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Journal articles on the topic 'Molecular interaction effects'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Xiaowei Jia, Xiaowei Jia, Jianqi Shen Jianqi Shen, Lufang Guo Lufang Guo, and Chen Wan Chen Wan. "Diffraction effects in planar wave-sphere interaction." Chinese Optics Letters 11, no. 5 (2013): 050501–50504. http://dx.doi.org/10.3788/col201311.050501.

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NAKANO, MASAYOSHI, SATORU YAMADA, MASAHIRO TAKAHATA, and KIZASHI YAMAGUCHI. "SECOND HYPERPOLARIZABILITIES OF MOLECULAR AGGREGATES: INTERMOLECULAR ORBITAL-INTERACTION AND SPIN-CONFIGURATION EFFECTS." International Journal of Nanoscience 01, no. 05n06 (2002): 545–49. http://dx.doi.org/10.1142/s0219581x02000644.

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Toward an understanding of intermolecular-interaction effects on the third-order nonlinear optical properties of nanostructured molecular aggregates, we investigate the longitudinal second hyperpolarizabilities (γ) of model dimers composed of neutral ( C 5 H 7) and charged [Formula: see text] monomers using ab initio molecular orbital methods. It is found that π–π orbital interaction in the stacking direction remarkably affects the γ values of dimers, while the difference in spin configuration hardly causes significant changes in γ for the present models due to weak exchange interactions betwe

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3

VASHISHTA, PRIYA, RAJIV K. KALIA, AIICHIRO NAKANO, and JIN YU. "MOLECULAR DYNAMICS AND QUANTUM MOLECULAR DYNAMICS SIMULATIONS ON PARALLEL ARCHITECTURES." International Journal of Modern Physics C 05, no. 02 (1994): 281–83. http://dx.doi.org/10.1142/s0129183194000325.

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Efficient parallel molecular dynamics (MD) algorithm based on the multiple-time-step (MTS) approach is developed. The MTS-MD algorithm is used to study structural correlations in porous silica at densities 2.2 g/cm3 to 1.6 g/cm3. Nature of phonons and effects of hydrostatic pressure in solid C60 is studied using the tight-binding MD method within a unified interaction model which includes intermolecular and intra-molecular interactions.

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Calvo, Jorge, David Zueco, and Luis Martin-Moreno. "Ultrastrong coupling effects in molecular cavity QED." Nanophotonics 9, no. 2 (2020): 277–81. http://dx.doi.org/10.1515/nanoph-2019-0403.

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AbstractThe spectrum and energy dynamics for a system that comprises a molecule interacting with a cavity photon is analyzed, taking into account the effect of both molecular vibrations and counter-rotating terms (CR) in the dipole Hamiltonian. The CR terms do not have a strong effect on the spectrum even for moderately large values of the exciton-photon interaction. However, it is shown that the polariton subspace is governed by an effective Quantum-Rabi Hamiltonian, where polaritons act as a two-level system and the phonons play the role of cavity photons. The effect of the CR terms is ampli

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5

S, Bhattacharjee. "Molecular Insights into the Interaction of Vitamin C (Ascorbic Acid) with Glutathione Peroxidase: A Comprehensive Computational Study." Medicinal and Analytical Chemistry International Journal 8, no. 1 (2024): 1–8. http://dx.doi.org/10.23880/macij-16000188.

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This research investigates the molecular interaction between vitamin C (ascorbic acid) and glutathione peroxidase (GPX), a key enzyme in the antioxidant defense system. Oxidative stress-induced damage, caused by an imbalance in reactive oxygen species (ROS) production, is implicated in various health issues. Vitamin C, a potent antioxidant, is known for its ability to neutralize free radicals and support overall cellular health. Despite numerous studies on the protective effects of vitamin C, the molecular details of its interaction with GPX remain unclear. In this study, we employ computation

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6

Mahmood, T., M. H. Rahman, G. R. Stringam, J. P. Raney, and A. G. Good. "Molecular markers for seed colour in Brassica juncea." Genome 48, no. 4 (2005): 755–60. http://dx.doi.org/10.1139/g04-122.

