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Journal articles on the topic 'Significant molecules'

Author: Grafiati

Published: 18 May 2024

Last updated: 31 July 2025

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1

Boldyreva, Yulia V., Ilya A. Lebedev, Ekaterina V. Zakharchuk, Javid F. Garaev, Sofia V. Adamchuk, and Arthur M. Smilyanin. "Oligopeptides as Biochemically Significant Molecules." Journal of Ural Medical Academic Science 18, no. 2 (2021): 138–46. http://dx.doi.org/10.22138/2500-0918-2021-18-2-138-146.

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Peptides are a class of organic substances consisting of two or more amino acid residues connected to each other by peptide bonds —C(O)NH—. Peptides were first mentioned in 1900 by the German organic chemist G. E. Fischer. He assumed that peptides consist of a chain of amino acids connected by a certain type of bond. In 1902, he was able to prove the presence of a peptide bond, and by 1905 he had developed a general method that allows synthesizing peptides in the laboratory. Friedrich Engels said the most succinctly about proteins: «Life is a way of existence of protein bodies...». It follows

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van den Berg, C. M. G. "Voltammetry of of biological significant molecules." TrAC Trends in Analytical Chemistry 12, no. 7 (1993): x. http://dx.doi.org/10.1016/0165-9936(93)87011-l.

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Wang, Shuhua. "Drug–drug interaction analysis based on information bottleneck graph neural network: A review." Medicine 104, no. 25 (2025): e42904. https://doi.org/10.1097/md.0000000000042904.

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The objective of learning drug–drug interactions is to understand the interaction behavior between compound molecules, which has garnered significant interest in the field of compound molecular science due to the potential harm adverse drug interactions may cause to organisms. Existing machine learning methods mostly rely on manually designed representations of compound molecules, overlooking the essence of compound molecules being composed of multiple molecular substructures and constrained by the knowledge of domain experts in the field of compound molecules. In this work, we propose a novel

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Pandey, Padmaker, Anamika Pandey, Shruti Singh, and Nikhil Kant Shukla. "Self Assembled Monolayers and Carbon Nanotubes: A Significant Tool’s for Modification of Electrode Surface." Sensor Letters 18, no. 9 (2020): 669–85. http://dx.doi.org/10.1166/sl.2020.4280.

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A compromising and well-organized model system is needed for investigating the molecular behaviour of biomolecules as many transduction processes and biological recognition occur at biological surfaces. The application of techniques in interfacial surfaces like one molecule thick films has made a feasible and significant tool for modern scientific studies. Self Assembling Monolayers (SAMs) technology is a very useful means for producing monomolecular films of various biological molecules on different substrates. Carbon Nanotubes (CNTs) have length-to-diameter aspect ratio property which provid

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Hilt, J. Zachary, and Mark E. Byrne. "Configurational biomimesis in drug delivery: molecular imprinting of biologically significant molecules." Advanced Drug Delivery Reviews 56, no. 11 (2004): 1599–620. http://dx.doi.org/10.1016/j.addr.2004.04.002.

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Uday, R. V. Sriram, Rajdip Misra, Annaram Harika, et al. "Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease." PLOS ONE 16, no. 9 (2021): e0257206. http://dx.doi.org/10.1371/journal.pone.0257206.

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Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding o

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S, Aravinth, Prakash Joshi, and Partha Pratim Mondal. "Detection of fortunate molecules induce particle resolution shift (PAR-shift) toward single-molecule limit in SMLM: A technique for resolving molecular clusters in cellular system." Review of Scientific Instruments 93, no. 9 (2022): 093704. http://dx.doi.org/10.1063/5.0101009.

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Molecules capable of emitting a large number of photons (also known as fortunate molecules) are crucial for achieving a resolution close to single molecule limit (the actual size of a single molecule). We propose a long-exposure single molecule localization microscopy (leSMLM) technique that enables detection of fortunate molecules, which is based on the fact that detecting a relatively small subset of molecules with large photon emission increases its localization precision [Formula: see text]. Fortunate molecules have the ability to emit a large burst of photons over a prolonged time ([Formu

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Chen, Min, Tao Zhang, Jinyuan Zhang, Chunyi Liu, Dong Chen, and Jin Zhang. "Unveiling the Micro-Mechanism of Functional Group Regulation for Enhanced Dielectric Properties in Novel Natural Ester Insulating Oil TME-C10." Molecules 30, no. 7 (2025): 1431. https://doi.org/10.3390/molecules30071431.

