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Journal articles on the topic 'Quantum Chemical Interactions'

Author: Grafiati

Published: 7 September 2023

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1

Khavryuchenko, Volodymyr D., Oleksiy V. Khavryuchenko, and Vladyslav V. Lisnyak. "Quantum Chemical Analysis of the Dielectric Constant Concept at Atomic Scale: an Interaction of Probing Point Charges with Silica Cristobalite-Like Cluster." Zeitschrift für Naturforschung A 61, no. 12 (December 1, 2006): 672–74. http://dx.doi.org/10.1515/zna-2006-1209.

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The quantum chemically simulated interaction of probing point charges with the silica cristobalite-like cluster Si48O122H52 [= Si48O70(OH)52] proves that the macroscopic dielectric constant can not be used at atomic scale distances due to quantum chemical interactions.

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2

Parthasarathi, R., Jianhui Tian, Antonio Redondo, and S. Gnanakaran. "Quantum Chemical Study of Carbohydrate–Phospholipid Interactions." Journal of Physical Chemistry A 115, no. 45 (November 17, 2011): 12826–40. http://dx.doi.org/10.1021/jp204015j.

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3

Brandenburg, Jan Gerit, Manuel Hochheim, Thomas Bredow, and Stefan Grimme. "Low-Cost Quantum Chemical Methods for Noncovalent Interactions." Journal of Physical Chemistry Letters 5, no. 24 (December 2014): 4275–84. http://dx.doi.org/10.1021/jz5021313.

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4

Tecmer, Paweł, Frank Schindler, Aleksandra Leszczyk, and Katharina Boguslawski. "Mixed uranyl and neptunyl cation–cation interaction-driven clusters: structures, energetic stability, and nuclear quadrupole interactions." Physical Chemistry Chemical Physics 22, no. 19 (2020): 10845–52. http://dx.doi.org/10.1039/d0cp01068e.

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5

Anugrah, Daru Seto Bagus, Laura Virdy Darmalim, Muhammad Rifky Irwanto Polanen, Permono Adi Putro, Nurwarrohman Andre Sasongko, Parsaoran Siahaan, and Zeno Rizqi Ramadhan. "Quantum Chemical Calculation for Intermolecular Interactions of Alginate Dimer-Water Molecules." Gels 8, no. 11 (October 31, 2022): 703. http://dx.doi.org/10.3390/gels8110703.

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The abundance of applications of alginates in aqueous surroundings created by their interactions with water is a fascinating area of research. In this paper, computational analysis was used to evaluate the conformation, hydrogen bond network, and stabilities for putative intermolecular interactions between alginate dimers and water molecules. Two structural forms of alginate (alginic acid, alg, and sodium alginate, SA) were evaluated for their interactions with water molecules. The density functional theory (DFT-D3) method at the B3LYP functional and the basis set 6-31++G** was chosen for calculating the data. Hydrogen bonds were formed in the Alg-(H2O)n complexes, while the SA-(H2O)n complexes showed an increase in Van der Walls interactions and hydrogen bonds. Moreover, in the SA-(H2O)n complexes, metal-nonmetal bonds existed between the sodium atom in SA and the oxygen atom in water (Na…O). All computational data in this study demonstrated that alginate dimers and water molecules had moderate to high levels of interaction, giving more stability to their complex structure.

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6

Pandey, Sarvesh Kumar, Mohammad Faheem Khan, Shikha Awasthi, Reetu Sangwan, and Sudha Jain. "A Quantum Theory of Atoms-in-Molecules Perspective and DFT Study of Two Natural Products: Trans-Communic Acid and Imbricatolic Acid." Australian Journal of Chemistry 70, no. 3 (2017): 328. http://dx.doi.org/10.1071/ch16406.

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The topological features of the charge densities, ρ(r), and the chemical reactivity of two most biologically relevant and chemically interesting scaffold systems i.e. trans-communic acid and imbricatolic acid have been determined using density functional theory. To identify, characterize, and quantify efficiently, the non-covalent interactions of the atoms in the molecules have been investigated quantitatively using Bader's quantum theory of atoms-in-molecules (QTAIM) technique. The bond path is shown to persist for a range of weak H···H as well as C···H internuclear distances (in the range of 2.0–3.0 Å). These interactions exhibit all the hallmarks of a closed-shell weak interaction. To get insights into both systems, chemical reactivity descriptors, such as HOMO–LUMO, ionization potential, and chemical hardness, have been calculated and used to probe the relative stability and chemical reactivity. Some other useful information is also obtained with the help of several other electronic parameters, which are closely related to the chemical reactivity and reaction paths of the products investigated. Trans-communic acid seems to be chemically more sensitive when compared with imbricatolic acid due to its experimentally observed higher half-maximal inhibitory concentration (bioactivity parameter) value, which is in accordance with its higher chemical reactivity as theoretically predicted using density functional theory-based reactivity index. The quantum chemical calculations have also been performed in solution using different solvents, and the relative order of their structural and electronic properties as well as QTAIM-based parameters show patterns similar to those observed in gas phase only. This study further exemplifies the use and successful application of the bond path concept and the quantum theory of atoms-in-molecules.