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A detailed RFLP map was used to map QTLs associated with seed colour in Brassica juncea using a doubled-haploid population derived from a cross between a black/brown-seeded cultivar and a yellow-seeded breeding line. Segregation analysis suggested that seed colour was under control of 2 unlinked loci with duplicate gene action. However, QTL analysis revealed 3 QTLs, SC-B4, SC-A10 and SC-A6, affecting seed colour. The QTLs were consistent across environments, and individually explained 43%, 31%, and 16%, respectively, and collectively 62% of the phenotypic variation in the population. Digenic i

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Szczȩśniak, M. M., Steve Scheiner, and Pavel Hobza. "Effects of electron correlation upon molecular interactions: Correction of the electrostatic interaction between DNA bases." Journal of Molecular Structure: THEOCHEM 179, no. 1 (1988): 177–84. http://dx.doi.org/10.1016/0166-1280(88)80122-2.

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8

Carroll, P. K., and Kh I. Hagim. "Configuration interaction effects in molecular spectra. N2: a case study." Physica Scripta 37, no. 5 (1988): 682–93. http://dx.doi.org/10.1088/0031-8949/37/5/005.

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Lai, Jing-jing, Huai-yu Yan, Yan Liu, and Yanbin Huang. "Effects of PEG molecular weight on its interaction with albumin." Chinese Journal of Polymer Science 33, no. 10 (2015): 1373–79. http://dx.doi.org/10.1007/s10118-015-1687-y.

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10

Minagawa, Keiji, Hirokazu Okamura, Seizo Masuda, and Masami Tanaka. "NMR Analysis of Molecular Motion of Polyurethane Fluid." International Journal of Modern Physics B 13, no. 14n16 (1999): 1975–82. http://dx.doi.org/10.1142/s0217979299002034.

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Urethane modified polyethers having hard-soft-hard structure were prepared as simple model compounds for homogeneous ER fluids. The NMR relaxation analysis was applied to these polyurethane ER fluids, and the molecular motions and interactions were studied with a series of the data of spin-lattice relaxation time T 1 and the spin-spin relaxation time T 2. Two hard-soft-hard urethanes, which showed opposite ER effects, were found to have similar relaxation behaviors under no electric field. The temperature dependence of T 1 indicated existence of significant intermolecular interaction and the c

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11

He, Yan, Hongfei Liu, Wangqing Bian, et al. "Molecular Interactions for the Curcumin-Polymer Complex with Enhanced Anti-Inflammatory Effects." Pharmaceutics 11, no. 9 (2019): 442. http://dx.doi.org/10.3390/pharmaceutics11090442.

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The molecular interactions between compound and polymeric carriers are expected to highly contribute to high drug load and good physical stability of solid dispersions. In this study, a series of amorphous solid dispersions (ASD) of Curcumin (Cur) were prepared with different polymers by the solvent evaporation method. With the carrier polyvinylpyrrolidone (PVP), the amorphous solid dispersion system exhibits a better solubility and stability than that with poloxamers and HP-β-CD due to the strong drug-polymer interaction. The drug/polymer interaction and their binding sites were investigated

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12

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 contri

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13

Illingworth, Christopher J., and Carmen Domene. "Many-body effects and simulations of potassium channels." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 465, no. 2106 (2009): 1701–16. http://dx.doi.org/10.1098/rspa.2009.0014.

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The electronic polarizability of an ion or a molecule is a measure of the relative tendency of its electron cloud to be distorted from its normal shape by an electric field. On the molecular scale, in a condensed phase, any species sits in an electric field due to its neighbours, and the resulting polarization is an important contribution to the total interaction energy. Electrostatic interactions are crucial for determining the majority of chemical–physical properties of the system and electronic polarization is a fundamental component of these interactions. Thus, polarization effects should

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Bu, Fanqiang, Lin Chen, Ying Sun, Bing Zhao та Ruige Wang. "Insight into the Binding Interaction between PEDCs and hERRγ Utilizing Molecular Docking and Molecular Dynamics Simulations". Molecules 29, № 14 (2024): 3256. http://dx.doi.org/10.3390/molecules29143256.

