindhan S, Shankar MK. A Structural and In Silico Investigation of Potential CDC7 Kinase Enzyme Inhibitors. ACS OMEGA 2023; 8:47187-47200. [PMID: 38107948 PMCID: PMC10719926 DOI: 10.1021/acsomega.3c07059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
A crucial role in the regulation of DNA replication is played by the highly conserved CDC kinase. The CDC7 kinase could serve as a target for therapeutic intervention in cancer. The primary heterocyclic substance is pyrazole, and its derivatives offer great potential as treatments for cancer cell lines. Here, we synthesized the two pyrazole derivatives: 4-(2-(4-chlorophenyl)hydrazinyl)-5-methyl-2-tosyl-1H-pyrazol-3(2H)-one (PYRA-1) and 4-(2-(2,4-difluorophenyl)hydrazinyl)-5-methyl-2-tosyl-1H-pyrazol-3(2H)-one (PYRA-2). The structural confirmation of both the compounds at the three-dimensional level is characterized using single crystal X-ray diffraction and density functional theory. Furthermore, the in silico chemical biological properties were derived using molecular docking and molecular dynamics (MD) simulations. PYRA-1 and PYRA-2 crystallize in the P-1 (a = 8.184(9), b = 14.251(13), c = 15.601(15), α = 91.57(8), β = 97.48(9), 92.67(9), V = 1801.1(3) 3, and Z = 2) and P21/n (a = 14.8648(8), b = 8.5998(4), c = 15.5586(8), β = 116.47(7), V = 1780.4(19) 3, and Z = 4), space groups, respectively. In both PYRA-1 and PYRA-2 compounds, C-H···O intermolecular connections are common to stabilize the crystal structure. In addition, short intermolecular interactions stabilizes with C-H···π and π-π stacking. Crystal packing analysis was quantified using Hirshfeld surface analysis resulting in C···H, O···H, and H···H contacts in PYRA-1 exhibiting more contribution than in PYRA-2. The conformational stabilities of the molecules are same in the gas and liquid phases (water and DMSO). The docking scores measured for PYRA-1 and PYRA-2 with CDC7 kinase complexes are -5.421 and -5.884 kcal/mol, respectively. The MD simulations show that PYRA-2 is a more potential inhibitor than PYRA-1 against CDC7 kinase.
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Affiliation(s)
- Mohanbabu Mookkan
- Department
of Physics, Presidency College (Autonomous), University of Madras, Chennai 600 005, India
| | - Saravanan Kandasamy
- Faculty
of Chemistry, University of Warsaw, Ludwika Pasteura 1, Warsaw 02-093, Poland
| | - Abdel-Basit Al-Odayni
- Department
of Restorative Dental Science, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11545, Saudi Arabia
| | - Naaser Ahmed Yaseen Abduh
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sugarthi Srinivasan
- Department
of Physics and Nanotechnology, SRM Institute
of Science and Technology, Kattankulathur 603203, India
| | - Bistuvalli Chandrashekara Revannasidappa
- Department
of Pharmaceutical Chemistry, NGSM Institute
of Pharmaceutical Sciences of Nitte - Deemed to be University, Paneer, Deralakatte, Mangalore 575018, Karnataka India
| | - Vasantha Kumar
- Department
of P.G. Chemistry, Sri Dharmasthala Manjunatheshwara
College (Autonomous), Ujire 574240, India
| | | | - Sanmargam Aravindhan
- Department
of Physics, Presidency College (Autonomous), University of Madras, Chennai 600 005, India
| | - Madan Kumar Shankar
- Department
of Chemistry-BMC, University of Uppsala, Husargatan 3, Uppsala 75237, Sweden
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7
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Kurbanova M, Saravanan K, Ahmad S, Sadigova A, Askerov R, Magerramov A, Bakri YE. Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA. Appl Biochem Biotechnol 2023; 195:5338-5354. [PMID: 35195835 DOI: 10.1007/s12010-022-03849-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/11/2022] [Indexed: 11/02/2022]
Abstract
In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.
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Affiliation(s)
- Malahat Kurbanova
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan.
| | | | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Arzu Sadigova
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan
| | - Rizvan Askerov
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan
| | - Abel Magerramov
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Lenin prospect 76, Chelyabinsk, 454080, Russian Federation.
