Log in

Relevant bibliographies by topics / Atoms-in-Molecule (AIM) / Journal articles

To see the other types of publications on this topic, follow the link: Atoms-in-Molecule (AIM).

Journal articles on the topic 'Atoms-in-Molecule (AIM)'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Atoms-in-Molecule (AIM).'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Chaudhary, Manoj Kumar, Tarun Chaudhary, and Bhawani Datt Joshi. "Simulated spectra (IR and Raman), NLO, AIM and molecular docking of carisoprodol from DFT approach." BIBECHANA 18, no. 1 (2021): 48–57. http://dx.doi.org/10.3126/bibechana.v18i1.29036.

Full text

Abstract:

The aim of this study to explore the spectroscopic behavior of carisoprodol in terms of simulated spectra (IR and Raman).. The intramolecular H-bond of the molecule has been inspected from the Atoms in Molecule (AIM) approach which infers that there exist partial covalent H-bond in nature. The protein-ligand binding activity of the drug molecule has been analyzed theoretically from the molecular docking approach with the predicted targets in terms of binding energy and conventional H-bond with residue. The molecular docking analysis of the title molecule explores that the binding energy with t

APA, Harvard, Vancouver, ISO, and other styles

2

Yuan, Chengqian, Haiming Wu, Meiye Jia, Peifeng Su, Zhixun Luo, and Jiannian Yao. "A theoretical study of weak interactions in phenylenediamine homodimer clusters." Physical Chemistry Chemical Physics 18, no. 42 (2016): 29249–57. http://dx.doi.org/10.1039/c6cp04922b.

Full text

Abstract:

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

APA, Harvard, Vancouver, ISO, and other styles

3

Felegari, Zahra, and Majid Monajjemi. "AIM and NBO analyses on the interaction between SWCNT and cyclophosphamide as an anticancer drug: A density functional theory study." Journal of Theoretical and Computational Chemistry 14, no. 03 (2015): 1550021. http://dx.doi.org/10.1142/s0219633615500212.

Full text

Abstract:

In this work, the molecular structures of single-walled carbon nanotube (SWCNT), cyclophosphamide and cyclophosphamide–SWCNT complex were optimized B3LYP/6–31G* level of theory. The nanotube used in this study was a (5,5) SWCNT including 150 C atoms. The NBO analysis showed that the transfer electron can be occurred from the lone pair of oxygen (donor atom) in the cyclophosphamide to the σ* or π* orbitals of the carbon atoms (acceptor atoms) in the SWCNT. The highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO) and energy gap (HOMO–LUMO) were calculated for the

APA, Harvard, Vancouver, ISO, and other styles

4

Srinivasan, P., and A. David Stephen. "DFT and Bader's AIM analysis of 2,5-,diphenyl-1,3,4-oxadizole molecule: A organic light emitting diode (OLED)." Journal of Theoretical and Computational Chemistry 14, no. 05 (2015): 1550038. http://dx.doi.org/10.1142/s0219633615500388.

Full text

Abstract:

The electron density and conductivity studies of 2,5-diphenyl-1,3,4-oxadizole organic light emitting diode (OLED) based molecule have been calculated from the quantum chemical calculations and combined with the Bader's AIM theory. Density functional theory calculations with B3LYP/aug-cc-PVDZ basis sets was used to determine ground state gas space molecular geometries (bond lengths and bond angles), electron density and bonding features of this molecule. The electron densities at the bond critical point (BCP) of aromatic Car–Car bonds are much stronger than the other bonds in the molecule. The

APA, Harvard, Vancouver, ISO, and other styles

5

Mottaghi, A., and Ali R. Ashrafi. "Topological edge properties of C60+12 n fullerenes." Beilstein Journal of Nanotechnology 4 (June 26, 2013): 400–405. http://dx.doi.org/10.3762/bjnano.4.47.

Full text

Abstract:

A molecular graph M is a simple graph in which atoms and chemical bonds are the vertices and edges of M, respectively. The molecular graph M is called a fullerene graph, if M is the molecular graph of a fullerene molecule. It is well-known that such molecules exist for even integers n ≥ 24 or n = 20. The aim of this paper is to investigate the topological properties of a class of fullerene molecules containing 60 + 12n carbon atoms.

APA, Harvard, Vancouver, ISO, and other styles

6

Putz, Mihai V. "Chemical Bonding by the Chemical Orthogonal Space of Reactivity." International Journal of Molecular Sciences 22, no. 1 (2020): 223. http://dx.doi.org/10.3390/ijms22010223.

Full text

Abstract:

The fashionable Parr–Pearson (PP) atoms-in-molecule/bonding (AIM/AIB) approach for determining the exchanged charge necessary for acquiring an equalized electronegativity within a chemical bond is refined and generalized here by introducing the concepts of chemical power within the chemical orthogonal space (COS) in terms of electronegativity and chemical hardness. Electronegativity and chemical hardness are conceptually orthogonal, since there are opposite tendencies in bonding, i.e., reactivity vs. stability or the HOMO-LUMO middy level vs. the HOMO-LUMO interval (gap). Thus, atoms-in-molecu

APA, Harvard, Vancouver, ISO, and other styles

7

Raghu, Nath Behera, and Michael Kaley Nisheal. "Computational study of some diselenide-based glutathione peroxidase mimics: Effect of E…N (E = Se/Te) intramolecular interaction and E–E bond strength." Journal of Indian Chemical Society Vol. 97, Mar 2020 (2020): 311–16. https://doi.org/10.5281/zenodo.5652922.