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Phenolic environmental endocrine-disrupting chemicals (PEDCs) are persistent EDCs that are widely found in food packaging materials and environmental media and seriously threaten human health and ecological security. Human estrogen-related receptor γ (hERRγ) has been proposed as a mediator for the low-dose effects of many environmental PEDCs; however, the atomic-level descriptions of dynamical structural features and interactions of hERRγ and PEDCs are still unclarified. Herein, how three PEDCs, 4-(1-methylpropyl)phenol (4-sec-butylphenol), 5,6,7,8-tetrahydro-2-naphthol (tetrahydro-2-napthol),

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Shirakawa, Masayuki, Takayoshi Kobayashi, and Eiji Tokunaga. "Solvent Effects in Highly Efficient Light-Induced Molecular Aggregation." Applied Sciences 9, no. 24 (2019): 5381. http://dx.doi.org/10.3390/app9245381.

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It has been reported that when irradiated with laser light non-resonant with the main absorption peaks, porphyrin molecules (4-[10,15,20-tris(4-sulfophenyl)-21,24-dihydroporphyrin-5-yl]benzenesulfonic acid, TPPS) in an aqueous solution become 10,000 to 100,000 times more efficient in light-induced molecular aggregation than expected from the ratio of gradient force potential to the thermal energy of molecules at room temperature. To determine the mechanism of this phenomenon, experiments on the light-induced aggregation of TPPS in alcohol solutions (methanol, ethanol, and butanol) were perform

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LIU, M. B., J. Z. CHANG, H. T. LIU, and T. X. SU. "MODELING OF CONTACT ANGLES AND WETTING EFFECTS WITH PARTICLE METHODS." International Journal of Computational Methods 08, no. 04 (2011): 637–51. http://dx.doi.org/10.1142/s0219876211002733.

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The physics of fluid–fluid–solid contact line dynamics and wetting behaviors are closely related to the inter-particle and intra-molecular hydrodynamic interactions of the concerned multiple phase system. Investigation of surface tension, contact angle, and wetting behavior using molecular dynamics (MD) is practical only on extremely small time scales (nanoseconds) and length scales (nanometers) even if the most advanced high-performance computers are used. In this article we introduce two particle methods, which are smoothed particle hydrodynamics (SPH) and dissipative particle dynamics (DPD)

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Shoda, Takayuki, and Tetsuo Murayama. "Intermolecular Interaction and Molecular Structure Deformation Effects on Hole Mobility in Molecular Doped Polymers." NIP & Digital Fabrication Conference 16, no. 1 (2000): 443–46. http://dx.doi.org/10.2352/issn.2169-4451.2000.16.1.art00007_2.

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Pivovarova, Nadezhda Anatolievna. "Characteristics of molecular interaction in oil dispersed systems." Oil and gas technologies and environmental safety 2023, no. 2 (2023): 23–33. http://dx.doi.org/10.24143/1812-9498-2023-2-23-33.

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Oil, gas condensates, oil products present a complex colloidal-dispersed system which often demonstrates the abnormally changing properties when external conditions change. Mixing the petroleum products can be accompanied by a non-linear behavior accompanied by synergistic and antagonistic effects. Understanding of the oil and oil products as oil dispersed systems, the specific features of intermolecular interaction largely clarify their behavior, changes in properties, chemistry and mechanism of reactions occurring in them. Petroleum systems are polydisperse, in which the components can coexi

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19

Hai, Ying, Kaili Qu, Yaquan Liu, and Chunyan Zhao. "Binding mechanism of single-walled carbon nanotubes (SWCNTs) to serum albumin: spectroscopy and molecular modelling exploration." Environmental Chemistry 15, no. 5 (2018): 278. http://dx.doi.org/10.1071/en18043.

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Environmental contextSingle-walled carbon nanotubes can have adverse physiological effects by interacting with proteins. Using serum bovine albumin as a model protein, we investigate the conformational changes in proteins at the tertiary structure level upon interaction with carbon nanotubes. This specific study of a model protein helps our understanding of the general binding mechanisms involved, and allows us to predict the potential adverse effects of carbon nanotubes interacting with other proteins. AbstractConsidering the large-scale production of diversified nanomaterials, it is of param

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20

Gao, Qi, and Dangling Ming. "Protein-protein interactions enhance the thermal resilience of SpyRing-cyclized enzymes: A molecular dynamic simulation study." PLOS ONE 17, no. 2 (2022): e0263792. http://dx.doi.org/10.1371/journal.pone.0263792.