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Saifina AF, Kartashov SV, Saifina LF, Fayzullin RR. Applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. Chemical bonding and binding features in the crystal and dimer of 1,3-bis(2-hydroxyethyl)-6-methyluracil. IUCRJ 2023; 10:584-602. [PMID: 37668216 PMCID: PMC10478519 DOI: 10.1107/s2052252523007108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
We considered it timely to test the applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. The procedure was carried out on the crystal of 1,3-bis(2-hydroxyethyl)-6-methyluracil, and some derived properties of the scalar potential and vector force fields were compared with those obtained from the experimental multipole model and from the aspherical pseudo-atom model with parameters fitted to the calculated structure factors. The procedure was shown to accurately replicate the general vector-field behavior, the peculiarities of the quantum potentials and the characteristics of the force-field pseudoatoms, such as charge, shape and volume, as well as to reproduce the relative arrangement of atomic and pseudoatomic zero-flux surfaces along internuclear regions. It was found that, in addition to the quantum-topological atoms, the force-field pseudoatoms are spatially reproduced within a single structural fragment and similar environment. In addition, the classical and nonclassical hydrogen bonds in the uracil derivative crystal, as well as the H...O, N...O and N...C interactions in the free π-stacked dimer of the uracil derivative molecules, were studied using the potential and force fields within the concepts of interatomic charge transfer and electron lone pair donation-acceptance. Remarkably, the nitrogen atoms in the N...O and N...C interactions behave rather like a Lewis base and an electron contributor. At the same time, the hydrogen atom in the H...O interaction, being a Lewis acid, also participates in the interatomic electron transfer by acting as a contributor. Thus, it has been argued that, when describing polar interatomic interactions within orbital-free considerations, it makes more physical sense to identify electronegative (electron occupier) and electropositive (electron contributor) atoms or subatomic fragments rather than nucleophilic and electrophilic sites.
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Affiliation(s)
- Alina F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Sergey V. Kartashov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Liliya F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
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Mohamed SK, El Bakri Y, Alfayomy AM, Karthikeyan S, Saravanan K, Abdel-Aziz SA, Abou-Seri SM, Ragab FA, Mague JT, Aboelmagd M. Insights into the crystal structure and computational studies of newly synthesized thiazolopyrimidine derivatives against adenosine receptor (Thermostabilised HUMAN A2a). J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135372] [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]
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10
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El Bakri Y, Mohamed SK, Saravanan K, Ahmad S, Mahmoud AA, Abdel-Raheem SAA, El-Sayed WM, Mague JT, Goumri Said S. 1,4,9,9-tetramethyloctahydro-4,7-(epoxymethano)azulen-5(1 H)-one, a natural product as a potential inhibitor of COVID-19: Extraction, crystal structure, and virtual screening approach. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2023; 35:102628. [PMID: 36908997 PMCID: PMC9984236 DOI: 10.1016/j.jksus.2023.102628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 05/28/2023]
Abstract
In the present work, we describe the extraction of a natural product namely 1,4,9,9-tetramethyloctahydro-4,7-(epoxymethano)azulen-5(1H)-one, and its structure was confirmed by single crystal X-ray diffraction analysis. The conformations of the 5-, 6-, and 7-membered rings in the title compound, C15H24O2, have been probed by a Cremer-Pople puckering analysis. C-H···O hydrogen bonds generate chains in the crystal that stretch along the c-axis direction. The Hirshfeld surface analysis method was used to stabilize the crystal packing of the natural compound. Accompanied by experimental studies, quantum chemical calculations were also performed to compare the structural elucidation and the results of these geometrical parameters exhibited excellent agreement. The compound was also docked with several drug targets of the SARS-CoV-2 virus and found to show the best binding with the main protease enzyme, having a binding energy of -12.31 kcal/mol and interacting with His41 and Cys145 residues. The dynamic stability deciphered the complex to be stable with an average RMSD of 3.8 Å. The compound dynamics with the enzyme showed the compound conformation to be highly stable. The intermolecular binding free energy determined the compound-main protease enzyme to show high interaction energy of < 40 kcal/mol. Together, these studies demonstrate the compound to be a lead structure against SARS-CoV-2.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, United Kingdom
- Chemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt
| | | | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Ahmed A Mahmoud
- Department of Chemistry, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | | | - Wael M El-Sayed
- Department of Zoology, Faculty of Science, University of Ain Shams, Abbassia 11566, Cairo, Egypt
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Souraya Goumri Said
- Physics Department, College of Science and General Studies, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
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11
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Makhlouf J, Bakri YE, Saravanan K, Valkonen A, Smirani W. Self-assembly, physico-chemical characterization, biological and computational approach of novel 2-Amino pyridine derivatives. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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12