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7

Parthasarathi, Ramakrishnan, Jianhui Tian, and S. Gnanakaran. "Elucidation of Carbohydrate-Phospholipid Interactions - a Quantum Chemical Study." Biophysical Journal 100, no. 3 (February 2011): 332a. http://dx.doi.org/10.1016/j.bpj.2010.12.2017.

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8

Beran, S., and L. Kubelkova. "Quantum chemical study of interactions of ketones with zeolites." Journal of Molecular Catalysis 39, no. 1 (January 1987): 13–19. http://dx.doi.org/10.1016/0304-5102(87)80043-3.

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9

Buglak, Andrey A., Ruslan R. Ramazanov, and Alexei I. Kononov. "Silver cluster–amino acid interactions: a quantum-chemical study." Amino Acids 51, no. 5 (March 21, 2019): 855–64. http://dx.doi.org/10.1007/s00726-019-02728-z.

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10

Moha, Verena, Michael Giese, Richard Moha, Markus Albrecht, and Gerhard Raabe. "Quantum-Chemical Investigations on the Structural Variability of Anion–π Interactions." Zeitschrift für Naturforschung A 69, no. 7 (July 1, 2014): 339–48. http://dx.doi.org/10.5560/zna.2014-0031.

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The structural versatility of anion-p interactions was investigated computationally. Employing quantum-chemically optimized structures of a series of C6H6-nFn/Br- complexes and the Coulomb law together with the London formula to calculate the electrostatic and the dispersion energy of the interaction between the anion and the π-system led to the result that up to the number of n = 2 due to a significantly repulsive electrostatic energy of interaction the dispersion energy is not sufficient to stabilize such structures in the gas phase where the anion is located above the plane defined by the aromatic ring. The energy surfaces resulting from the interaction of bromide anions with isolated arenes bearing varying numbers of fluorine atoms in different positions of the aromatic ring also show a pronounced dependency on the subsitution pattern of the aromatic system. Depending on the nature of the electron withdrawing group and its position, the energy surface can have a sharply defined energetically low minimum, in which the anion is ‘fixed’. Other substitution patterns result in very flat energy surfaces, and even a surface with more than two local minima within the scanned area was found. Thus, our study reveals the reason for the experimentally observed structural versatility depending on the substitution pattern in the solid state.

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11

Cukras, Janusz, and Joanna Sadlej. "Towards Quantum-Chemical Modeling of the Activity of Anesthetic Compounds." International Journal of Molecular Sciences 22, no. 17 (August 27, 2021): 9272. http://dx.doi.org/10.3390/ijms22179272.

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The modeling of the activity of anesthetics is a real challenge because of their unique electronic and structural characteristics. Microscopic approaches relevant to the typical features of these systems have been developed based on the advancements in the theory of intermolecular interactions. By stressing the quantum chemical point of view, here, we review the advances in the field highlighting differences and similarities among the chemicals within this group. The binding of the anesthetics to their partners has been analyzed by Symmetry-Adapted Perturbation Theory to provide insight into the nature of the interaction and the modeling of the adducts/complexes allows us to rationalize their anesthetic properties. A new approach in the frame of microtubule concept and the importance of lipid rafts and channels in membranes is also discussed.

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12

Lee, Kayoung, Babak Fallahazad, Jiamin Xue, David C. Dillen, Kyounghwan Kim, Takashi Taniguchi, Kenji Watanabe, and Emanuel Tutuc. "Chemical potential and quantum Hall ferromagnetism in bilayer graphene." Science 345, no. 6192 (July 3, 2014): 58–61. http://dx.doi.org/10.1126/science.1251003.

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Bilayer graphene has a distinctive electronic structure influenced by a complex interplay between various degrees of freedom. We probed its chemical potential using double bilayer graphene heterostructures, separated by a hexagonal boron nitride dielectric. The chemical potential has a nonlinear carrier density dependence and bears signatures of electron-electron interactions. The data allowed a direct measurement of the electric field–induced bandgap at zero magnetic field, the orbital Landau level (LL) energies, and the broken-symmetry quantum Hall state gaps at high magnetic fields. We observe spin-to-valley polarized transitions for all half-filled LLs, as well as emerging phases at filling factors ν = 0 and ν = ±2. Furthermore, the data reveal interaction-driven negative compressibility and electron-hole asymmetry in N = 0, 1 LLs.