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Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the assembly of biostructures, cancer cell recognition and other fields. It was believed that the covalent cyclization of protein skeleton caused by SpyRing reduces the conformational entropy of biological structure and improves its rigidity, thus improving the thermal resilience of the target enzyme. However, the effects of SpyTag/ SpyCatcher interaction with this enzyme are poorly understood, and th

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21

Kano, Koji. "Molecular complexes of water-soluble porphyrins." Journal of Porphyrins and Phthalocyanines 08, no. 02 (2004): 148–55. http://dx.doi.org/10.1142/s1088424604000143.

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Water-soluble porphyrins tend to form self-aggregates under certain conditions. The structure of the self-aggregate (H-type dimer, H-type higher aggregate, or J-aggregate) sensitively depends on the structure of the peripheral substituents at the meso-positions of the porphyrin. Water-soluble porphyrins also form relatively stable π-stacked complexes with various aromatics. Polar effects are important in complexation of anionic porphyrins with anthraquinonesulfonates. The results suggest that the main attractive interaction for formation of π-stacked complexes of water-soluble porphyrins is th

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22

Godiksen, Rasmus B., Zachary T. Trautt, Moneesh Upmanyu, Søren Schmidt, and Dorte Juul Jensen. "Simulation of Recrystallization Using Molecular Dynamics; Effects of the Interatomic Potential." Materials Science Forum 558-559 (October 2007): 1081–86. http://dx.doi.org/10.4028/www.scientific.net/msf.558-559.1081.

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Recrystallization is governed by the migration of high angle grain boundaries traveling through a deformed material driven by the excess energy located primarily in dislocation structures. A method for investigating the interaction between a migrating grain boundary and dislocation boundaries using molecular dynamics (MD) was recently developed. During simulations migrating high angle grain boundaries interact with dislocation boundaries, and individual dislocations from the dislocation boundaries are absorbed into the grain boundaries. Results obtained previously, using a simple Lennard-Jones

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23

Heindel, Joseph P., Kristina M. Herman, and Sotiris S. Xantheas. "Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development." Annual Review of Physical Chemistry 74, no. 1 (2023): 337–60. http://dx.doi.org/10.1146/annurev-physchem-062422-023532.

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Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born–

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24

Hanai, Toshihiko. "In Silico Chromatography: Modeling a New Support for Alkyl-Bonded Phases and a Solvent Phase." Journal of Analytical, Bioanalytical and Separation Techniques 2, no. 2 (2017): 111–17. http://dx.doi.org/10.15436/2476-1869.17.1743.

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Chromatography is a tool to measure molecular interactions, and computational chemistry is a tool to explain molecular interactions. Therefore, reversed-phase liquid chromatography of acidic drugs using a pentyl- and an octyl-bonded silica gels was quantitatively analyzed in silico. A model pentyl- and an octyl-bonded silica gel and a methanol phases were constructed for docking with acidic drugs. Molecular interaction energy values based on van der Waals energy were obtained after docking an acidic drug into the model pentyl- or octyl-phases. Solvent effects, hydrogen bonding, and electrostat

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Mikheev, Yu A., L. N. Guseva, and G. E. Zaikov. "Sponge Effects at the Interaction of Polymers with Low-molecular Compounds." International Journal of Polymeric Materials 43, no. 3-4 (1999): 169–93. http://dx.doi.org/10.1080/00914039908009684.

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Liu, Zilong, Tatiana Rios-Carvajal, Martin P. Andersson, Marcel Ceccato, Susan L. S. Stipp, and Tue Hassenkam. "Ion effects on molecular interaction between graphene oxide and organic molecules." Environmental Science: Nano 6, no. 7 (2019): 2281–91. http://dx.doi.org/10.1039/c9en00274j.

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Bae, Je Hyun, Yu Rim Lim, and Jaeyoung Sung. "Statistical Mechanics of Molecular Adsorption: Effects of Adsorbate Interaction on Isotherms." Langmuir 24, no. 6 (2008): 2569–72. http://dx.doi.org/10.1021/la703372t.

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28

Rino, José Pedro, Paulo S. Branício, and Denílson S. Borges. "Classical Molecular Dynamics Simulation of Structural and Dynamical Properties of II-VI and III-V Semiconductors." Defect and Diffusion Forum 258-260 (October 2006): 522–30. http://dx.doi.org/10.4028/www.scientific.net/ddf.258-260.522.