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The functional groups in the molecular structure of natural ester insulating oil have a significant impact on its physicochemical and electrical properties. This article takes the novel synthetic ester TME-C10 and traditional natural ester GT molecules as research objects, and based on density functional theory (DFT) calculations, systematically explores the micro-mechanism of the effects of C=C double bonds, ester groups (-COOC), and β-H groups on the performance of insulating oils. The results show that the chemical stability and anti-aging ability of the TME-C10 molecule are significantly i

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Friederich, Pascal, Reinder Coehoorn, and Wolfgang Wenzel. "Molecular Origin of the Anisotropic Dye Orientation in Emissive Layers of Organic Light Emitting Diodes." Chemistry of Materials 29, no. 21 (2017): 9528–35. https://doi.org/10.1021/acs.chemmater.7b03742.

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Molecular orientation anisotropy of the emitter molecules used in organic light emitting diodes (OLEDs) can give rise to an enhanced light-outcoupling efficiency, when their transition dipole moments are oriented preferentially parallel to the substrate, and to a modified internal quantum efficiency, when their static dipole moments give rise to a locally modified internal electric field. Here, the orientation anisotropy of state-of-the-art phosphorescent dye molecules is investigated using a simulation approach which mimics the physical vapor deposition process of amorphous thin films. The si

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ShirsathPriya .K, ShirsathPriya K., AhirraoSangita A. AhirraoSangita .A, Wankhede Neha B. Wankhede Neha. B, et al. "Molecular Docking: A Gateway to Rational Drug Design and Precision Medicine." International Journal of Pharmaceutical Research and Applications 10, no. 2 (2025): 2054–61. https://doi.org/10.35629/4494-100220542061.

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In essence, molecular docking describes how one molecule is oriented in relation to another, such as when they bind to one another to form a stable complex. The preferred orientation of the two molecules is used to predict the power of alliance or the irreversible affinity of the distinct molecules through the use of scoring systems. Signal transmission depends on these interactions, which are accomplished via molecular docking between significant biological constituents such proteins, peptides, nucleic acids, carbohydrates, and lipids. Additionally, these molecular docking-assisted interactio

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Cheng, Yaming. "Analyze molecular interaction for mixture of argon and particles with different sizes." Theoretical and Natural Science 18, no. 1 (2023): 30–37. http://dx.doi.org/10.54254/2753-8818/18/20230290.

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This article elaborates on molecular dynamics simulation, which is a technology that supports us in analyzing the structure and dynamics of materials and their properties at a microscopic level. In this article, the molecular dynamics simulation develops on Lennard-Jones potential. The simulation is based on the fundamental understanding between Argon-Argon molecules. The application for running molecular dynamics simulation is Moldy. The Argon particles size is changed by altering van der Waals radius from Lennard-Jones potential parameters, and the mixture of Argon and different sizes partic

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ABADIR, G. B., K. WALUS, R. F. B. TURNER, and D. L. PULFREY. "BIOMOLECULAR SENSING USING CARBON NANOTUBES: A SIMULATION STUDY." International Journal of High Speed Electronics and Systems 18, no. 04 (2008): 879–87. http://dx.doi.org/10.1142/s0129156408005849.

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A simulation study using molecular dynamics and the density-functional-theory/non-equilibrium-Green's-function approach has been carried out to investigate the potential of carbon nanotubes (CNT) as molecular-scale biosensors. Single molecules of each of two amino acids (isoleucine and asparagine) were used as the target molecules in two separate simulations. The results show a significant suppression of the local density of states (LDOS) in both cases, with a distinct response for each molecule. This is promising for the prospect of CNT-based single-molecule sensors that might depend on the L

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Medcraft, Chris, and Melanie Schnell. "A Comparative Study of Two Bicyclic Ethers, Eucalyptol and 1,4-Cineole, by Broadband Rotational Spectroscopy." Zeitschrift für Physikalische Chemie 230, no. 1 (2016): 1–14. http://dx.doi.org/10.1515/zpch-2015-0643.