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Saravanan K, Sugarthi S, Suganya S, Kumaradhas P. Probing the intermolecular interactions, binding affinity, charge density distribution and dynamics of silibinin in dual targets AChE and BACE1: QTAIM and molecular dynamics perspective. J Biomol Struct Dyn 2022; 40:12880-12894. [PMID: 34637680 DOI: 10.1080/07391102.2021.1977699] [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] [Indexed: 12/27/2022]
Abstract
Alzheimer's disease (AD) is the grievous neurodegenerative disorder. Reportedly, many enzymes are responsible for this disease, in which notably, acetylcholinesterase (AChE) and β-secretase (BACE1) are largely involved for AD. An experimental study reports that silibinin molecule inhibits both AChE and BACE1 enzymes. Present study aims to understand the dual binding mechanism of silibinin in the active site of AChE and BACE1 from the intermolecular interactions, conformational flexibility, charge density distribution, binding energy and the stability of molecule. To obtain the above information, the molecular docking, molecular dynamics (MD) and QTAIM (quantum theory of atoms in molecules) calculations have been performed. The molecular docking reveals that silibinin molecule is forming strong and weak intermolecular interactions with the catalytic site of both enzymes. The QTAIM analysis for the binding pockets of both complexes shows the charge density distribution of intermolecular interactions. The electrostatic potential map displays the electronegative/positive regions at the interaction zone of silibinin with AChE and BACE1 complexes. The MD simulation confirms that the silibinin molecule is stable in the active site of AChE and BACE1 enzymes. The binding free energies of silibinin with both enzymes are more favorable to have the interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India.,Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Srinivasan Sugarthi
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, India
| | - Suresh Suganya
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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13
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Poddel’sky AI, Fukin GK, Baranov EV. Triphenylantimony(V) Complexes Based on o-Aminophenols with the Ambivalent N-Aryl Group. RUSS J COORD CHEM+ 2022. [DOI: 10.1134/s1070328422700166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Gajda R, Piekara A, Tchoń D, Woźniak K, Sławiński WA. Charge density studies of single and transient (single to double) boron-oxygen bonds in (NH 4) 2B 4O 5(OH) 4·2H 2O. Dalton Trans 2022; 51:14865-14874. [PMID: 36165128 DOI: 10.1039/d2dt02442j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A H4B4O92- ion which makes up the (NH4)2B4O5(OH)4·2H2O crystal structure has two types of boron-oxygen bonds, i.e. single B-O bonds and an intermediate between single and double BO bonds. Differences between these two bond types are visible not only because they differ by their lengths but also a topology of electron density distribution differs. This also gives a hint as to how to distinguish between these two bond types. Experimental results based on multipole model refinement gave excellent agreement with theoretical calculations and literature data. Calculations at bond critical points for B-O and BO (electron density, the Laplacian of electron density and the localized-orbital locator function) suggest us how boron-oxygen bonds should be categorised with respect to compounds previously reported in the literature. Additionally, a novel synthesis method for the investigated compound has been developed, which involves crystallization from an aqueous solution of BH3NH3 dissolved in a mixture of tetrahydrofuran and water.
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Affiliation(s)
- Roman Gajda
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Anna Piekara
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Daniel Tchoń
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Krzysztof Woźniak
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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15
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Ferchichi A, Makhlouf J, El Bakri Y, Saravanan K, Valkonen A, Hashem HE, Ahmad S, Smirani W. Self-assembly of new cobalt complexes based on [Co (SCN) 4], synthesis, empirical, antioxidant activity, and quantum theory investigations. Sci Rep 2022; 12:15828. [PMID: 36138056 PMCID: PMC9500081 DOI: 10.1038/s41598-022-18471-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/12/2022] [Indexed: 11/09/2022] Open
Abstract
The cobalt (II) complexes have been synthesized from the reaction of the cationic entities (3,4-dimethylaniline (1) and histamine (2)) with metallic salt CoCl2⋅6H2O and thiocyanate ion (SCN−) as a ligand in H2O/ethanolic solution and processing by the evaporation crystal growth method at room temperature to get crystals. The synthesized complex has been fully characterized by single-crystal X-ray diffraction. UV–Visible, FTIR spectroscopy, TGA analysis, and DFT circulations were also performed. The crystal structural analysis reveals that the solid (1) {[Co(SCN)4] (C8H12N)3}·Cl crystallizes in the monoclinic system with the space group P21/n and the solid (2) {[Co(SCN)4](C5H11N3)2}·2Cl crystallizes in the monoclinic space group P21/m. Metal cations are joined into corrugated chains parallel to the b-axis direction in (1) and (2) by four thiocyanate anions. The crystal structures of (1) and (2) were calculated using XRPD data, indicating that they are closely connected to the DRX mono-crystal results. Different interactions pack the system into a ring formed by N–H⋯Cl and N–H⋯S hydrogen bonds. C–H⋯π and the π⋯π stacking of anilinuim ring for (1) and N–H⋯S intermolecular interactions for (1) and (2) increase the crystals' robustness. Hirshfeld surface analysis cum 2D fingerprint plots visualize the main intermolecular interactions with their contributions in the solid-state phase. The molecular geometries of both complexes obtained from the crystal structure were used for quantum chemical calculation. Here, frontier orbital analysis and electrostatic potential illustrate the chemical reactivities of metal–organic complexes. QTAIM and NCI analysis reveal the strength of interactions at the electronic level.