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An effective inter-atomic potential is proposed in order to describe structural and dynamical properties of II-VI and III-V semiconductors. The interaction potential consists of twoand three-body interactions. The two-body term takes into account steric repulsion, charge-induce dipole interaction due to the electronic polarizability of ions, Coulomb interaction due to charge transfer between ions, and dipole-dipole (van der Waals) interactions. The three-body term, which has a modified Stillinger-Weber form, describes bond-bending as well as bond-stretching effects. Here we report the fitting

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Hossain, Md Jamal, Mohammad A. Rashid, and Md Zakir Sultan. "Transition Metal Chelation Augments the Half-life of Secnidazole: Molecular Docking and Fluorescence Spectroscopic Approaches." Drug Research 70, no. 12 (2020): 583–92. http://dx.doi.org/10.1055/a-1252-2322.

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AbstractThis current research aimed to establish the most required pharmacodynamics parameters of two transition metal complexes of an antimicrobial drug secnidazole. The spectroscopic fluorescence quenching strategy was outlined to evaluate the binding mechanism and binding affinity of nickel (II) and chromium (III) complexes of secnidazole with bovine serum albumin (BSA). The conformational modifications and the interacting patterns of the protein due to the interaction of the parent compound of the metal complexes have been investigated by molecular docking approach. The ligand-protein inte

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Lof, R. W., M. A. van Veenendaal, B. Koopmans, A. Heessels, H. T. Jonkman, and G. A. Sawatzky. "CORRELATION EFFECTS IN SOLID C60." International Journal of Modern Physics B 06, no. 23n24 (1992): 3915–21. http://dx.doi.org/10.1142/s0217979292002000.

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The bandgap of solid C 60 is found to be 2.3±0.1 eV . The on-site molecular C 60 Coulomb interaction (U) as determined from the KVV C 60 Auger spectrum is found to be 1.6 ±.2 eV . This value of U is shown to be consistent with Frenkel type molecular excitons in the 1.5–2 eV range. These results lead us to suggest that doped C 60 should be considered as a highly correlated system with U/W comparable to that in high T c cuprates. The Auger spectroscpoy results are consistent with a rather long range Coulomb interaction on a single bucky ball indicating that a Hubbard model is not suitable to des

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Szczęśniak, Małgorzata M., and Steve Scheiner. "Accurate evaluation of SCF and MP2 components of interaction energies. Complexes of HF, OH2, and NH3 with Li+." Collection of Czechoslovak Chemical Communications 53, no. 10 (1988): 2214–29. http://dx.doi.org/10.1135/cccc19882214.

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High-quality Gaussian basis sets of the well-tempered type, containing three sets of polarization functions on all atoms, are used to investigate the interaction of Li+ with HF, OH2, and NH3. These sets reproduce the SCF and MP2 energies of the various monomers very well and, moreover, accurately treat the multipole moments and polarizabilities of the monomers. When applied to the complexes, the sets are essentially free of primary and secondary basis set superposition error at the SCF level; MP2 extension effects are also completely negligible while basis set superposition effects are small b

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Sumanta, Kumar Ghatak, Chattopadhyay Pabitra, and Sen Kamalika. "Molecular interaction of peanut proteins with some bio-pesticides: A comparative spectral study." Journal of Indian Chemical Society Vol. 97, No. 12a, Dec 2020 (2020): 2593–600. https://doi.org/10.5281/zenodo.5655906.

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Department of Chemistry, The University of Burdwan, Golapbag, Burdwan-713 104, West Bengal, India Department of Chemistry, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata-700 009, India <em>E-mail: </em>kamalchem.roy@gmail.com <em>Manuscript received online 15 November 2020, revised and accepted 25 December 2020</em> Safety and quality of food supplies is an essential part of consumer protection. Due to proven toxicity of synthetic pesticides, bio-pesticides are slowly capturing the agro-economy. It is now time to evaluate the different aspects of bio-pesticides that might h

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Ma, Lu-Yan, Glenn King, and Lawrence Rothfield. "Mapping the MinE Site Involved in Interaction with the MinD Division Site Selection Protein of Escherichia coli." Journal of Bacteriology 185, no. 16 (2003): 4948–55. http://dx.doi.org/10.1128/jb.185.16.4948-4955.2003.