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13

Balasubramanian, Krishnan, and Satya P. Gupta. "Quantum Molecular Dynamics, Topological, Group Theoretical and Graph Theoretical Studies of Protein-Protein Interactions." Current Topics in Medicinal Chemistry 19, no. 6 (May 2, 2019): 426–43. http://dx.doi.org/10.2174/1568026619666190304152704.

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Background: Protein-protein interactions (PPIs) are becoming increasingly important as PPIs form the basis of multiple aggregation-related diseases such as cancer, Creutzfeldt-Jakob, and Alzheimer’s diseases. This mini-review presents hybrid quantum molecular dynamics, quantum chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these theoretical studies facilitate the discovery of some PPI inhibitors of therapeutic importance. Objective: The objective of this review is to present hybrid quantum molecular dynamics, quantum chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these theoretical studies enable the discovery of some PPI inhibitors of therapeutic importance. Methods: This article presents a detailed survey of hybrid quantum dynamics that combines classical and quantum MD for PPIs. The article also surveys various developments pertinent to topological, graph theoretical, group theoretical and docking studies of PPIs and highlight how the methods facilitate the discovery of some PPI inhibitors of therapeutic importance. Results: It is shown that it is important to include higher-level quantum chemical computations for accurate computations of free energies and electrostatics of PPIs and Drugs with PPIs, and thus techniques that combine classical MD tools with quantum MD are preferred choices. Topological, graph theoretical and group theoretical techniques are shown to be important in studying large network of PPIs comprised of over 100,000 proteins where quantum chemical and other techniques are not feasible. Hence, multiple techniques are needed for PPIs. Conclusion: Drug discovery and our understanding of complex PPIs require multifaceted techniques that involve several disciplines such as quantum chemistry, topology, graph theory, knot theory and group theory, thus demonstrating a compelling need for a multi-disciplinary approach to the problem.

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14

Ibrahim, Mahmoud A. A., Ossama A. M. Ahmed, Nayra A. M. Moussa, Sabry El-Taher, and Hussien Moustafa. "Comparative investigation of interactions of hydrogen, halogen and tetrel bond donors with electron-rich and electron-deficient π-systems." RSC Advances 9, no. 56 (2019): 32811–20. http://dx.doi.org/10.1039/c9ra08007d.

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15

RANGEL-VÁZQUEZ, N. A., and F. RODRÍGUEZ-FÉLIX. "ANALYSIS OF CHITOSAN/POLYVINYLPYRROLIDONE (STRUCTURE, FTIR, ELECTROSTATIC POTENTIAL, HOMO/LUMO ORBITALS) USING COMPUTATIONAL CHEMISTRY." Latin American Applied Research - An international journal 45, no. 1 (January 30, 2015): 39–44. http://dx.doi.org/10.52292/j.laar.2015.368.

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Chitosan and PVP oligomers were analyzed by means of the HyperChem software 8.0v to determine the theoretical structure. Quantum chemical calculation of geometrical structure and energies were studied using PM3 and AM1 methods in where the Gibbs free energy was calculated with a value of -9028 and -5796 Kcal/mol, respectively; these values showed that the reaction was carried out. Quantum chemical calculations are applied to study the (CT) complexes in order to obtain information on structures and other molecular properties like specific interaction of donor and acceptor. The interaction energy contribution comes from the effects of donor– acceptor interactions and π−π interactions. The HOMO and LUMO were simulated by determinate the transition state and energy band gap. Vibrational analysis shows that the band in 3185 cm-1 and shifting of band to lower wave number clearly indicates strong intermolecular interactions between chitosan and PVP. When the PVP oligomers is blended with chitosan, this absorption signal, which is assigned to the stretching vibration of a C=O group in the pyrrolidone ring, tends to shift to a position of somewhat lower frequency.

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16

Agudelo, W. A., and M. E. Patarroyo. "Quantum Chemical Analysis of MHC-Peptide Interactions for Vaccine Design." Mini-Reviews in Medicinal Chemistry 10, no. 8 (July 1, 2010): 746–58. http://dx.doi.org/10.2174/138955710791572488.

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17

Wang, Linjun, and Oleg V. Prezhdo. "Accurate and Efficient Quantum Chemistry by Locality of Chemical Interactions." Journal of Physical Chemistry Letters 5, no. 24 (December 18, 2014): 4317–18. http://dx.doi.org/10.1021/jz5024256.