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AbstractThe rotational spectra of the two structurally related molecules, 1,4-cineole and 1,8-cineole (eucalyptol), were measured between 2–8.5 GHz with chirped pulse Fourier transform microwave spectroscopy. The structures of these two molecules only differ in the connectivity of an ether functional group. This results in a significant change in the three dimensional structure of the molecule and consequently large differences in the rotational spectra. Only one conformer of each molecule was detected in the molecular jet and no line splittings due to internal rotations were detected. A subst

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KANDIGOWDA, DR JAGADEESHA, M. PREMSINGH, R. J. ANILKUMAR, and Y. L. RAMU. "Computational Analysis of Excited State Intramolecular Hydrogen Atom Transfer and Microsolvation Studies on 8-Acetyl-7-hydroxy-4-methylcoumarin using DFT and TDDFT." Asian Journal of Chemistry 35, no. 10 (2023): 2365–74. http://dx.doi.org/10.14233/ajchem.2023.28130.

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The computational calculations were carried out on 8-acetyl-7-hydroxy-4-methyl coumarin (AHM) and its water complex AHM+(H2O)4- [AHMH] at ground and excited states by employing density functional theory (DFT)/specific state time-dependent density functional theory (SS-TDDFT). In AHM and AHMH molecules, there is an intramolecular hydrogen bond between hydroxyl group and acetyl group along with inter-molecular hydrogen bonds in the hydrated molecule. The computational studies of molecular structural parameters, molecular electrostatic potential, natural bond orbital (NBO) analysis, the molecular

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Chappell, Sarah, Carly Brooke, Richard J. Nichols, et al. "Evidence for a hopping mechanism in metal|single molecule|metal junctions involving conjugated metal–terpyridyl complexes; potential-dependent conductances of complexes [M(pyterpy)2]2+ (M = Co and Fe; pyterpy = 4′-(pyridin-4-yl)-2,2′:6′,2′′-terpyridine) in ionic liquid." Faraday Discussions 193 (2016): 113–31. http://dx.doi.org/10.1039/c6fd00080k.

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Extensive studies of various families of conjugated molecules in metal|molecule|metal junctions suggest that the mechanism of conductance is usually tunnelling for molecular lengths < ca. 4 nm, and that for longer molecules, coherence is lost as a hopping element becomes more significant. In this work we present evidence that, for a family of conjugated, redox-active metal complexes, hopping may be a significant factor for even the shortest molecule studied (ca. 1 nm between contact atoms). The length dependence of conductance for two series of such complexes which differ essentially in the

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Khalilov, Ali N., Victor N. Khrustalev, Tatiana A. Tereshina, et al. "Crystal structure and Hirshfeld surface analysis of 1-(tert-butylamino)-3-mesitylpropan-2-ol hemihydrate." Acta Crystallographica Section E Crystallographic Communications 78, no. 5 (2022): 525–29. http://dx.doi.org/10.1107/s2056989022004297.

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The title compound, 2C16H27NO·H2O, crystallizes in the monoclinic P21/c space group with two independent molecules (A and B) in the asymmetric unit. In the crystal, molecules A and B are linked through the water molecules by intermolecular O—H...O and O—H...N hydrogen bonds, producing chains along the b-axis direction. These chains are linked with neighboring chains parallel to the (103) plane via C—H...π interactions, generating ribbons along the b-axis direction. The stability of the molecular packaging is ensured by van der Waals interactions between the ribbons. According to the Hirshfeld

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Robson, Alex, Kevin Burrage, and Mark C. Leake. "Inferring diffusion in single live cells at the single-molecule level." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1611 (2013): 20120029. http://dx.doi.org/10.1098/rstb.2012.0029.

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The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single-molecule and single-cell level can add significant insight into understanding molecular architectures of diffusing molecules and the nanoscale environment in which the molecules diffuse. The tool of choice for monitoring dynamic molecular localization in live cells is fluorescence microscopy, especially so combining total internal reflection fluorescence with the use of fluorescent protein (FP) reporters

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Baumann, Gerd, and Zeno Földes-Papp. "Single-Molecule Tracking in Live Cell without Immobilization or without Hydrodynamic Flow by Simulations: Thermodynamic Jitter." Biophysica 4, no. 3 (2024): 442–52. http://dx.doi.org/10.3390/biophysica4030028.