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ABSTRACT Interactions between the MinD and MinE proteins are required for proper placement of the Escherichia coli division septum. The site within MinE that is required for interaction with MinD was mapped by studying the effects of site-directed minE mutations on MinD-MinE interactions in yeast two-hybrid and three-hybrid experiments. This confirmed that the MinE N-terminal domain is responsible for the interaction of MinE with MinD. Mutations that interfered with the interaction defined an extended surface on one face of the α-helical region of the MinE N-terminal domain, consistent with th

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Xu, Yixue, Jiyuan Cui, Huiqun Yu, and Wansong Zong. "Insight into the Molecular Mechanism for the Discrepant Inhibition of Microcystins (MCLR, LA, LF, LW, LY) on Protein Phosphatase 2A." Toxins 14, no. 6 (2022): 390. http://dx.doi.org/10.3390/toxins14060390.

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Microcystins (MCs) exhibit diversified inhibition effects on protein phosphatases (PPs) due to their structural differences. To fully evaluate the potential mechanism for the discrepant inhibition effects, the five most frequent MCs with varying residues at position Z4 were selected as the tested toxins. Their inhibition sequence on PP2A was detected as follows: MCLR > MCLW > MCLA > MCLF > MCLY. Combined with homology modeling and molecular docking technology, the major interaction parameters between the MCs and PP2A were obtained. The correlation analysis for the major interaction

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Hiranyakorn, Methanee, Maho Yagi-Utsumi, Saeko Yanaka, et al. "Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains." International Journal of Molecular Sciences 24, no. 7 (2023): 6075. http://dx.doi.org/10.3390/ijms24076075.

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In multidomain proteins, individual domains connected by flexible linkers are dynamically rearranged upon ligand binding and sensing changes in environmental factors, such as pH and temperature. Here, we characterize dynamic domain rearrangements of Lys48-linked ubiquitin (Ub) chains as models of multidomain proteins in which molecular surfaces mediating intermolecular interactions are involved in intramolecular domain–domain interactions. Using NMR and other biophysical techniques, we characterized dynamic conformational interconversions of diUb between open and closed states regarding solven

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Li, Zoe, Ruili Huang, Menghang Xia, Tucker A. Patterson, and Huixiao Hong. "Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery." Biomolecules 14, no. 1 (2024): 72. http://dx.doi.org/10.3390/biom14010072.

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Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) struc

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Patil, Prajakta, Mrunal Desai, Gayathri Baburaj, et al. "Optimizing Cardiovascular Treatment in Non-Small Cell Lung Cancer: A Comprehensive Computational Approach for Assessment of Drug-Drug Interactions between Tyrosine Kinase Inhibitors and Cardiovascular Drugs." F1000Research 14 (March 19, 2025): 309. https://doi.org/10.12688/f1000research.162353.1.

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Background As lung cancer treatment has progressed, there has been an increase in awareness of the short- and long-term adverse effects of targeted cancer therapies of tyrosine kinase inhibitors, particularly cardiovascular toxicities. Methods The current study assessed the potential drug interactions using interaction drug-interaction checkers (IBM Micromedex and Drugs.com). Molecular docking was employed to further investigate the involvement of human ether-à-go-go-related gene (hERG) and pregnane X receptor (PXR) proteins to elucidate their potential interactions and underlying mechanisms.

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Gelhausen, Rick, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, and Martin Raden. "IntaRNAhelix-composing RNA–RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction." Journal of Bioinformatics and Computational Biology 17, no. 05 (2019): 1940009. http://dx.doi.org/10.1142/s0219720019400092.

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Efficient computational tools for the identification of putative target RNAs regulated by prokaryotic sRNAs rely on thermodynamic models of RNA secondary structures. While they typically predict RNA–RNA interaction complexes accurately, they yield many highly-ranked false positives in target screens. One obvious source of this low specificity appears to be the disability of current secondary-structure-based models to reflect steric constraints, which nevertheless govern the kinetic formation of RNA–RNA interactions. For example, often — even thermodynamically favorable — extensions of short in

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Gurina, Darya, Oleg Surov, Marina Voronova, Anatoly Zakharov, and Mikhail Kiselev. "Water Effects on Molecular Adsorption of Poly(N-vinyl-2-pyrrolidone) on Cellulose Nanocrystals Surfaces: Molecular Dynamics Simulations." Materials 12, no. 13 (2019): 2155. http://dx.doi.org/10.3390/ma12132155.