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18

González, Ronald, and Maria A. Mroginski. "Fully Quantum Chemical Treatment of Chromophore–Protein Interactions in Phytochromes." Journal of Physical Chemistry B 123, no. 46 (November 2019): 9819–30. http://dx.doi.org/10.1021/acs.jpcb.9b08938.

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19

Šponer, Jiří, and Pavel Hobza. "Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies." Collection of Czechoslovak Chemical Communications 68, no. 12 (2003): 2231–82. http://dx.doi.org/10.1135/cccc20032231.

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Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.

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20

Zheng, Kang, Danping Li, Liu Jiang, Xiaowei Li, Changjian Xie, Ling Feng, Jie Qin, Shaosong Qian, and Qiuxiang Pang. "Revisiting stacking interactions in tetrathiafulvalene and selected derivatives using tight-binding quantum chemical calculations and local coupled-cluster method." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 77, no. 3 (May 13, 2021): 311–20. http://dx.doi.org/10.1107/s2052520621003085.

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The engineering of supramolecular architectures needs accurate descriptions of the intermolecular interactions in crystal structures. Tetrathiafulvalene (TTF) is an effective building block used in the construction of promising functional materials. The parallel packing of the neutral TTF–TTF system was studied previously using the high-level quantum chemical method, advancing it as a valuable model system. The recently developed tight-binding quantum chemical method GFN2-xTB and local coupled-cluster method DLPNO-CCSD(T) were used to investigate the stacking interactions of TTF and selected derivatives deposited in the Cambridge Structural Database. Using the interaction energy of the TTF–TTF dimer calculated at the CCSD(T)/CBS level as the reference, the accuracies of the two methods are investigated. The energy decomposition analysis within the DLPNO-CCSD(T) framework reveals the importance of dispersion interaction in the TTF-related stacking systems. The dispersion interaction density plot vividly shows the magnitude and distribution of the dispersion interaction, providing a revealing insight into the stacking interactions in crystal structures. The results show that the GFN2-xTB and DLPNO-CCSD(T) methods could achieve accuracy at an affordable computational cost, which would be valuable in understanding the nature of parallel stacking in supramolecular systems.

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21

de Rezende, Fátima M. P., Marilua A. Moreira, Rodrigo A. Cormanich, and Matheus P. Freitas. "Conformational analysis, stereoelectronic interactions and NMR properties of 2-fluorobicyclo[2.2.1]heptan-7-ols." Beilstein Journal of Organic Chemistry 8 (August 2, 2012): 1227–32. http://dx.doi.org/10.3762/bjoc.8.137.

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Four diastereoisomers of 2-fluorobicyclo[2.2.1]heptan-7-ols were computationally investigated by using quantum-chemical calculations, and their relative energies were analyzed on the basis of stereoelectronic interactions, particularly the presence or otherwise of the F∙∙∙HO intramolecular hydrogen bond in the syn-exo isomer. It was found through NBO and AIM analyses that such an interaction contributes to structural stabilization and that the 1h J F,H(O) coupling constant in the syn-exo isomer is modulated by the n F→σ*OH interaction, i.e., the quantum nature of the F∙∙∙HO hydrogen bond.

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22

Veljković, Ivana S., Dušan Ž. Veljković, Gordana G. Sarić, Ivana M. Stanković, and Snežana D. Zarić. "What is the preferred geometry of sulfur–disulfide interactions?" CrystEngComm 22, no. 43 (2020): 7262–71. http://dx.doi.org/10.1039/d0ce00211a.

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23

Grabowski, Sławomir J. "Hydrogen Bond and Other Lewis Acid–Lewis Base Interactions as Preliminary Stages of Chemical Reactions." Molecules 25, no. 20 (October 13, 2020): 4668. http://dx.doi.org/10.3390/molecules25204668.

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Various Lewis acid–Lewis base interactions are discussed as initiating chemical reactions and processes. For example, the hydrogen bond is often a preliminary stage of the proton transfer process or the tetrel and pnicogen bonds lead sometimes to the SN2 reactions. There are numerous characteristics of interactions being first stages of reactions; one can observe a meaningful electron charge transfer from the Lewis base unit to the Lewis acid; such interactions possess at least partly covalent character, one can mention other features. The results of different methods and approaches that are applied in numerous studies to describe the character of interactions are presented here. These are, for example, the results of the Quantum Theory of Atoms in Molecules, of the decomposition of the energy of interaction or of the structure-correlation method.

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24

Clark, Timothy, Jane S. Murray, and Peter Politzer. "A perspective on quantum mechanics and chemical concepts in describing noncovalent interactions." Physical Chemistry Chemical Physics 20, no. 48 (2018): 30076–82. http://dx.doi.org/10.1039/c8cp06786d.