Full text

Abstract:

Department of Chemistry, Birla Institute of Technology & Science, Pilani – K. K. Birla Goa Campus, Zuarinagar-403 726, Goa, India <em>E-mail:</em> rbehera@goa.bits-pilani.ac.in Present address: Tarragona, Spain <em>Manuscript received online 01 December 2019, revised and accepted 26 December 2019</em> There have been growing interests in studying small molecular weight organoselenium compounds as potential mimetics of glutathione peroxidase (GPx). In this regards, the intramolecular E…N (E = Se/Te) interactions and their effect on the E-E bond strengths in a series of diaryl d

APA, Harvard, Vancouver, ISO, and other styles

8

Wzgarda-Raj, Kinga, Agnieszka J. Rybarczyk-Pirek, Sławomir Wojtulewski, and Marcin Palusiak. "C—Br...S halogen bonds in novel thiourea N-oxide cocrystals: analysis of energetic and QTAIM parameters." Acta Crystallographica Section C Structural Chemistry 76, no. 2 (2020): 170–76. http://dx.doi.org/10.1107/s2053229620000947.

Full text

Abstract:

Cocrystals of thiourea with 4-nitropyridine N-oxide, C5H4N2O3·2CH4N2S, (I), and 3-bromopyridine N-oxide, C5H4BrNO·CH4N2S, (II), crystallize in the monoclinic space group P21/c. In the crystals, molecules of both components are linked by N—H...O hydrogen bonds, creating R 2 1(6) synthons. The bromine substituent of the N-oxide component in (II) is a centre for C—Br...S halogen bonding to the thiourea molecule. Computations based on quantum chemistry methods (quantum theory of atoms in molecules, QTAIM) and atoms in molecules (AIM) theory were performed for a more detailed description of the obs

APA, Harvard, Vancouver, ISO, and other styles

9

Herich, Peter, Lenka Kucková, Jan Moncol, and Jozef Kožíšek. "Charge density study of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex." Zeitschrift für Kristallographie - Crystalline Materials 233, no. 9-10 (2018): 745–52. http://dx.doi.org/10.1515/zkri-2018-2070.

Full text

Abstract:

Abstract An experimental electronic structure of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex, [Cu(cln)2(im)2(EtOH)2] (cln=clonixato, im=imidazole) (1) has been obtained from single-crystal X-ray diffraction data collected at 100 K using an Incoatec IμS Ag microfocus source. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the experimental electron density with the atoms in molecules (AIM) approach. The central copper atom is octahedrally coordinated by two oxygen atoms from two clonixato anions and two nitrogen atoms from two imi

APA, Harvard, Vancouver, ISO, and other styles

10

McWeeny, Roy. "The Quantum Mechanics of Cohesion." Collection of Czechoslovak Chemical Communications 72, no. 2 (2007): 252–68. http://dx.doi.org/10.1135/cccc20070252.

Full text

Abstract:

We consider the fundamental problem of "what makes atoms stick together in molecules, crystals, or clusters?" The Heitler and London paper (1927) on the hydrogen molecule marked a first attempt to discuss, in terms of quantum mechanics, the interaction of two atoms with unpaired spins. The aim of this note is to show how the primitive concepts used eighty years ago still retain a certain validity even in a much more general context. We consider in fact the interaction of two arbitrary systems, each with a resultant spin angular momentum, and show how the interaction energy depends on the scala

APA, Harvard, Vancouver, ISO, and other styles

11

AMZOIU, MANUEL, FLORENTINA CRISTOVICI, DENISA AMZOIU, FLORICA POPESCU, ALEXANDRA NITULESCU, and EMIN CADAR. "STUDY OF THE INTERACTION BETWEEN OXICAM DERIVATIVES AND COX1 USING FINGERPRINT DESCRIPTORS AND MOLECULAR DOCKING." Journal of Science and Arts 21, no. 2 (2021): 529–38. http://dx.doi.org/10.46939/j.sci.arts-21.2-b02.

Full text

Abstract:

Oxicam derivatives play an important role in the treatment of pain and inflammation. The mechanism of action of these compounds consists in the inhibition of cyclooxygenase (COX) and the blockade of isoform 1 of this enzyme (COX-1) is considered to generate adverse effects. The aim of this paper is to establish which of the atoms in the oxicams molecules are responsible for their inhibitory activities, using electronegativity as fingerprint descriptor. Using this descriptor and molecular docking programs, the atoms in the molecule that have a greater contribution to COX-1 inhibition have been

APA, Harvard, Vancouver, ISO, and other styles

12

Abdualkader, Abdualrahman Mohammed, Muhammad Taher, and Nik Idris Nik Yusoff. "MESOIONIC SYDNONE: A REVIEW IN THEIR CHEMICAL AND BIOLOGICAL PROPERTIES." International Journal of Pharmacy and Pharmaceutical Sciences 9, no. 8 (2017): 1. http://dx.doi.org/10.22159/ijpps.2017v9i8.18774.

Full text

Abstract:

Various literature sources have documented sydnones as important molecules with exclusive chemical properties and a wide spectrum of bioactivities. Sydnone can be defined as a five-membered pseudo-aromatic heterocyclic molecule. Classically, 1,2,3-oxadiazole forms the main skeleton of sydnone. The molecule has delocalized balanced positive and negative charges. The five annular atoms share the positive charge and the enolate-like exocyclic oxygen atom bears the negative charge. The hydrogen atom at the position C4 was proved to have acidic and nucleophilic functionalities making the sydnone ri

APA, Harvard, Vancouver, ISO, and other styles

13

Blokhin, Igor V., Yury M. Atroshchenko, Irina V. Shakhkeldyan, et al. "Quantum-chemical simulation of the interaction of 2-methyl-5,7-dinitrobenzo[d]oxazole with tetrahydride borate ion by DFT method." Butlerov Communications 59, no. 8 (2019): 40–46. http://dx.doi.org/10.37952/roi-jbc-01/19-59-8-40.