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Affiliation(s)
- Amal Ferchichi
- Labortory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage, Bizerte Zarzouna, Tunisia
| | - Jawher Makhlouf
- Labortory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage, Bizerte Zarzouna, Tunisia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Lenin Prospect 76, Chelyabinsk, Russian Federation, 454080
| | | | - Arto Valkonen
- Department of Chemistry, University of Jyvaskyla, 40014, Jyvaskyla, Finland
| | - Heba E Hashem
- Department of Chemistry, Faculty of Women, Ain Shams University, Cairo, Egypt.
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Wajda Smirani
- Labortory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage, Bizerte Zarzouna, Tunisia
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16
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Growth, single crystal investigations, Hirshfeld surface analysis, DFT studies, molecular dynamics simulations, molecular docking, physico-chemical characterization and biological activity of novel thiocyanic complex with zinc transition metal precursor. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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El Bakri Y, Saravanan K, Ahmad S, Mague JT. Synthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme. J Biomol Struct Dyn 2022:1-14. [PMID: 35665631 DOI: 10.1080/07391102.2022.2084456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Infection by the human immunodeficiency virus still represents a continuous serious concern and a global threat to human health. Due to the appearance of multi-resistant virus strains and the serious adverse side effects of the antiretroviral therapy administered, there is an urgent need for the development of new treatment agents that are more active, less toxic, and with increased tolerability to mutations. Quinoxaline derivatives are a class of heterocyclic compounds with a wide range of organic and remedial applications. In addition, they are known to significantly inhibit HIV reverse transcriptase (RT) and HIV replication in cell cultures. For these reasons, we are investigating the synthesis and computational studies of quinoxaline derivatives with a focus on their effects on the HIV RT enzyme, and we present here the structure of one such molecule, methyl 2-[(2E)-3-oxo-1,2,3,4-tetrahydroquinoalin-2-ylidene] acetate, which was confirmed by X-ray diffraction studies. In the crystal, N-H···O and C-H···O hydrogen bonds form ribbons whose mean planes are inclined to (111) by 25.69(8)°. The ribbons are formed into stacks by C-H···π(ring) interactions and π-stacking interactions between carbonyl groups. The Hirshfeld surface map allows us to understand the nature of interactions in the contribution to crystal packing. A density functional theory (DFT) calculation was performed to optimize the geometrical parameters and then they were compared with the solid-state phase. The molecular electrostatic potential map displays reactive sites on the surface, which are responsible for intermolecular interaction in the chemical species. Computational molecular docking, in addition to molecular dynamics simulations and MMGB/PBSA binding energy techniques, was used to assess the affinity of the molecule for the HIV reverse transcriptase enzyme. The new quinoxaline derivative is more powerful in terms of binding affinity and binding conformation stability with the HIV reverse transcriptase enzyme, which suggests the molecule is a good candidate for further biological optimization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | | | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, Los Angeles, USA
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18
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Semenov VV, Zolotareva NV, Novikova OV, Petrov BI, Lazarev NM, Fukin GK, Cherkasov AV, Razov EN. Decomposition of zinc (1-hydroxyethylidene)diphosphonate induced by aliphatic amines and ammonia. Molecular structures of ammonium (1-hydroxyethylidene)diphosphonates. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3500-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Stash AI, Tsirelson VG. WinXPRO, 3DPlot and TrajPlot computer software: new options for orbital-free quantum crystallography studies. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576722002321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A multipurpose computer software package for orbital-free quantum crystallography has been developed. Based on multipole experimental electron-density parameters, this software allows users to extract the chemical-bonding information that was previously unavailable for X-ray single-crystal diffraction analysis.
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20
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Complexes of 1-(2-R(F, CH3, Cl)-phenyl)-1,4-dihydro-5H-tetrazole-5-thiones with cadmium chloride: Synthesis, molecular, crystal structures and computational investigation approach. J Inorg Biochem 2022; 231:111791. [DOI: 10.1016/j.jinorgbio.2022.111791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/20/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022]
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21
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Influence of pseudo-polymorphism on the structure and thermal behavior of the new barium β-diketonate complexes [Ba(adtfa)2(18-crown-6)] and [Ba(adtfa)2(18-crown-6)](CDCl3)2. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Akram S, Mehmood A, Noureen S, Ahmed M. Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis. Acta Crystallogr C Struct Chem 2022; 78:72-80. [DOI: 10.1107/s2053229621013607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/27/2021] [Indexed: 11/10/2022] Open
Abstract
Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.