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Since quantum mechanical calculations do not typically lend themselves to chemical interpretation, analyses of bonding interactions depend largely upon models (the octet rule, resonance theory, charge transfer, etc.). This sometimes leads to a blurring of the distinction between mathematical modelling and physical reality.

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25

Hanafy, Mahmoud, and Muhammad Maher. "An Approach of Statistical Corrections to Interactions in Hadron Resonance Gas." Advances in High Energy Physics 2021 (May 26, 2021): 1–10. http://dx.doi.org/10.1155/2021/6660872.

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We propose a new model for hadrons with quantum mechanical attractive and repulsive interactions sensitive to some spatial correlation length parameter inspired by the Beth-Uhlenbeck quantum mechanical nonideal gas model (Uhlenbeck and Beth, 1937). We confront the thermodynamics calculated using our model with a corresponding recent lattice data at four different values of the baryon chemical potential, μ b = 0 , 170 , 340 , 425 MeV over temperatures ranging from 130 MeV to 200 MeV and for five values for the correlation length ranging from 0 to 0.2 fm. For equilibrium temperatures up to the vicinity of the chiral phase transition temperature ≃160 MeV, a decent fitting between the model and the lattice data is observed for different values of r , especially at μ b , r = 170 , 0.05 , 340 , 0.1 , and 340 , 0.15 , where μ b is in MeV and r is in fm. For the vanishing chemical potential, the uncorrelated model r = 0 , which corresponds to the ideal hadron resonance gas model, seems to offer the best fit. The quantum hadron correlations seem to be more probable at nonvanishing chemical potentials, especially within the range μ b ∈ 170 , 340 MeV .

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26

Ivanova, Bojidarka, and Michael Spiteller. "Physical Properties and Molecular Conformations of Indole Alkaloids and Model Protein Interactions – Theoretical vs. Experimental Study." Natural Product Communications 7, no. 2 (February 2012): 1934578X1200700. http://dx.doi.org/10.1177/1934578x1200700206.

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The physical properties and molecular structure of five natural indole alkaloids (IAs) and their interaction with protein targets have been studied, experimentally and theoretically. Electronic absorption (EAs) and CD spectroscopy, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), as well as imaging mass spectrometric techniques (IMS) were used, analyzing the isolated alkaloids and corresponding IAs/protein molecular complexes. Theoretical quantum chemical DFT calculations were also applied. The mechanism of their biological activity and structure-activity relationship as potential neurologically active compounds were studied, using the model interactions with 5HT2A receptors. The gas-phase stable molecular fragments of the IAs are discussed comparing the experimental mass spectrometric data and theoretical quantum chemical DFT calculations of the different molecular fragments of the IAs.

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27

Pham, Nhat Vu, Nguyen Thanh Si, Mai Mac Son, Pham Thi Bich Thao, Nguyen Van Hong, and Pham Tran Nguyen Nguyen. "Quantum chemical studies of interactions between Au6 cluster and DNA bases." Science and Technology Development Journal - Natural Sciences 4, no. 2 (June 22, 2020): First. http://dx.doi.org/10.32508/stdjns.v4i2.871.

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Density functional theory (DFT) is employed to examine the adsorption mechanism of DNA bases (adenine, guanine, cytosine, and thymine) on the gold surface using Au6 cluster as model reactant. Geometries of resulting complexes are optimized using the PBE functional in conjunction with the cc-pVTZ-PP consistent-correlation pseudopotential basis set for gold and the cc-pVTZ basis set for the non-metals. The binding sites and energies, along with several quantum chemical indicators are also investigated at the same level of theory. The binding energies between Au6 cluster and DNA bases are computed to be around 14–25 kcal/mol in gas-phase and slightly reduced to 10 – 20 kcal/mol in the water environment. Cytosine has the highest affinity with gold cluster, decreasing as follows cytosine > adenine guanine > thymine. If a visible light with a frequency of Hz (500 nm) is applied, the time for the recovery of Au6 from the complexes will be in the range of (for thymine) to 10 (for cytosine) seconds at 298 K in water. In addition, the geometric structures of both the gold cluster and DNA bases are almost unchanged during the complexation. The gold cluster is found to benefit from a larger change of energy gap that could be converted to an electrical signal for the detection of these molecules. Current results could provide us with fundamentals for understanding the DNA bases absorption on gold nanoparticle surfaces at the atomic and molecular levels.

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Wójcik, G., I. Mossakowska, J. Szymczak, S. Roszak, and J. Leszczynski. "X-ray diffraction and quantum chemical studies of interactions in polymorphs." Acta Crystallographica Section A Foundations of Crystallography 62, a1 (August 6, 2006): s180. http://dx.doi.org/10.1107/s0108767306096413.