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Experiments to measure a single molecule/particle, i.e., an individual molecule/particle, at room temperature or under physiological conditions without immobilization—for example, on a surface or without significant hydrodynamic flow—have so far failed. This failure has given impetus to the underlying theory of Brownian molecular motion towards its stochastics due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a

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Yoshida, Norimasa, Kyoichi Kassai, Hironobu Murase, et al. "Effects ofHelicobacter pyloriWater Extract on Expression of Endothelial Adhesion Molecules." Canadian Journal of Gastroenterology 18, no. 6 (2004): 387–91. http://dx.doi.org/10.1155/2004/158638.

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The present study investigated whetherHelicobacter pyloriwater extract induces the upregulation of intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin on human umbilical vein endothelial cells, using an ELISA. The nature of the substances mediating this upregulation was also analyzed.H pyloriwater extract derived from type strain (NCTC 11637) significantly upregulated intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin to the same extent as interleukin-1. Treatments with extracts from clinical strains showed no significant increas

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Ramos Silva, Manuela, Vânia M. Moreira, Cláudia Cardoso, Ana Matos Beja та Jorge A. R. Salvador. "3-Oxoandrosta-4,6-dien-17β-yl 2-methyl-1H-imidazole-1-carboxylate and 3-oxo-5α-androst-17β-yl 2-methyl-1H-imidazole-1-carboxylate: C—H...π and π–π intermolecular interactions". Acta Crystallographica Section C Crystal Structure Communications 65, № 3 (2009): o88—o91. http://dx.doi.org/10.1107/s0108270109003278.

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The title compounds, C24H30N2O3, (I), and C24H34N2O3, (II), both contain an androstane backbone and a 2-methylimidazole-1-carboxylate moiety at the 17-position. Compound (I) contains two symmetry-independent molecules (denoted 1 and 2), while compound (II) contains just one molecule in the asymmetric unit. The C—C—O—C torsion angle that reflects the twisting of the 2-methylimidazole-1-carboxylate moiety from the mean steroid plane is 143.1 (2)° for molecule 1 of (I), 73.1 (3)° for molecule 2 of (I) and 86.63 (17)° for (II). The significance of this study lies in its observation of significant

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Itami, Kenichiro. "(Invited, Digital Presentation) Molecular Nanocarbon Synthesis and Beyond." ECS Meeting Abstracts MA2022-01, no. 10 (2022): 789. http://dx.doi.org/10.1149/ma2022-0110789mtgabs.

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Our goal is the creation of super molecules, innovative functional molecules with significant properties and/or beautiful molecules. To this end, we have focused on catalyst-enabling synthetic chemistry with broad directions, including applications in molecular nanocarbons, pharmaceuticals, and plant/animal chemical biology, and the development of rapid molecule-assembly methods using unique catalysts. In particular, we have pioneered molecular nanocarbon science by the bottom-up synthesis of structurally uniform nanocarbons of fundamental and practical importance. Representative achievements

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Tao, Feng. "Nanoscale surface chemistry in self- and directed-assembly of organic molecules on solid surfaces and synthesis of nanostructured organic architectures." Pure and Applied Chemistry 80, no. 1 (2008): 45–57. http://dx.doi.org/10.1351/pac200880010045.

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This article briefly reviews the interplay of weak noncovalent interactions involved in the formation of self-assembled monolayers of organic molecules and the strong chemical binding in directed-assembly of organic molecules on solid surfaces. For a self-assembled monolayer, each molecule involves at least three categories of weak interactions, including molecule-substrate interactions, molecule-molecule interactions in a lamella, and molecule-molecule interactions between two adjacent lamellae. Basically, molecule-substrate interactions play a major role in determining molecular configuratio

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Watanabe, Go, Akane Yamazaki, and Jun Yoshida. "The Missing Relationship between the Miscibility of Chiral Dopants and the Microscopic Dynamics of Solvent Liquid Crystals: A Molecular Dynamics Study." Symmetry 15, no. 5 (2023): 1092. http://dx.doi.org/10.3390/sym15051092.