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23
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Bilal A, Mehmood A, Noureen S, Lecomte C, Ahmed M. Crystal engineering of a co-crystal of antipyrine and 2-chlorobenzoic acid: relative energetic contributions based on multipolar refinement. CrystEngComm 2022. [DOI: 10.1039/d2ce01179d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The growth and stability of a new 1 : 1 antipyrene–dichlorobenzoic acid cocrystal system has been analyzed in terms of electron density analysis and electrostatic interaction energy contributions.
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Affiliation(s)
- Aqsa Bilal
- Materials Chemistry Laboratory, Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, 63100, Pakistan
| | - Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, Texas, 76129, USA
| | - Sajida Noureen
- Materials Chemistry Laboratory, Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, 63100, Pakistan
| | - Claude Lecomte
- Laboratoire CRM2, UMR CNRS 7036, Université de Lorraine, Boulevard des Aiguillettes BP70239, Vandoeuvre-les-Nancy, 54506, France
- CNRS, Laboratoire CRM2, UMR CNRS 7036, Boulevard des Aiguillettes, BP70239, Vandoeuvre-les-Nancy, 54506, France
| | - Maqsood Ahmed
- Materials Chemistry Laboratory, Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, 63100, Pakistan
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24
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Bartashevich EV, Mukhitdinova SE, Tsirelson VG. Bond orders and electron delocalization indices for S–N, S–C and S–S bonds in 1,2,3-dithiazole systems. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.09.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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26
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Shteingolts SA, Saifina AF, Saifina LF, Semenov VE, Fukin GK, Fayzullin RR. X-ray charge density study of the 6-methyluracil derivative in the crystal: Revealing, consequences, and multipole refinement of minor static disorder. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Murugan K, Vijayapritha S, Viswanathamurthi P, Saravanan K, Vijayan P, Ojwach SO. Ru(II) complexes containing (2-(pyren-1-ylmethylene)hydrazinyl)benzothiazole: Synthesis, solid-state structure, computational study and catalysis in N-alkylation reactions. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Murugan K, Vijayapritha S, Kavitha V, Viswanathamurthi P. Versatile formation of Ru(II) hydrazone complexes: Structure, theoretical studies and catalytic activity in α-alkylation. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Experimental distribution of electron density in crystals of Ph3Sb(O2CCH=CH–CH=CH–CH3)2 complex: the selection of a reference point for the source function in the absence of a bond critical point between atoms. Struct Chem 2020. [DOI: 10.1007/s11224-020-01548-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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31
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Tsirelson V, Stash A. Orbital-free quantum crystallography: view on forces in crystals. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2020; 76:769-778. [DOI: 10.1107/s2052520620009178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/06/2020] [Indexed: 11/11/2022]
Abstract
Quantum theory of atoms in molecules and the orbital-free density functional theory (DFT) are combined in this work to study the spatial distribution of electrostatic and quantum electronic forces acting in stable crystals. The electron distribution is determined by electrostatic electron mutual repulsion corrected for exchange and correlation, their attraction to nuclei and by electron kinetic energy. The latter defines the spread of permissible variations in the electron momentum resulting from the de Broglie relationship and uncertainty principle, as far as the limitations of Pauli principle and the presence of atomic nuclei and other electrons allow. All forces are expressed via kinetic and DFT potentials and then defined in terms of the experimental electron density and its derivatives; hence, this approach may be considered as orbital-free quantum crystallography. The net force acting on an electron in a crystal at equilibrium is zero everywhere, presenting a balance of the kinetic
F
kin(
r
) and potential forces
F
(
r
). The critical points of both potentials are analyzed and they are recognized as the points at which forces
F
kin(
r
) and
F
(
r
) individually are zero (the Lagrange points). The positions of these points in a crystal are described according to Wyckoff notations, while their types depend on the considered scalar field. It was found that
F
(
r
) force pushes electrons to the atomic nuclei, while the kinetic force
F
kin(
r
) draws electrons from nuclei. This favors formation of electron concentration bridges between some of the nearest atoms. However, in a crystal at equilibrium, only kinetic potential v
kin(
r
) and corresponding force exhibit the electronic shells and atomic-like zero-flux basins around the nuclear attractors. The force-field approach and quantum topological theory of atoms in molecules are compared and their distinctions are clarified.