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29

Plasser, Felix, and Hans Lischka. "Analysis of Excitonic and Charge Transfer Interactions from Quantum Chemical Calculations." Journal of Chemical Theory and Computation 8, no. 8 (July 17, 2012): 2777–89. http://dx.doi.org/10.1021/ct300307c.

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Wang, Huanjiang, Haiyan Xu, Weihong Jia, Juan Liu, and Sili Ren. "Revealing the Intermolecular Interactions of Asphaltene Dimers by Quantum Chemical Calculations." Energy & Fuels 31, no. 3 (February 24, 2017): 2488–95. http://dx.doi.org/10.1021/acs.energyfuels.6b02738.

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31

Tam, S. W., J. Wright, L. A. Curtiss, and C. E. Johnson. "Investigations of hydrogen/Li2O surface interactions via quantum chemical cluster methods." Journal of Nuclear Materials 179-181 (March 1991): 859–62. http://dx.doi.org/10.1016/0022-3115(91)90224-u.

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32

Petukhov, V. N., S. A. Shchelkunov, O. A. Malyshev, D. A. Kubak, and T. I. Yushina. "Influence of Water on the Quantum Chemical Interactions in Coal Flotation." Coke and Chemistry 65, no. 11 (November 2022): 538–44. http://dx.doi.org/10.3103/s1068364x22700272.

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33

Heßelmann, Andreas. "Correlation effects and many-body interactions in water clusters." Beilstein Journal of Organic Chemistry 14 (May 2, 2018): 979–91. http://dx.doi.org/10.3762/bjoc.14.83.

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Background: The quantum-chemical description of the interactions in water clusters is an essential basis for deriving accurate and physically sound models of the interaction potential for water to be used in molecular simulations. In particular, the role of many-body interactions beyond the two-body interactions, which are often not explicitly taken into account by empirical force fields, can be accurately described by quantum chemistry methods on an adequate level, e.g., random-phase approximation electron correlation methods. The relative magnitudes of the different interaction energy contributions obtained by accurate ab initio calculations can therefore provide useful insights that can be exploited to develop enhanced force field methods. Results: In line with earlier theoretical studies of the interactions in water clusters, it has been found that the main contribution to the many-body interactions in clusters with a size of up to N = 13 molecules are higher-order polarisation interaction terms. Compared to this, many-body dispersion interactions are practically negligible for all studied sytems. The two-body dispersion interaction, however, plays a significant role in the formation of the structures of the water clusters and their stability, since it leads to a distinct compression of the cluster sizes compared to the structures optimized on an uncorrelated level. Overall, the many-body interactions amount to about 13% of the total interaction energy, irrespective of the cluster size. The electron correlation contribution to these, however, amounts to only about 30% to the total many-body interactions for the largest clusters studied and is repulsive for all structures considered in this work. Conclusion: While this shows that three- and higher-body interactions can not be neglected in the description of water complexes, the electron correlation contributions to these are much smaller in comparison to the two-body electron correlation effects. Efficient quantum chemistry approaches for describing intermolecular interactions between water molecules may therefore describe higher-body interactions on an uncorrelated Hartree–Fock level without a serious loss in accuracy.

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Zheng, Min, Nigel W. Moriarty, Yanting Xu, Jeffrey R. Reimers, Pavel V. Afonine, and Mark P. Waller. "Solving the scalability issue in quantum-based refinement: Q|R#1." Acta Crystallographica Section D Structural Biology 73, no. 12 (November 30, 2017): 1020–28. http://dx.doi.org/10.1107/s2059798317016746.

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Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately asnm, wherenis the number of atoms andm(≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package calledQ|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach inQ|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

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Sulimov, Alexey, Danil Kutov, Ivan Ilin, and Vladimir Sulimov. "Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations." Nanomaterials 12, no. 2 (January 15, 2022): 274. http://dx.doi.org/10.3390/nano12020274.

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The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

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Zhou, Yujing, and Ming Wah Wong. "Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations." Molecules 27, no. 3 (January 21, 2022): 706. http://dx.doi.org/10.3390/molecules27030706.

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Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future.

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Chibisov, Andrey, Maxim Aleshin, and Mary Chibisova. "DFT Analysis of Hole Qubits Spin State in Germanium Thin Layer." Nanomaterials 12, no. 13 (June 29, 2022): 2244. http://dx.doi.org/10.3390/nano12132244.