Full text

Abstract:

The aim of the work was quantum chemical modeling by the theory of the functional density functional of the interaction of 2-methyl-5,7-dinitrobenzo[d]oxazole with tetrahydride borate ion. For this, geometric optimization and calculation of the total energies of the 2-methyl-5,7-dinitrobenzo[d]oxazole molecule in the gas phase and water were carried out using the DFT/B3LYP/aug-cc-pVDZ method. To determine the likely reaction centers for a nucleophile attack, atomic charges according to Mulliken and NBO charges in the molecule of the initial substrate were established. The largest positive char

APA, Harvard, Vancouver, ISO, and other styles

14

Anuar, Nornizar, Wan Nor Asyikin Wan Mohamed Daid, Sopiah Ambong Khalid, Sarifah Fauziah Syed Draman, and Siti Rozaimah Sheikh Abdullah. "Prediction of Interaction of Citric Acid Modified Cellulose with Water Region Using Molecular Modelling Technique." Key Engineering Materials 797 (March 2019): 118–26. http://dx.doi.org/10.4028/www.scientific.net/kem.797.118.

Full text

Abstract:

In this paper, chemically modified cellulose was used instead of cellulose as it offers higher adsorption capacities, great chemical strength and good resistance to heat. As part of Phyto-Adsorption Remediation Method, citric acid modified cellulose (CAMC) was used to treat ferric ion. However, there is a large possibility that CAMC molecule might interact with water molecule that contain hydrogen bond and hence pose as a competitor to ferric acid and reduces the efficiency of CAMC in ferric ion removal. Thus, the aim of this work is to identify the most stable hydrogen bond between CAMC and w

APA, Harvard, Vancouver, ISO, and other styles

15

Farrugia, Louis J., Paul R. Mallinson, and Brian Stewart. "Experimental charge density in the transition metal complex Mn2(CO)10: a comparative study." Acta Crystallographica Section B Structural Science 59, no. 2 (2003): 234–47. http://dx.doi.org/10.1107/s0108768103000892.

Full text

Abstract:

An accurate experimental charge density study at 100 K of Mn2(CO)10 [bis(pentacarbonylmanganese)(Mn—Mn)] has been undertaken. A comparison with previously reported structural determinations reveals no evidence for significant Mn—Mn bond lengthening between 100 and 296 K. The nature of the metal–metal and metal–ligand atom interactions has been studied by topological analysis using the Atoms in Molecules (AIM) approach of Bader [(1990), Atoms in Molecules: a Quantum Theory.Oxford: Clarendon Press]. An analysis of the density ρ(r), the Laplacian of the density ∇2ρ(r b ) and the total energy dens

APA, Harvard, Vancouver, ISO, and other styles

16

Kumar, Anmol, and Shridhar R. Gadre. "Molecular Electrostatic Potential-Based Atoms in Molecules: Shielding Effects and Reactivity Patterns." Australian Journal of Chemistry 69, no. 9 (2016): 975. http://dx.doi.org/10.1071/ch16226.

Full text

Abstract:

The Atoms in Molecules (AIM) concept based on the zero-flux surface (ZFS) of the gradient of molecular electrostatic potential (MESP) has been recently proposed by the present authors. The nature of MESP-based atomic basins brings out the asymmetric electronic distribution in a molecule. An electron-rich atom among the two bonded atoms is seen to possess a completely closed MESP-based atomic basin. The present article illustrates the nature of atomic basins for a variety of molecules such as BF, BH3, AlCl3, B2H6, and Al2Cl6, and a Lewis acid–base pair, viz. NH3BH3 wherein the electronic distri

APA, Harvard, Vancouver, ISO, and other styles

17

Grabowsky, Simon, Manuela Weber, Jürgen Buschmann, and Peter Luger. "Experimental electron density study of ethylene oxide at 100 K." Acta Crystallographica Section B Structural Science 64, no. 3 (2008): 397–400. http://dx.doi.org/10.1107/s0108768108010197.

Full text

Abstract:

The experimental electron density of ethylene oxide was derived from a multipole refinement of 100 K X-ray data and complemented by density-functional calculations at experimental and optimized geometry. Atomic and bond-topological properties were derived using the atoms-in-molecules (AIM) formalism. The high strain in the three-membered ring molecule is mainly expressed by the high ellipticities of the three bonds in this ring, while the bond paths are only slightly bent for the C—C bond, but are virtually straight for the C—O bond.

APA, Harvard, Vancouver, ISO, and other styles

18

Hervé du Penhoat, Marie-Anne, Anis Hamila, Marie-Pierre Gaigeot, et al. "Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays." Quantum Beam Science 3, no. 4 (2019): 24. http://dx.doi.org/10.3390/qubs3040024.

Full text

Abstract:

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation

APA, Harvard, Vancouver, ISO, and other styles

19

Vank, Judith C., Carlos P. Sosa, Andras Perczel та Imre G. Csizmadia. "Peptide models XXVII. An exploratory ab initio study on the 21st amino acid side-chain conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe) in their γL backbone conformation". Canadian Journal of Chemistry 78, № 3 (2000): 395–408. http://dx.doi.org/10.1139/v00-029.