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32
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Bol’shakov OI, Yushina ID, Stash AI, Aysin RR, Bartashevich EV, Rakitin OA. Structure and properties of 4-phenyl-5H-1,2,3-dithiazole-5-thione polyiodide with S−I+−S bridged complex. Struct Chem 2020. [DOI: 10.1007/s11224-020-01584-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Bartashevich E, Sobalev S, Matveychuk Y, Tsirelson V. Variations of quantum electronic pressure under the external compression in crystals with halogen bonds assembled in Cl3-, Br3-, I3-synthons. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2020; 76:514-523. [DOI: 10.1107/s2052520620006113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/05/2020] [Indexed: 11/10/2022]
Abstract
The inner-crystal quantum electronic pressure was estimated for unstrained C6Cl6, C6Br6, and C6I6 crystals and for those under external compression simulated from 1 to 20 GPa. The changes in its distribution were analyzed for the main structural elements in considered crystals: for triangles of the typical halogen bonds assembled in Hal3-synthons, where Hal = Cl, Br, I; for Hal...Hal stacking interactions, as well as for covalent bonds. Under simulated external compression, the quantum electronic pressure in the intermolecular space reduces as the electron density increases, indicating spatial areas of relatively less crystal resistance to external compression. The most compliant C6Cl6 crystal shows the largest changes of quantum electronic pressure in the centre of Cl3-synthon while the deformation of rigid I3-synthon under external compression depends only on the features of I...I halogen bonds.
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Saravanan K, Sivanandam M, Hunday G, Pavan MS, Kumaradhas P. Exploring the different environments effect of piperine via combined crystallographic, QM/MM and molecular dynamics simulation study. J Mol Graph Model 2019; 92:280-295. [PMID: 31425905 DOI: 10.1016/j.jmgm.2019.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 12/20/2022]
Abstract
Piperine is a pungent alkaloid, largely present in the skin of pepper. It is the most active component of pepper and being used as a medicine in many Asian countries. The effect of piperine on memory impairment and neurodegeneration in Alzheimer's disease model has been investigated. In the present study, we aim to investigate the effect of piperine molecule in different environments (crystal and active site of proteins) from crystallography, molecular docking, QM/MM based charge density analysis and molecular dynamic simulation. The crystal structure of piperine has been used to determine the topological electron density of intermolecular interactions. The O-atoms of piperine is forming C-H⋅⋅⋅O interactions with the neighboring molecules in the crystal, these interactions also confirmed from the Hirshfeld surface. Further, to understand the nature of interactions and the conformational flexibility of piperine in the active site of recombinant human acetylcholinesterase (rhAChE), molecular docking analysis has been performed. The selected docked complex suggests favorable hydrogen bonding and hydrophobic interactions with rhAChE enzyme; notably, the O3 atom of piperine molecule forms strong hydrogen bonding interaction with Glu202 at 1.8 Å. To determine the charge density distribution and the electrostatic properties of piperine molecule in the active site of rhAChE, the piperine-rhAChE complex was minimized at QM/MM energy level; in which, the binding pocket with piperine was considered as QM region. The charge density analysis of piperine and the interacting amino acid groups have been carried out. The topological analysis of O3⋯H-O/Glu202 hydrogen bonding interaction exhibits strong interactions and the electron density ρcp(r): 0.242 eÅ-3 and the Laplacian ∇2ρcp(r): 3.176 eÅ-5 respectively. These results were compared with the corresponding molecule present in the crystal and gas phase environments of piperine. The comparison of active site structure with the corresponding crystal phase and gas phase structures reveal that piperine exhibits large conformational modification in the active site. The molecular dynamics simulation and binding free energy calculations were performed, this gives the stability, binding affinity of the molecule in the active site of rhAChE. The O3⋯H-O/Glu202 interaction shows the high stability (89.2%), this was confirmed from the stability of hydrogen bond analysis. The binding free energy was used to measure the rate of inhibition of enzyme in the presence of ligand molecule. The comparative study allows to understand the nature of piperine molecule in the gas and crystal phases, and amino acids environment.
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Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Mysore S Pavan
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India.
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35
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Hasil A, Mehmood A, Ahmed M. Experimental and theoretical charge-density analysis of hippuric acid: insight into its binding with human serum albumin. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:750-762. [PMID: 32830731 DOI: 10.1107/s2052520619007911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/02/2019] [Indexed: 11/10/2022]
Abstract
In order to comprehend the binding of an important metabolite, hippuric acid, with human serum albumin and to understand its chemical and electronic nature, an experimental charge-density analysis has been carried out using high-resolution diffraction data collected under cryogenic conditions, and all the results have been compared with theoretical findings using the B3LYP/6-311++g(2d,2p) level of theory. The structure displays very strong classical hydrogen bonds as well as other noncovalent interactions, which have been fully characterized using Hirshfeld surface analysis and Bader's quantum theory of atoms in molecules. Contact analysis on the Hirshfeld surfaces shows that the O...H, C...H and C...N intermolecular interactions are enriched and gives their relative strengths. Topological analysis of the electron density shows the charge concentration/depletion of hippuric acid bonds in the crystal structure. Electrostatic parameters such as atomic charges and dipole moments were calculated. The mapping of atomic basins and the calculation of respective charges show the atomic volumes of each atom as well as their charge contributions in the hippuric acid crystal structure. The dipole-moment calculations show that the molecule is very polar in nature. Calculations of the electrostatic potential show that the chain part of the molecule has a higher concentration of negative charge than the ring, which might be instrumental in its strong binding with the polar residues of site II of human serum albumin.