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Nematic liquid crystals (LCs) are known to undergo a phase transition to chiral nematic LCs possessing helices upon doping with enantiomeric molecules known as chiral dopants. The relationship between the helical pitch (p), the molar fraction (x), and the power of the chiral dopant to induce a helix in a nematic solvent (βM) is expressed as p=1/(x·βM). The helical pitch is easily controlled by the concentration of the chiral dopant when the dopant molecule is miscible with the host nematic LC. However, it has not yet been clarified what the miscibility of the chiral dopant molecules with the n

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Danielson, J. R., S. Ghosh, and C. M. Surko. "Influence of geometry on positron binding to molecules." Journal of Physics B: Atomic, Molecular and Optical Physics 54, no. 22 (2021): 225201. http://dx.doi.org/10.1088/1361-6455/ac3e78.

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Abstract Annihilation studies have established that positrons bind to most molecules. They also provide measurements of the positron-molecule binding energies, which are found to vary widely and depend upon molecular size and composition. Trends of binding energy with global parameters such as molecular polarizability and dipole moment have been discussed previously. In this paper, the dependence of binding energy on molecular geometry is investigated by studying resonant positron annihilation on selected pairs of isomers. It is found that molecular geometry can play a significant role in dete

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Qian, Ying, Minghua Shi, and Qian Zhang. "CONSMI: Contrastive Learning in the Simplified Molecular Input Line Entry System Helps Generate Better Molecules." Molecules 29, no. 2 (2024): 495. http://dx.doi.org/10.3390/molecules29020495.

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In recent years, the application of deep learning in molecular de novo design has gained significant attention. One successful approach involves using SMILES representations of molecules and treating the generation task as a text generation problem, yielding promising results. However, the generation of more effective and novel molecules remains a key research area. Due to the fact that a molecule can have multiple SMILES representations, it is not sufficient to consider only one of them for molecular generation. To make up for this deficiency, and also motivated by the advancements in contras

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Posch, Phillip E., Hugo A. Araujo, Karen Creswell, Chantai Praud, Armead H. Johnson, and Carolyn Katovich Hurley. "Microvariation creates significant functional differences in the DR3 Molecules." Human Immunology 42, no. 1 (1995): 61–71. http://dx.doi.org/10.1016/0198-8859(94)00074-z.

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Anderson, Brian J., Jeffrey R. Hall, and Jerry P. Jasinski. "N-Ethyl-2-[1-(2-hydroxy-4-methylphenyl)ethylidene]hydrazinecarbothioamide." Acta Crystallographica Section E Structure Reports Online 70, no. 6 (2014): o735. http://dx.doi.org/10.1107/s1600536814012203.

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The title compound, C12H17N3OS, crystallizes with two independent molecules (AandB) in the asymmetric unit. The dihedral angle between the mean planes of the benzene ring and the hydrazinecarbothioamide group are 6.9 (4) and 37.2 (5)° in moleculesAandB, respectively. An intramolecular O—H...N hydrogen bond is observed in each molecule. This serves to maintain an approximately planar conformation for moleculeA, but leaves a significant twist between these two groups in moleculeB. In the crystal, a weak N—H...S interaction is observed, forming inversion dimers among theBmolecules and resulting i

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Qiao, Anjie, Zhen Wang, Jiahua Rao, Yuedong Yang, and Zhewei Wei. "Advancing Retrosynthesis with Retrieval-Augmented Graph Generation." Proceedings of the AAAI Conference on Artificial Intelligence 39, no. 19 (2025): 20004–13. https://doi.org/10.1609/aaai.v39i19.34203.

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Diffusion-based molecular graph generative models have achieved significant success in template-free, single-step retrosynthesis prediction. However, these models typically generate reactants from scratch, often overlooking the fact that the scaffold of a product molecule typically remains unchanged during chemical reactions. To leverage this useful observation, we introduce a retrieval-augmented molecular graph generation framework. Our framework comprises three key components: a retrieval component that identifies similar molecules for the given product, an integration component that learns

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Eremin, Roman A., Kholmirzo Kholmurodov, Viktor I. Petrenko, László Rosta, and Mikhail V. Avdeev. "Effect of the solute–solvent interface on small-angle neutron scattering from organic solutions of short alkyl chain molecules as revealed by molecular dynamics simulation." Journal of Applied Crystallography 46, no. 2 (2013): 372–78. http://dx.doi.org/10.1107/s002188981205131x.