Full text

Abstract:

Selenocysteine is expected to have 9 × 9 = 81 conformations [3 × 3 = 9 backbone: ψ (g+,a,g-) × ϕ (g+,a,g-) and 3 × 3 = 9 side-chain: χ1 (g+,a,g-) × χ2 (g+,a,g-)]. In the present study, all the torsional modes of the side-chain (χ1: rotation about the Cα-Cβ and χ2: rotation about the Cβ-Se bonds) were investigated in the relaxed γL backbone [(ϕ,ψ); (g-,g+)] conformation. Seven out of the nine expected minima were found at the RHF/3-21G level of theory for N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe). The stabilization energy exerted b

APA, Harvard, Vancouver, ISO, and other styles

20

Capa-Cobos, Luis Fernando, Ximena Jaramillo-Fierro, and Silvia González. "Computational Study of the Adsorption of Phosphates as Wastewater Pollutant Molecules on Faujasites." Processes 9, no. 10 (2021): 1821. http://dx.doi.org/10.3390/pr9101821.

Full text

Abstract:

The adsorption of sodium dihydrogen phosphate (NaH2PO4) onto X- and Y-type faujasite zeolites was computationally studied using the Density Functional Theory (DFT) method. The structures were modeled using the Materials Studio software. The Si/Al ratios for the X- and Y-type zeolite models were 1.2 and 2.5, respectively. The central pore of the zeolite provided a more favorable coordination for adsorbing NaH2PO4. Full molecular optimization and adsorption energy calculations were performed using the VASP code. The adsorption was more effective on zeolite Y, with an adsorption energy of 161 kJ/

APA, Harvard, Vancouver, ISO, and other styles

21

Soler, Philippe, Franck Fuster, and Hilaire Chevreau. "Fast topological analysis of 2D and 3D grids of data: Application to the atoms in molecule (AIM) and the electron localization function (ELF)." Journal of Computational Chemistry 25, no. 15 (2004): 1920–25. http://dx.doi.org/10.1002/jcc.20102.

Full text

APA, Harvard, Vancouver, ISO, and other styles

22

Kumar, Mukesh, Satyavir Singh, Nazia Siddiqui, and Saleem Javed. "Quantum Computational, Spectroscopic, NHO and Molecular Docking Studies on 1-Methyl-nicotinamide (MNA): An Antithrombotic, Anti-inflammatory, Gastroprotective and Vasoprotective Compound." Asian Journal of Organic & Medicinal Chemistry 6, no. 2 (2021): 128–40. http://dx.doi.org/10.14233/ajomc.2021.ajomc-p326.

Full text

Abstract:

In present work, 1-methylnicotinamide (1-MNA) has been investigated theoretically by density functional theory approach and investigated its vibrational spectroscopy. To complete the structure optimization, determination of vibrational frequencies and other valuable parameters, B3LYP method used with the 6-311++G(d,p) basis set. Atoms in molecules theory (AIM) had been used to evaluate ellipticity, isosurface projection by electron localization function and binding energies. The IR and Raman spectra have also been calculated computationally. NBO analysis employed to determine interactions of d

APA, Harvard, Vancouver, ISO, and other styles

23

Karimov, O. K., G. Y. Kolchina, G. A. Teptereva, I. A. Chetvertneva, E. K. Karimov, and A. R. Badretdinov. "The reactivity of cinnamic acid derivatives as lignin precursors." Fine Chemical Technologies 15, no. 4 (2020): 7–13. http://dx.doi.org/10.32362/2410-6593-2020-15-4-7-13.

Full text

Abstract:

Objectives. Cinnamic acid derivatives belong to a large class of phenolic compounds, which are widely distributed in plants and have high potential for use in the medical and industrial fields. They have various useful practical properties, e.g., antioxidant, anti-inflammatory, antiplatelet, and anti-melanogenic properties. Hydroxycinnamic acids are of particular interest as phenylpropanoids, which are the starting compounds of lignin. The aim of this work was to study the electronic structure and analyze the reactivity of the simplest representatives of phenylpropanoids formed during the bios

APA, Harvard, Vancouver, ISO, and other styles

24

Masaryk, Lukáš, Ján Moncol, Radovan Herchel, and Ivan Nemec. "Halogen Bonding in New Dichloride-Cobalt(II) Complex with Iodo Substituted Chalcone Ligands." Crystals 10, no. 5 (2020): 354. http://dx.doi.org/10.3390/cryst10050354.

Full text

Abstract:

The synthesis and properties of new chalcone ligand 4I-L ((2E)-1-[4-(1H-imidazol-1-yl)phenyl]-3-(4-iodophenyl)prop-2-en-1-one) and tetracoordinate Co(II) complex [Co(4I-L)2Cl2], (1a), are reported in this article. Upon recrystallization of 1a, the single crystals of [Co(4I-L)4Cl2]·2DMF·3Et2O (1b) were obtained and crystal structure was determined using X-ray diffraction. The non-covalent interactions in 1b were thoroughly analyzed and special attention was dedicated to interactions formed by the peripheral iodine substituents. The density functional theory (DFT), atoms in molecule (AIM) and no

APA, Harvard, Vancouver, ISO, and other styles

25

Osipov, E. M., K. M. Polyakov, T. V. Tikhonova, et al. "Incorporation of copper ions into crystals of T2 copper-depleted laccase fromBotrytis aclada." Acta Crystallographica Section F Structural Biology Communications 71, no. 12 (2015): 1465–69. http://dx.doi.org/10.1107/s2053230x1502052x.