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Due to the presence of a strong spin–orbit interaction, hole qubits in germanium are increasingly being considered as candidates for quantum computing. These objects make it possible to create electrically controlled logic gates with the basic properties of scalability, a reasonable quantum error correction, and the necessary speed of operation. In this paper, using the methods of quantum-mechanical calculations and considering the non-collinear magnetic interactions, the quantum states of the system 2D structure of Ge in the presence of even and odd numbers of holes were investigated. The spatial localizations of hole states were calculated, favorable quantum states were revealed, and the magnetic structural characteristics of the system were analyzed.

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38

Macha, Prathyushakrishna, Maricris L. Mayes, Benjoe Rey B. Visayas, Vikas Soni, Vamshikrishna Reddy Sammeta, and Milana C. Vasudev. "Influence of dityrosine nanotubes on the expression of dopamine and differentiation in neural cells." Journal of Materials Chemistry B 9, no. 18 (2021): 3900–3911. http://dx.doi.org/10.1039/d0tb02680h.

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This study reports the quantum chemical calculations of interactions and self-assembly of dityrosine nanotubes. These nanotubes were studied for application as a biologically functional scaffold and their interactions with neural cells.

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39

Agrawal, Megha, Amit Kumar, and Archana Gupta. "Conformational stability, spectroscopic signatures and biological interactions of proton pump inhibitor drug lansoprazole based on structural motifs." RSC Advances 7, no. 66 (2017): 41573–84. http://dx.doi.org/10.1039/c7ra00130d.

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40

Biesner, Tobias, and Ece Uykur. "Pressure-Tuned Interactions in Frustrated Magnets: Pathway to Quantum Spin Liquids?" Crystals 10, no. 1 (December 18, 2019): 4. http://dx.doi.org/10.3390/cryst10010004.

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Quantum spin liquids are prime examples of strongly entangled phases of matter with unconventional exotic excitations. Here, strong quantum fluctuations prohibit the freezing of the spin system. On the other hand, frustrated magnets, the proper platforms to search for the quantum spin liquid candidates, still show a magnetic ground state in most of the cases. Pressure is an effective tuning parameter of structural properties and electronic correlations. Nevertheless, the ability to influence the magnetic phases should not be forgotten. We review experimental progress in the field of pressure-tuned magnetic interactions in candidate systems. Elaborating on the possibility of tuned quantum phase transitions, we further show that chemical or external pressure is a suitable parameter in these exotic states of matter.

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Yokogawa, Daisuke, Hirofumi Sato, Sergey Gusarov, and Andriy Kovalenko. "Development of additive isotropic site potential for exchange-repulsion energy, based on intermolecular perturbation theory." Canadian Journal of Chemistry 87, no. 12 (December 2009): 1727–32. http://dx.doi.org/10.1139/v09-131.

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We have developed an additive spherical site potential for exchange-repulsion energy by applying the local density approximation in Hilbert space, the local-site approximation, and the s-type auxiliary basis set to the equation derived from intermolecular perturbation theory. The method efficiently addresses the decomposition of molecular interactions derived from quantum chemistry into additive spherical site potentials, required as force field input in a statistical-mechanical, reference interaction site model (RISM and 3D-RISM), molecular theory of solvation. The present method reproduces the exchange-repulsion energy between simple molecules obtained from quantum chemical calculations.

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Wylie, Luke, Zoe L. Seeger, Amber N. Hancock, and Ekaterina I. Izgorodina. "Increased stability of nitroxide radicals in ionic liquids: more than a viscosity effect." Physical Chemistry Chemical Physics 21, no. 6 (2019): 2882–88. http://dx.doi.org/10.1039/c8cp04854a.

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43

Molčanov, Krešimir, and Biserka Kojić-Prodić. "Towards understanding π-stacking interactions between non-aromatic rings." IUCrJ 6, no. 2 (February 2, 2019): 156–66. http://dx.doi.org/10.1107/s2052252519000186.

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The first systematic study of π interactions between non-aromatic rings, based on the authors' own results from an experimental X-ray charge-density analysis assisted by quantum chemical calculations, is presented. The landmark (non-aromatic) examples include quinoid rings, planar radicals and metal-chelate rings. The results can be summarized as: (i) non-aromatic planar polyenic rings can be stacked, (ii) interactions are more pronounced between systems or rings with little or no π-electron delocalization (e.g. quinones) than those involving delocalized systems (e.g. aromatics), and (iii) the main component of the interaction is electrostatic/multipolar between closed-shell rings, whereas (iv) interactions between radicals involve a significant covalent contribution (multicentric bonding). Thus, stacking covers a wide range of interactions and energies, ranging from weak dispersion to unlocalized two-electron multicentric covalent bonding (`pancake bonding'), allowing a face-to-face stacking arrangement in some chemical species (quinone anions). The predominant interaction in a particular stacked system modulates the physical properties and defines a strategy for crystal engineering of functional materials.