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The problem of describing the experimental small-angle neutron scattering (SANS) from diluted solutions of saturated monocarboxylic acids with short chain lengths (myristic and stearic acids) in deuterated decalin is considered. The method of classical molecular dynamics simulation (MDS) is used to obtain the atomic number density distributions, and, as a consequence, the scattering length density (SLD) distribution in the solute–solvent interface area (about 1 nm around the acid molecules), assuming the acid molecules to be rigid and non-associated in the solutions. MDS is performed for solut

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Boontham, Pisake, Adrian Robins, Palanichamy Chandran, et al. "Significant immunomodulatory effects of Pseudomonas aeruginosa quorum-sensing signal molecules: possible link in human sepsis." Clinical Science 115, no. 11 (2008): 343–51. http://dx.doi.org/10.1042/cs20080018.

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Pathogenic bacteria use quorum-sensing signal molecules to co-ordinate the expression of virulence genes. Animal-based studies have demonstrated the immunomodulatory effects of quorum-sensing signal molecules. In the present study, we have examined the impact of these molecules on normal human immune function in vitro and compared this with immune changes in patients with sepsis where quorum-sensing signal molecules were detected in the sera of patients. Quorum-sensing signal molecules inhibited normal dendritic cell and T-cell activation and proliferation, and down-regulated the expression of

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Crawford, John M., and Keiko Watanabe. "Cell Adhesion Molecules in Inflammation and Immunity: Relevance to Periodontal Diseases." Critical Reviews in Oral Biology & Medicine 5, no. 2 (1994): 91–123. http://dx.doi.org/10.1177/10454411940050020301.

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Inflammatory and immune responses involve close contact between different populations of cells. These adhesive interactions mediate migration of cells to sites of inflammation and the effector functions of cells within the lesions. Recently, there has been significant progress in understanding the molecular basis of these intercellular contacts. Blocking interactions between cell adhesion molecules and their ligands has successfully suppressed inflammatory reactions in a variety of animal models in vivo. The role of the host response in periodontal disease is receiving renewed attention, but l

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Cristian, Gavrilă Vlad, та Teodor Octavian Nicolescu. "New Equations for Rapid Calculation of π-bonds, σ-bonds, Single, Double and Triple Bonds in Open Chain Alcohols and Cycloamines". International Journal of Chemistry, Mathematics and Physics 8, № 3 (2024): 9–15. https://doi.org/10.22161/ijcmp.8.3.2.

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Molecules are chemical structures composed of atoms, and in order to improve the understanding of the classical organic chemistry concepts it is necessary to have accessible mathematical models that contain all the important structural elements of a molecule. An interesting tool for organic chemistry is represented by the prediction of the number of π-bonds, σ-bonds, single, double and triple bonds for organic compounds based on their molecular formulas in order to solve different kinds of problems regarding the representation of molecules. In this manuscript we try to present a simple method

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Rousou, Charis, Josanne de Maar, Boning Qiu, et al. "The Effect of Microbubble-Assisted Ultrasound on Molecular Permeability across Cell Barriers." Pharmaceutics 14, no. 3 (2022): 494. http://dx.doi.org/10.3390/pharmaceutics14030494.

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The combination of ultrasound and microbubbles (USMB) has been applied to enhance drug permeability across tissue barriers. Most studies focused on only one physicochemical aspect (i.e., molecular weight of the delivered molecule). Using an in vitro epithelial (MDCK II) cell barrier, we examined the effects of USMB on the permeability of five molecules varying in molecular weight (182 Da to 20 kDa) and hydrophilicity (LogD at pH 7.4 from 1.5 to highly hydrophilic). Treatment of cells with USMB at increasing ultrasound pressures did not have a significant effect on the permeability of small mol

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Liu, Lu, Xi Zhao, and Xuri Huang. "Generating Potential RET-Specific Inhibitors Using a Novel LSTM Encoder–Decoder Model." International Journal of Molecular Sciences 25, no. 4 (2024): 2357. http://dx.doi.org/10.3390/ijms25042357.