Full text

Abstract:

Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase fromBotrytis acladahas been solved previously. With the aim of obtaining the structure of the native form of the enzyme, crystals of the depleted laccase were soaked in Cu+- and Cu2+-containing solutions. Copper ions were found to be incorporated into the active site only when Cu+

APA, Harvard, Vancouver, ISO, and other styles

26

Maslehat, Sholeh, Soroush Sardari, and Mahboube Ganji Arjenaki. "Frequency and Importance of Six Functional Groups that Play a Role in Drug Discovery." Biosciences, Biotechnology Research Asia 15, no. 3 (2018): 541–48. http://dx.doi.org/10.13005/bbra/2659.

Full text

Abstract:

Small molecules are composed of chemical functional groups; they are sets of connected atoms or atom groups that determine properties and reactivity of the parent molecule. DrugBank is a rich source of information that containing molecular data about small molecules, their mechanisms, pharmaceutical interaction and targets. In this study, After collecting data of small drug molecules from DrugBank database and classifying them in different categories based on their mechanism of action, the therapeutic properties of the molecules were recorded. Finally, the functional group from the pharmaceuti

APA, Harvard, Vancouver, ISO, and other styles

27

Ma, Shumeng, Shymaa Damfo, Matthew W. Bowler, Vitaliy Mykhaylyk, and Frank Kozielski. "High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms." Acta Crystallographica Section D Structural Biology 80, no. 6 (2024): 451–63. http://dx.doi.org/10.1107/s2059798324004480.

Full text

Abstract:

Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hi

APA, Harvard, Vancouver, ISO, and other styles

28

Zhukov, N. D., A. A. Kletsov, D. S. Mosiyash, and V. V. Belyaev. "Modelling of nanocrystals atomic configurations at nuclei formation." Bulletin of State University of Education. Series: Physics and Mathematics, no. 2 (June 13, 2024): 6–18. https://doi.org/10.18384/2949-5067-2024-2-6-18.

Full text

Abstract:

Aim. Study of the model of nucleus-sized nanocrystal and identification of its properties and patterns.Methodology. A model was developed and numerical calculations were carried out on the example of the binary semiconductor GaAs, which showed that during the spontaneous formation of a nanocrystal, the crystal lattice with an elementary cell size of 0.4 – 0.5 nm is formed, which is greater than the length of the bond of both gallium and arsenic atoms when they are possible combined in the molecule (the sum of atomic radii is 0.273 nm) and less than the lattice constant of gallium arsenide (0.5

APA, Harvard, Vancouver, ISO, and other styles

29

Burguera, Sergi, Antonio Bauzá, and Antonio Frontera. "Tuning the Nucleophilicity and Electrophilicity of Group 10 Elements through Substituent Effects: A DFT Study." International Journal of Molecular Sciences 24, no. 21 (2023): 15597. http://dx.doi.org/10.3390/ijms242115597.

Full text

Abstract:

In this study, a series of electron donor (–NH2, –NMe2 and –tBu) and electron-withdrawing substituents (–F, –CN and –NO2) were used to tune the nucleophilicity or electrophilicity of a series of square planar Ni2+, Pd2+ and Pt2+ malonate coordination complexes towards a pentafluoroiodobenzene and a pyridine molecule. In addition, Bader’s theory of atoms in molecules (AIM), noncovalent interaction plot (NCIplot), molecular electrostatic potential (MEP) surface and natural bond orbital (NBO) analyses at the PBE0-D3/def2-TZVP level of theory were carried out to characterize and discriminate the r

APA, Harvard, Vancouver, ISO, and other styles

30

Jarzembska, Katarzyna N., Radosław Kamiński, Łukasz Dobrzycki, and Michał K. Cyrański. "First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 70, no. 5 (2014): 847–55. http://dx.doi.org/10.1107/s2052520614017570.

Full text

Abstract:

The aim of this study was to test the applicability of a Bruker AXS CMOS-type PHOTON 100 detector for the purpose of a fine charge density quality data collection. A complex crystal containing oxalic acid, ammonium oxalate and two water molecules was chosen as a test case. The data was collected up to a resolution of 1.31 Å−1with high completeness (89.1%;Rmrg= 0.0274). The multipolar refinement and subsequent quantum theory of atoms in molecules (QTAIM) analysis resulted in a comprehensive description of the charge density distribution in the crystal studied. The residual density maps are flat

APA, Harvard, Vancouver, ISO, and other styles

31

Agaeva, G., and G. Najafova. "ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)." Russian Journal of Biological Physics and Chemisrty 8, no. 1 (2024): 21–26. http://dx.doi.org/10.29039/rusjbpc.2023.0583.

Full text

Abstract:

The electronic characteristics of stable conformational states of beta-amyloid peptide (25-35) have been studied by molecular modeling methods. Beta-amyloid peptide (Aβ) is the main component of senile plaques found in the brains of patients with Alzheimer's disease. Aβ (25-35) fragment of a molecule with the amino acid sequence Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met. It has been shown that the conformational features of a molecule are largely determined by its environment; therefore, the aim of this work was to study the differences in the conformations of amyloid beta-peptide (25-35) in

APA, Harvard, Vancouver, ISO, and other styles

32

DE OLIVEIRA, BOAZ GALDINO, REGIANE DE CÁSSIA MARITAN UGULINO DE ARAÚJO, VERNECK MAIA SOARES, and MOZART NEVES RAMOS. "A THEORETICAL STUDY ABOUT THE ELECTRONIC COOPERATIVE EFFECT ON HYDROCYANIDE CHAINS USING DFT CALCULATIONS AND AIM TOPOLOGICAL PARAMETERS." Journal of Theoretical and Computational Chemistry 07, no. 02 (2008): 247–56. http://dx.doi.org/10.1142/s0219633608003605.