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Models of interaction between a poly(N-vinyl-2-pyrrolidone) macromolecule and a fragment of Iβ-cellulose were built in a vacuum and water environment. The models were made to interpret the mechanism of interaction of the polymer and cellulose nanocrystals by the classical molecular dynamics method. The structural behavior of a poly(N-vinyl-2-pyrrolidone) macromolecule in water has been studied in terms of the radius of gyration, atom–atom radial distribution functions and number of hydrogen bonds. It was found that the polymer has a high affinity with the solvent and each monomer unit has on a

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Trapp, Melissa L., Jonathan K. Watts, Noham Weinberg, and B. Mario Pinto. "Component analysis of the X-C-Y anomeric effect (X = O, S; Y = F, OMe, NHMe) by DFT molecular orbital calculations and natural bond orbital analysis." Canadian Journal of Chemistry 84, no. 4 (2006): 692–701. http://dx.doi.org/10.1139/v06-048.

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Six 2-Y-substituted oxacyclohexane and thiacyclohexane heterocycles (Y = F, OMe, NHMe) were examined using DFT molecular orbital calculations. Natural bond orbital (NBO) analysis of the total energy behaviour yielded the orbital-interaction factors contributing to the conformational equilibria. The dipole moments of the optimized systems were used to estimate the electrostatic contributions to the anomeric effect. The primary determinant of the X-C-Y anomeric effect was found to be the orbital interaction components associated with the combined endo- and exo-anomeric effects acting in concert

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Conrad, Marcus, Anselm H. C. Horn, and Heinrich Sticht. "Computational Analysis of Histamine Protonation Effects on H1R Binding." Molecules 28, no. 9 (2023): 3774. http://dx.doi.org/10.3390/molecules28093774.

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Despite numerous studies investigating histamine and its receptors, the impact of histamine protonation states on binding to the histamine H1-receptor (H1R) has remained elusive. Therefore, we assessed the influence of different histamine tautomers (τ-tautomer, π-tautomer) and charge states (mono- vs. dicationic) on the interaction with the ternary histamine-H1R-Gq complex. In atomistic molecular dynamics simulations, the τ-tautomer formed stable interactions with the receptor, while the π-tautomer induced a rotation of the histamine ring by 180° and formed only weaker hydrogen bonding interac

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Nenna, Antonio, Francesco Nappi, Mario Lusini, et al. "Effect of Statins on Platelet Activation and Function: From Molecular Pathways to Clinical Effects." BioMed Research International 2021 (January 23, 2021): 1–10. http://dx.doi.org/10.1155/2021/6661847.

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Purpose. Statins are a class of drugs widely used in clinical practice for their lipid-lowering and pleiotropic effects. In recent years, a correlation between statins and platelet function has been unveiled in the literature that might introduce new therapeutic indications for this class of drugs. This review is aimed at summarizing the mechanisms underlying statin-platelet interaction in the cardiologic scenario and building the basis for future in-depth studies. Methods. We conducted a literature search through PubMed, Embase, EBSCO, Cochrane Database of Systematic Reviews, and Web of Scien

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Sharma, Ketan, Oleg A. Vasilyev, Terry A. Miller, and John F. Stanton. "Molecules with Spin and Vibronic Coupling Effects: A Computational Perspective." Journal of Physics: Conference Series 2769, no. 1 (2024): 012002. http://dx.doi.org/10.1088/1742-6596/2769/1/012002.

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Abstract While fundamental to molecular quantum mechanics, limitations of the Born-Oppenheimer Approximation (BOA) have long been known. Nonetheless, calculations that include molecular interactions, such as vibronic coupling and electron spin effects, that violate the BOA have remained a challenge due to their large demand on computational resources. The purpose of this paper is to describe two complementary software programs, SOCJT and XSIM, designed for efficient calculations that include these interactions. The programs are sufficiently general and user friendly that they can be readily ap

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Balakshy, Vladimir I. "Polarization effects in acousto-optic interaction." Optical Engineering 32, no. 4 (1993): 746. http://dx.doi.org/10.1117/12.61058.