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Affiliation(s)
- Asma Hasil
- Materials Chemistry Laboratory, Department of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus 63100, Pakistan
| | - Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, USA
| | - Maqsood Ahmed
- Materials Chemistry Laboratory, Department of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus 63100, Pakistan
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36
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Sivakumar M, Saravanan K, Saravanan V, Sugarthi S, kumar SM, Alhaji Isa M, Rajakumar P, Aravindhan S. Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics. J Biomol Struct Dyn 2019; 38:1903-1917. [DOI: 10.1080/07391102.2019.1620128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Kandasamy Saravanan
- X-Ray Crystallography and Computational Molecular Biology Lab, Department of Physics, Periyar University, Salem, India
| | | | - Srinivasan Sugarthi
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, Tamil Nadu, India
| | | | - Mustafa Alhaji Isa
- Bioinformatics and Computational Biology Lab, Department of Microbiology, Faculty of Sciences, University of Maiduguri, Maiduguri, Nigeria
| | - Perumal Rajakumar
- Department of Organic Chemistry, University of Madras, Chennai, India
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37
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Saravanan K, Hunday G, Kumaradhas P. Binding and stability of indirubin-3-monoxime in the GSK3β enzyme: a molecular dynamics simulation and binding free energy study. J Biomol Struct Dyn 2019; 38:957-974. [DOI: 10.1080/07391102.2019.1591301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
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38
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Tsirelson VG, Stash AI, Tokatly IV. Quantum pressure focusing in solids: a reconstruction from experimental electron density. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:201-209. [PMID: 32830745 DOI: 10.1107/s2052520619001471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/25/2019] [Indexed: 06/11/2023]
Abstract
Here an approach is presented for reconstructing the distribution of electronic internal quantum pressure in the electronic continuum of solids from the experimental electron density. Using the formalism of the density functional theory, the spatial inner-crystal map of the quantum pressure is obtained. The results are visualized via the indicator of quantum pressure focusing (IQPF) which reveals the regions where the pressure is concentrated or depleted due to quantum effects. IQPF contains all quantum electron-shell structure-forming contributions resulting from kinetic, exchange and correlation effects, and presents a clear picture of the chemical bond features in crystals with different type of bonding mechanisms.
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Affiliation(s)
- Vladimir G Tsirelson
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, 125047, Russian Federation
| | - Adam I Stash
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, 125047, Russian Federation
| | - Ilya V Tokatly
- Departamento de Fisica de Materials, Universidad del Pais Vasco UPV/EHU, San Sebastian, 20018, Spain
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39
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Bartashevich E, Mukhitdinova S, Yushina I, Tsirelson V. Electronic criterion for categorizing the chalcogen and halogen bonds: sulfur–iodine interactions in crystals. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2019; 75:117-126. [DOI: 10.1107/s2052520618018280] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/24/2018] [Indexed: 11/10/2022]
Abstract
Diversity of mutual orientations of Y–S and I–X and covalent bonds in molecular crystals complicate categorizing noncovalent chalcogen and halogen bonds. Here, the different types of S...I interactions with short interatomic distances are analysed. The selection of S...I interactions for the categorization of the chalcogen and halogen bonds has been made using angles that determine the mutual orientation of electron lone pairs and σ-holes interacted S and I atoms. In complicated cases of noncovalent interactions with `hole-to-hole' of S and I orientations, distinguishing the chalcogen and halogen bonds is only possible if the atom is uniquely determined, which also provides the electrophilic site. The electronic criterion for chalcogen/halogen bonds categorizing that is based on analysis of dispositions of electron density and electrostatic potential minima along the interatomic lines has been suggested and its effectiveness has been demonstrated.
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40
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Acylguanidine-BACE1 complex: Insights of intermolecular interactions and dynamics. J Theor Biol 2019; 464:33-49. [DOI: 10.1016/j.jtbi.2018.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/09/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022]
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Lübben J, Wandtke CM, Hübschle CB, Ruf M, Sheldrick GM, Dittrich B. Aspherical scattering factors for SHELXL - model, implementation and application. Acta Crystallogr A Found Adv 2019; 75:50-62. [PMID: 30575583 PMCID: PMC6302932 DOI: 10.1107/s2053273318013840] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/29/2018] [Indexed: 11/23/2022] Open
Abstract
A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.