Full text

Abstract:

A theoretical investigation about the cooperative effect on ( HCN )n homo and ( HCN )n ⋯ HF heterochains was performed in terms of structural parameters and topological properties obtained in concordance with the protocol of Bader's atoms in molecules theory. Initially, the hydrogen bonding distances, electronic densities, and Laplacian descriptors were used to characterize small ( HCN )n and ( HCN )n ⋯ HF chains formed by n = 2–4 units of HCN . Hydrogen bond distances and distribution of charge density have revealed that the cooperative effect on ( HCN )n ⋯ HF heterochains is ruled by the pol

APA, Harvard, Vancouver, ISO, and other styles

33

Altowyan, Mezna Saleh, Jörg H. Albering, Assem Barakat, Saied M. Soliman, and Morsy A. M. Abu-Youssef. "Synthesis, Supramolecular Structural Investigations of Co(II) and Cu(II) Azido Complexes with Pyridine-Type Ligands." Crystals 13, no. 2 (2023): 346. http://dx.doi.org/10.3390/cryst13020346.

Full text

Abstract:

Two new Co(II) and Cu(II) azido complexes with 4-picoline (4-Pic) and pyridine-2-carboxaldoxime (HAld) were synthesized by self-assembly of the organic ligand and the M(II) nitrate in the presence of azide as a co-ligand. Their structures were determined to be [Co(4-Pic)4(H2O)(N3)]NO3*H2O*4-Pic (1) and [Cu(HAld)(Ald)(N3)] (2) using X-ray single crystal diffraction. In complex 1, the coordination geometry is a slightly distorted octahedron with a water molecule and azide ion located trans to one another. On the other hand, complex 2 has a distorted square pyramid CuN5 coordination sphere with N

APA, Harvard, Vancouver, ISO, and other styles

34

C.D. Tibambre-Heredia, H. Olaya-Dávila, A.C. Sevilla, et al. "Radon Progeny Recoil Effect in Retrospective Indoor Glass Dosimetry." Journal of Nuclear Physics, Material Sciences, Radiation and Applications 7, no. 1 (2020): 35–41. http://dx.doi.org/10.15415/jnp.2019.71004.

Full text

Abstract:

Radon gas diffusion and progeny transport in air, are mechanisms to be considered in retrospective glass dosimetry. With the aim to contribute to the understanding of the Rn progeny recoil energy role in this dosimetry methodology, we carried out a simulation employing GEANT4 code. In that, we assumed the chemical compound of the glass that is used commonly in households. Results are compared to experimentally measured 210Bi concentration to show that the recoil energy helps the progenies incrustation, mainly for the 218,214Po alpha emitters but do not influence bismuth-210 diffusion directly.

APA, Harvard, Vancouver, ISO, and other styles

35

Stephen, A. D., S. M. Shankar, R. N. Devi, et al. "Evaluation of diflunisal a difluoro-derivative of salicylic acid as an inhibitor of human serum albumin using molecular docking tools." Journal of Environmental Biology 43, no. 4 (2022): 527–35. http://dx.doi.org/10.22438/jeb/43/4/mrn-3006.

Full text

Abstract:

Aim: To evaluate the binding interaction of diflunisal at active site of Human Serum Albumin (HSA), an important enzyme responsible for osteoarthritis disease. Methodology: The gas phase molecule was optimized with B3LYP/6-311G** basis set, while a single point energy calculation was carried out for the molecule lifted from the active site. Bader’s theory of atoms in molecules (AIM) was used to determine the electron density and Laplacian of electron density. The protein was assigned with polar hydrogens and Kollman charges. Iterated local search procedure was performed during docking, during

APA, Harvard, Vancouver, ISO, and other styles

36

TAN, YING, LIJUAN ZHU, XIUCHAN XIAO, et al. "A COMPARATIVE STUDY OF META/PARA SUBSTITUTION EFFECTS ON THE HYDROGEN-BONDED COMPLEX OF ANILINE-H2O: OBSERVATIONS FROM COMPUTATION." Journal of Theoretical and Computational Chemistry 10, no. 05 (2011): 567–79. http://dx.doi.org/10.1142/s0219633611006645.

Full text

Abstract:

Compared with para-substitution, substituent effects ( R = NH 2, OH , CH 3, F , Cl , H , SiH 3, CHO , CN , NO 2) of meta-position effects on hydrogen-bonded complex of aniline with one water molecule are studied at B3LYP/6-311++G(d,p) level of theory. The differences in hydrogen bonding and some properties associated with the H -bond (such as bond length, vibrational frequency, binding energies, p K a values of aniline derivatives) are discussed between meta and para substitutions. Natural bond orbital (NBO) and atoms in molecules (AIM) analysis are applied to investigate the physical origin o

APA, Harvard, Vancouver, ISO, and other styles

37

Ichimura, S. "Development of Atom Counting Technique by Laser Ionization." Microscopy and Microanalysis 3, S2 (1997): 1077–78. http://dx.doi.org/10.1017/s1431927600012277.

Full text

Abstract:

The aim of the present study is to discuss the possibility of “counting atoms” by laser ionization technique, which has been applied to post-ionization in sputtered neutral mass spectrometry. The detection of one H2 molecule was tried under an extremely high vacuum (XHV) condition, since the molecule has a higher ionization energy (15.4 eV) than most of elements and the existence probability of it within laser ionization region is less than one under the condition.Fig.1 shows schematically the experimental setup. The second harmonics (SH) of a picosecond YAG laser was focused with a spherical

APA, Harvard, Vancouver, ISO, and other styles

38

Wojtkowiak, Kamil, Mariusz Michalczyk, Wiktor Zierkiewicz, Aneta Jezierska, and Jarosław J. Panek. "Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic." International Journal of Molecular Sciences 23, no. 22 (2022): 13701. http://dx.doi.org/10.3390/ijms232213701.