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Csaki, Andrea, Thomas Schneider, Janina Wirth, et al. "Molecular plasmonics: light meets molecules at the nanoscale." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 369, no. 1950 (2011): 3483–96. http://dx.doi.org/10.1098/rsta.2011.0145.

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Certain metal nanoparticles exhibit the effect of localized surface plasmon resonance when interacting with light, based on collective oscillations of their conduction electrons. The interaction of this effect with molecules is of great interest for a variety of research disciplines, both in optics and in the life sciences. This paper attempts to describe and structure this emerging field of molecular plasmonics, situated between the molecular world and plasmonic effects in metal nanostructures, and demonstrates the potential of these developments for a variety of applications.

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Zhang, Ning, Haoyu Lu, Yuting Chen, et al. "PremPRI: Predicting the Effects of Missense Mutations on Protein–RNA Interactions." International Journal of Molecular Sciences 21, no. 15 (2020): 5560. http://dx.doi.org/10.3390/ijms21155560.

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Protein–RNA interactions are crucial for many cellular processes, such as protein synthesis and regulation of gene expression. Missense mutations that alter protein–RNA interaction may contribute to the pathogenesis of many diseases. Here, we introduce a new computational method PremPRI, which predicts the effects of single mutations occurring in RNA binding proteins on the protein–RNA interactions by calculating the binding affinity changes quantitatively. The multiple linear regression scoring function of PremPRI is composed of three sequence- and eight structure-based features, and is param

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Fatriani, Rizka, Yopi Haryandi, Iffa Afiqa Khairani, and Hida Arliani Nur Anisa. "Caffeine Molecular Target Identification and Protein Interaction Analysis in Alzheimer's Disease." MAXIMUS: Journal of Biological and Life Sciences 3, no. 1 (2025): 9. https://doi.org/10.35472/maximus.v3i1.2143.

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Caffeine is known to have various biological effects, including its potential to modulate the central nervous system. This study aims to identify the molecular targets of caffeine and explore their relationship with Alzheimer's disease using a bioinformatics approach. The methods used include target prediction using SwissTargetPrediction and SuperPred, target relationship analysis with disease through the DAVID database, protein interaction exploration and enrichment analysis using STRING-DB, and network analysis using Cytoscape. The results showed that from the total targets obtained, there w

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Sánchez, Manuel, Miguel Romero, Manuel Gómez-Guzmán, Juan Tamargo, Francisco Pérez-Vizcaino, and Juan Duarte. "Cardiovascular Effects of Flavonoids." Current Medicinal Chemistry 26, no. 39 (2019): 6991–7034. http://dx.doi.org/10.2174/0929867326666181220094721.

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: Cardiovascular Disease (CVD) is the major cause of death worldwide, especially in Western society. Flavonoids are a large group of polyphenolic compounds widely distributed in plants, present in a considerable amount in fruit and vegetable. Several epidemiological studies found an inverse association between flavonoids intake and mortality by CVD. The antioxidant effect of flavonoids was considered the main mechanism of action of flavonoids and other polyphenols. In recent years, the role of modulation of signaling pathways by direct interaction of flavonoids with multiple protein targets, n

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Marforio, Tainah Dorina, Alessandro Calza, Edoardo Jun Mattioli, Francesco Zerbetto, and Matteo Calvaresi. "Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60." International Journal of Molecular Sciences 22, no. 21 (2021): 11567. http://dx.doi.org/10.3390/ijms222111567.

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Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol−1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were g

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MIYAZAKI, AKIRA, та TOSHIAKI ENOKI. "π–d INTERACTION BASED MOLECULAR CONDUCTING MAGNETS: HOW TO INCREASE THE EFFECTS OF THE π–d INTERACTION". COSMOS 04, № 02 (2008): 131–40. http://dx.doi.org/10.1142/s0219607708000330.

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The crystal structures and electronic and magnetic properties of conducting molecular magnets developed by our group are reviewed from the viewpoints of our two current strategies for increasing the efficiency of the π–d interaction. (EDTDM)2 FeBr 4 is composed of quasi-one-dimensional donor sheets sandwiched between magnetic anion sheets. The ground state of the donor layer changes from the insulator state to the metallic state by the application of pressure. When it is near to the insulator–metal phase boundary pressure, the magnetic order of the anion spins considerably affects the transpor

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