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Rimola, Albert, Mariona Sodupe, and Piero Ugliengo. "Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies." Life 9, no. 1 (January 17, 2019): 10. http://dx.doi.org/10.3390/life9010010.

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There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic–mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic–mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic–mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.

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Jiménez, Eddy I., Wilmer E. Vallejo Narváez, Tomás Rocha-Rinza, and Marcos Hernández-Rodríguez. "Design and application of a bifunctional organocatalyst guided by electron density topological analyses." Catalysis Science & Technology 7, no. 19 (2017): 4470–77. http://dx.doi.org/10.1039/c7cy00430c.

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46

YANG, SHI-JIE, YUECHAN LIU, and SHIPING FENG. "THERMODYNAMICAL PROPERTIES OF A TRAPPED INTERACTING BOSE GAS." Modern Physics Letters B 26, no. 08 (March 30, 2012): 1250053. http://dx.doi.org/10.1142/s0217984912500534.

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The thermodynamical properties of interacting Bose atoms in a harmonic potential are studied within the mean-field approximation. For weak interactions, the quantum statistics is equivalent to an ideal gas in an effective mean-field potential. The eigenvalue of the Gross–Pitaevskii equation is identified as the chemical potential of the ideal gas. The condensation temperature and density profile of atoms are calculated. It is found that the critical temperature Tc decreases as the interactions increase. Below the critical point, the condensation fraction exhibits a universal relation of N0/N = 1-(T/Tc)γ, with the index γ ≈ 2.3 independent of the interaction strength, the chemical potential, as well as the frequency of the confining potential.

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47

He, Zhicong, Cheng Xu, Wenhao He, Jinhu He, Yunpeng Zhou, and Fang Li. "Principle and Applications of Multimode Strong Coupling Based on Surface Plasmons." Nanomaterials 12, no. 8 (April 7, 2022): 1242. http://dx.doi.org/10.3390/nano12081242.

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In the past decade, strong coupling between light and matter has transitioned from a theoretical idea to an experimental reality. This represents a new field of quantum light–matter interaction, which makes the coupling strength comparable to the transition frequencies in the system. In addition, the achievement of multimode strong coupling has led to such applications as quantum information processing, lasers, and quantum sensors. This paper introduces the theoretical principle of multimode strong coupling based on surface plasmons and reviews the research related to the multimode interactions between light and matter. Perspectives on the future development of plasmonic multimode coupling are also discussed.

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Đorđević, Ivana S., Marko Popadić, Mirjana Sarvan, Marija Petković-Benazzouz, and Goran V. Janjić. "Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 76, no. 1 (January 29, 2020): 122–36. http://dx.doi.org/10.1107/s2052520619016287.

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Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C—H...Se and C—H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C—H...Se (∼−0.8 kcal mol−1) and C—H...S interactions are weaker than the most stable parallel interaction (∼−3.3 kcal mol−1) and electrostatic interactions of σ/π type (∼−2.6 kcal mol−1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O—H...Se (∼−4.4 kcal mol−1) and N—H...Se interactions (∼−2.2 kcal mol−1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

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Ganesamoorthy, C., S. Heimann, S. Hölscher, R. Haack, C. Wölper, G. Jansen, and S. Schulz. "Synthesis, structure and dispersion interactions in bis(1,8-naphthalendiyl)distibine." Dalton Transactions 46, no. 28 (2017): 9227–34. http://dx.doi.org/10.1039/c7dt02165h.

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Naph₂Sb₂1shows intermolecular interactions in the solid state. Quantum chemical calculations of1and the lighter (P, As) and heavier (Bi) congeners showed that intermolecular E⋯E interactions (E = P, As, Sb, Bi) are dispersion dominated, while E⋯π interactions additionally contained a significant electrostatic contribution.

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50

YF, Chang. "Information, Entropy Decrease and Simulations of Astrophysical Evolutions." Physical Science & Biophysics Journal 5, no. 2 (2021): 1–11. http://dx.doi.org/10.23880/psbj-16000181.

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Entropy is a great development in science. We proposed that entropy decrease due to internal interactions in the isolated system is possible. We define the entangled scale, which mainly involves the number n and entangled degree. Since coherence, entanglement and correlation are all internal interactions in information systems, we discuss quantitatively entropy decrease along coherence, and entropy increase only for incoherence. From beginning quantum heat engine, we must systematically study quantum thermodynamics. Based on some astrophysical simulation models, they shown that the universe evolves from disorder to structures, which correspond to entropy decrease. This is consistence with theoretical result. The simulation must be an isolated system only using internal gravitational interactions.

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