Full text

Abstract:

It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum–chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting

APA, Harvard, Vancouver, ISO, and other styles

39

Nguyen, Thao, Mario Aparicio, and Mahmoud A. Saleh. "Gas Phase Ionization of Toluene: Benzylium Versus Tropylium Pathway." Current Physical Chemistry 9, no. 2 (2019): 138–50. http://dx.doi.org/10.2174/1877946809666190722140957.

Full text

Abstract:

Aim: In this investigation, we used accurate mass high-resolution gas chromatography mass spectrometry to study the gas phase carbocations rearrangements and fragmentation of toluene and halo-toluenes as well as their deuterium labeled compounds. Objective: Accurate mass of selected ions from ionization of toluene and related compounds revealed that the initially formed radical cation C7H8 +. does not rearrange to tropylium radical cation contradicting published literature. Methods: When the toluene radical cation was purely selected, it was found to lose a free radical (hydrogen atom) at coll

APA, Harvard, Vancouver, ISO, and other styles

40

Lim, Victoria T., David F. Hahn, Gary Tresadern, Christopher I. Bayly, and David L. Mobley. "Benchmark assessment of molecular geometries and energies from small molecule force fields." F1000Research 9 (December 3, 2020): 1390. http://dx.doi.org/10.12688/f1000research.27141.1.

Full text

Abstract:

Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures o

APA, Harvard, Vancouver, ISO, and other styles

41

Tilavov, Husan Shomurodovich, and Hasan Irgashevich Kadirov. "CATALYTIC SYN TIC SYNTHESIS OF PYRIDINES BASED ON THE CRO THESIS OF PYRIDINES BASED ON THE CROTON FRACTION." Scientific Reports of Bukhara State University 4, no. 5 (2020): 34–40. http://dx.doi.org/10.52297/2181-1466/2020/4/5/2.

Full text

Abstract:

Background. The presence in the molecule of pyridine bases of nitrogen atoms having the properties of the bases determines the specificity of the products of this class and gives ample opportunities for their use in various industries. . The chemistry of pyridine bases is associated with such general theoretical issues as the electronic structure of the cycle, aromaticity, the effect of substituents on the reactivity of heterocycles in nucleophilic substitution reactions, and tautomerism. At the same time, systematic data on the reactions of alkylation with dihalo-alkanes, acylation under low-

APA, Harvard, Vancouver, ISO, and other styles

42

Yavari, Morteza, S. Beyramabadi, Ali Morsali, and Mohammad Bozorgmehr. "(E)-4-(((2-amino-5-chlorophenyl)imino)methyl)-5-(hydroxy-methyl)-2-methylpyridin-3-ol and its Cu(II) complex: Synthesis, DFT calculations and AIM analysis." Journal of the Serbian Chemical Society 85, no. 8 (2020): 1033–46. http://dx.doi.org/10.2298/jsc191010022y.

Full text

Abstract:

Herein, (E)-4-{[(2-amino-5-chlorophenyl)imino]methyl}-5-(hydroxymethyl)- 2-methylpyridin-3-ol [HL] Schiff base and its [Cu(L)Cl] complex were newly synthesized and characterized by several spectroscopic methods. In addition, density functional theory (DFT) methods were used for investigation of the tautomerization of the HL Schiff base, structural parameters of HL and [Cu(L)Cl] species, assignment of the IR vibrational bands and the NMR chemical shifts as well as natural bond orbital (NBO) analyses. The most stable tautomer of the HL Schiff base is the enol form of the meta isomer. The optimiz

APA, Harvard, Vancouver, ISO, and other styles

43

Rudenok, V. A., N. P. Kondrateva, M. G. Krasnolutskaya, S. A. Ovchukova, and R. S. Zeynalov. "Treatment of animals without antibiotics." ТЕНДЕНЦИИ РАЗВИТИЯ НАУКИ И ОБРАЗОВАНИЯ 77, no. 1 (2021): 25–28. http://dx.doi.org/10.18411/trnio-09-2021-06.

Full text

Abstract:

The aim of our study was to develop a technology for treating animals with direct electrochemical blood oxidation. The process of direct electrochemical oxidation of blood occurs on the surface of a platinum wire electrode inserted into the blood vessel along its axis. The wire electrode is not in electrical contact with the DC power source. It is polarized by the current flowing between the additional electrodes. A solution containing a culture of staphylococci was poured into a test tube. After the passage of current through the system, staphylococci die. The cause of their death was not the

APA, Harvard, Vancouver, ISO, and other styles

44

Krasnenko, Veera, Leonid L. Rusevich, Aleksander Platonenko, Yuri A. Mastrikov, Maksim Sokolov, and Eugene A. Kotomin. "Water Splitting on Multifaceted SrTiO3 Nanocrystals: Calculations of Raman Vibrational Spectrum." Materials 15, no. 12 (2022): 4233. http://dx.doi.org/10.3390/ma15124233.

Full text

Abstract:

Various photocatalysts are being currently studied with the aim of increasing the photocatalytic efficiency of water splitting for production of hydrogen as a fuel and oxygen as a medical gas. A noticeable increase of hydrogen production was found recently experimentally on the anisotropic faces (facets) of strontium titanate (SrTiO3, STO) nanoparticles. In order to identify optimal sites for water splitting, the first principles calculations of the Raman vibrational spectrum of the bulk and stepped (facet) surface of a thin STO film with adsorbed water derivatives were performed. According to

APA, Harvard, Vancouver, ISO, and other styles

45

Ono, Ryusei, Hiroto Suzuki, Kenji Miyatake, and Takashi Tokumasu. "Transport Mechanism of Hydroxide Ions Focused on the Vehicle Mechanism Near the Cation Sites in Anion Exchange Membranes." ECS Meeting Abstracts MA2024-02, no. 43 (2024): 2892. https://doi.org/10.1149/ma2024-02432892mtgabs.