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Affiliation(s)
- Jens Lübben
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstrasse 4, Göttingen, D-37077, Germany
- Bruker AXS Inc., 5465 E. Cheryl Parkway, Madison, WI 53711, USA
| | - Claudia M. Wandtke
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstrasse 4, Göttingen, D-37077, Germany
| | | | - Michael Ruf
- Bruker AXS Inc., 5465 E. Cheryl Parkway, Madison, WI 53711, USA
| | - George M. Sheldrick
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstrasse 4, Göttingen, D-37077, Germany
| | - Birger Dittrich
- Heinrich-Heine Universität Düsseldorf, Institut für Anorganische Chemie und Strukturchemie, Material- und Strukturforschung, Gebäude: 26.42, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Saravanan K, Sivanandam M, Hunday G, Mathiyalagan L, Kumaradhas P. Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis. J Biomol Struct Dyn 2018; 37:2339-2354. [DOI: 10.1080/07391102.2018.1479661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Lakshmanan Mathiyalagan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
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43
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Jarzembska KN, Kamiński R, Durka K, Woźniak K. Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline. J Phys Chem A 2018; 122:4508-4520. [PMID: 29672046 DOI: 10.1021/acs.jpca.8b00832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å-1) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.
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Affiliation(s)
- Katarzyna N Jarzembska
- Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Radosław Kamiński
- Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Krzysztof Durka
- Department of Chemistry , Warsaw University of Technology , Noakowskiego 3 , 00-664 Warsaw , Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
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44
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Modern level for properties prediction of iodine-containing organic compounds: the halogen bonds formed by iodine. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1898-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Charge density studies of an inorganic-organic hybrid p-phenylenediammonium tetrachlorocuprate. Struct Chem 2017. [DOI: 10.1007/s11224-017-0969-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Bartashevich E, Yushina I, Kropotina K, Muhitdinova S, Tsirelson V. Testing the tools for revealing and characterizing the iodine-iodine halogen bond in crystals. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:217-226. [PMID: 28362285 DOI: 10.1107/s2052520617002931] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/21/2017] [Indexed: 05/13/2023]
Abstract
To understand what tools are really suitable to identify and classify the iodine-iodine non-covalent interactions in solid organic polyiodides, we have examined the anisotropy of the electron density within the iodine atomic basin along and across the iodine-iodine halogen bond using the Laplacian of electron density, one-electron potential and electron localization function produced by Kohn-Sham calculations with periodic boundary conditions. The Laplacian of electron density exhibits the smallest anisotropy and yields a vague picture of the outermost electronic shells. The one-electron potential does not show such a deficiency and reveals that the valence electron shell for the halogen-bond acceptor iodine is always wider than that for the halogen-bond donor iodine along its σ-hole direction. We have concluded that the one-electron potential is the most suitable for classification of the iodine-iodine bonds and interactions in complicated cases, while the electron localization function allows to distinguish the diiodine molecule bonded with the monoiodide anion from the typical triiodide anion.
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Affiliation(s)
- Ekaterina Bartashevich
- Chemistry Department, South Ural State University, 76 Lenin ave, Chelyabinsk 454080, Russian Federation
| | - Irina Yushina
- Chemistry Department, South Ural State University, 76 Lenin ave, Chelyabinsk 454080, Russian Federation
| | - Kristina Kropotina
- Chemistry Department, South Ural State University, 76 Lenin ave, Chelyabinsk 454080, Russian Federation
| | - Svetlana Muhitdinova
- Chemistry Department, South Ural State University, 76 Lenin ave, Chelyabinsk 454080, Russian Federation
| | - Vladimir Tsirelson
- Quantum Chemistry, Mendeleev University of Chemical Technology of Russia, 9, Miusskaya Square, Moscow 125047, Russian Federation
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47
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Saravanan K, Kalaiarasi C, Kumaradhas P. Understanding the conformational flexibility and electrostatic properties of curcumin in the active site of rhAChE via molecular docking, molecular dynamics, and charge density analysis. J Biomol Struct Dyn 2017; 35:3627-3647. [DOI: 10.1080/07391102.2016.1264891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Chinnasamy Kalaiarasi
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
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48
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Landeros-Rivera B, Moreno-Esparza R, Hernández-Trujillo J. Theoretical study of intermolecular interactions in crystalline arene–perhaloarene adducts in terms of the electron density. RSC Adv 2016. [DOI: 10.1039/c6ra14957j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The intermolecular interactions in C6X6–arene crystals (X = F, Cl) and the halogen substitution effect can be quantified by the electron density.
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49
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Tsirelson VG, Stash AI, Tokatly IV. Bonding in molecular crystals from the local electronic pressure viewpoint. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1101173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Vladimir G. Tsirelson
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, Russia
| | - Adam I. Stash
- Laboratory of Oxide Materials, Karpov Research Institute of Physical Chemistry, Moscow, Russia
| | - Ilya V. Tokatly
- Departamento de Fisica de Materials, Universidad del Pais Vasco UPV/EHU, San Sebastian, Spain
- IKERBASQUE, Basgue Foundation for Science, Bilbao, Spain
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