Full text

Abstract:

Recently, interest in hydrogen usage and production has surged to achieve a sustainable society, with fuel cells and electrolyzers coming into focus. Fuel cells exhaust only water, offering an eco-friendly alternative. Electrolyzers, utilizing renewable sources like solar and wind, generate hydrogen from water, reducing environmental impact. We explore anion exchange membranes (AEM) used in the fuel cells and electrolyzers. While proton exchange membranes (PEM) are currently more common, AEMs offer advantages such as cost reduction through non-precious metal catalysts, operations with less cor

APA, Harvard, Vancouver, ISO, and other styles

46

Cheshkova, Tatiana V., Татyana А. Sagachenko, Elena Yu Kovalenko, Alexandra S. Vishnevich, Evgeniya B. Golushkova, and Raisa S. Min. "Characteristics of fuel oil obtained from oil of the Krapivinskoe oilfield (report 2)." Bulletin of the Tomsk Polytechnic University Geo Assets Engineering 336, no. 6 (2025): 158–73. https://doi.org/10.18799/24131830/2025/6/5012.

Full text

Abstract:

Relevance. The need to obtain new data on the pattern of thermal transformations of resin, asphaltene and oil components of the fuel oil subjected to thermal or thermocatalytical treatment. These data will help to improve the efficiency of thermal and thermocatalytic treatment of fuel oil for increasing the yield of desired products. Aim. To study the structural organization of resin-asphaltene substances and the molecular composition of oil components isolated from the residue of crude oil produced at the Krapivinskoe field and the products of its thermal destruction. Methods. Transmission el

APA, Harvard, Vancouver, ISO, and other styles

47

Cococcioni, Matteo, and Andrea Floris. "Magnetic Energy Landscape of Dimolybdenum Tetraacetate on a Bulk Insulator Surface." Applied Sciences 11, no. 9 (2021): 3806. http://dx.doi.org/10.3390/app11093806.

Full text

Abstract:

The magnetic states and the magnetic anisotropy barrier of a transition metal molecular complex, dimolybdenum tetraacetate, are investigated via density functional theory (DFT). Calculations are performed in the gas phase and on a calcite (10.4) bulk insulating surface, using the Generalized-Gradient Approximation (GGA)-PBE and the Hubbard-corrected DFT + U and DFT + U + V functionals. The molecular complex (denoted MoMo) contains two central metallic molybdenum atoms, embedded in a square cage of acetate groups. Recently, MoMo was observed to form locally regular networks of immobile molecule

APA, Harvard, Vancouver, ISO, and other styles

48

Nikmaram, Farrokh Roya, and Khadijeh Kalateh. "Aromaticity of C20H10-xFx Corannulene: A Comparative Study by NICS and EFG Methods." Letters in Organic Chemistry 16, no. 7 (2019): 592–99. http://dx.doi.org/10.2174/1570178615666181024115442.

Full text

Abstract:

Corannulene (C20H10) and its fluorinated derivatives, C20H10-xFx (x=1-10), are investigated at the B3LYP/6-31G level of density functional theory. The degree of electron delocalization is evaluated using Nucleus Independent Chemical Shift (NICS) method, Electric Field Gradient (EFG) method and factor of Ellipticity (ε). In this study, the benzene is the scale of comparison as a more aromatic structure. The aromaticity has been evaluated at three points of structures; center of five-member ring (5-MR), center of fluorine-substituted ring (6-MR), and center of other six-member rings. This compar

APA, Harvard, Vancouver, ISO, and other styles

49

Liu, Jia-Bao, Faisal Yasin, Adeel Farooq, and Absar Ul Haq. "Generators of Maximal Subgroups of Harada-Norton and some Linear Groups." Open Chemistry 17, no. 1 (2019): 1509–18. http://dx.doi.org/10.1515/chem-2019-0143.

Full text

Abstract:

AbstractGroup theory, the ultimate theory for symmetry, is a powerful tool that has a direct impact on research in robotics, computer vision, computer graphics and medical image analysis. Symmetry is very important in chemistry research and group theory is the tool that is used to determine symmetry. Usually, it is not only the symmetry of molecule but also the symmetries of some local atoms, molecular orbitals, rotations and vibrations of bonds, etc. that are important. Harada-Norton group is an example of a sporadic simple group. There are 14 maximal subgroups of Harada-Norton group. Generat

APA, Harvard, Vancouver, ISO, and other styles

50

Hikida, Kengo, Hiroto Suzuki, and Takashi Tokumasu. "Effects of Ionomer Film Thickness and Water Content on Oxygen Permeation Properties of PEFC Cathode Catalyst." ECS Meeting Abstracts MA2024-02, no. 43 (2024): 2891. https://doi.org/10.1149/ma2024-02432891mtgabs.

Full text

Abstract:

This study explores the effects of film thickness and water content on the oxygen permeation properties of ionomers in the cathode catalyst layer of Polymer Electrolyte Fuel Cells (PEFCs) using Molecular Dynamics (MD) simulations. The aim is to understand in detail how these parameters influence the efficiency of oxygen transport within the ionomer of the catalyst layer, which is important for optimizing the performance of PEFCs. In this study, we adopt the MD simulation, which computes the time evolution of the positions and velocities of particles based on Newton's equations of motion. In th

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!