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The receptor tyrosine kinase RET (rearranged during transfection) plays a vital role in various cell signaling pathways and is a critical factor in the development of the nervous system. Abnormal activation of the RET kinase can lead to several cancers, including thyroid cancer and non-small-cell lung cancer. However, most RET kinase inhibitors are multi-kinase inhibitors. Therefore, the development of an effective RET-specific inhibitor continues to present a significant challenge. To address this issue, we built a molecular generation model based on fragment-based drug design (FBDD) and a lo

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Shub, Ifat, Ehud Schreiber, and Yossef Kliger. "Saving Significant Amount of Time in MD Simulations by Using an Implicit Solvent Model and Elevated Temperatures." ISRN Computational Biology 2013 (March 31, 2013): 1–5. http://dx.doi.org/10.1155/2013/640125.

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Molecular dynamic simulations are used for investigating various aspects of biological processes. Such simulations often require intensive computer power; therefore several solutions were developed to minimize the computer power needed, including the usage of elevated temperatures. Yet, such simulations are still not commonly used by the wide scientific community of chemists and biochemists. For about two years now, the molecular simulations suite GROMACS enables conducting simulations using implicit solvent models to further decrease runtimes. In order to quantify the saving in computer power

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Oladimeji, Enock Oluwole, Emmanuel E. Etim, Emmanuel Chukwuebuka Umeh, et al. "Exploring the Thermodynamic Characteristics of Isoelectronic Diatomic Interstellar Molecular Species: Oxygen and Sulfur Containing Specie." UMYU Scientifica 3, no. 2 (2024): 146–58. http://dx.doi.org/10.56919/usci.2432.016.

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Study’s Excerpt/Novelty This study provides a comprehensive computational analysis of the thermodynamic properties of isoelectronic diatomic interstellar molecular species containing oxygen and sulfur atoms, spanning a wide range of interstellar temperatures. By investigating entropy, free energy, heat capacity, and internal energy, the research reveals unique trends, such as the earlier responsiveness of sulfur-containing molecules to temperature changes and the significant impact of molecular size on thermodynamic properties. These insights into the isoelectronic effects and thermodynamic be

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Barik, Debashis, Geethanjali Anand, Subba Rao Cheekatla, and Mintu Porel. "A Novel Class of Functionally Tuneable Star-Shaped Molecules for Interaction with Multiple Proteins." Organics 4, no. 2 (2023): 219–31. http://dx.doi.org/10.3390/org4020018.

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Molecules with tuneable properties are well known for their applications in the material and bio-medical fields; nevertheless, the structural and functional tunability makes them more significant in diverse applications. Herein, we designed and synthesized a novel class of star-shaped molecules via incorporating two important functional groups, i.e., triazole and dithiocarbamate (DTC). The rationale behind selecting these two key functional groups is their diverse applications, e.g., DTC having applications for therapeutics, pesticides, and vulcanizing agents, and triazole having applications

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Selvakumar, Jayaraman, Meredith H. Miles, David A. Grossie, and Kuppuswamy Arumugam. "Synthesis and molecular structure of biologically significant bis(1,3-dimesityl-4,5-naphthoquinoimidazol-2-ylidene)gold(I) complexes with chloride and dichloridoaurate counter-ions." Acta Crystallographica Section C Structural Chemistry 75, no. 4 (2019): 462–68. http://dx.doi.org/10.1107/s2053229619003292.

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Diffraction-quality single crystals of two gold(I) complexes, namely bis(1,3-dimesityl-4,5-naphthoquinoimidazol-2-ylidene)gold(I) chloride benzene monosolvate, [Au(C29H26N2O2)2]Cl·C6H6or [(NQMes)2Au]Cl·C6H6,2, and bis(1,3-dimesityl-4,5-naphthoquinoimidazol-2-ylidene)gold(I) dichloridoaurate(I) dichloromethane disolvate, [Au(C29H26N2O2)2][AuCl2]·2CH2Cl2or [(NQMes)2Au][AuCl2]·2CH2Cl2,4, were isolated and studied with the aid of single-crystal X-ray diffraction analysis. Compound2crystallizes in a monoclinic space groupC2/cwith eight molecules in the unit cell, while compound4crystallizes in the

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Kanemaru, Kodai, Keisuke Shiroshita, Haruyuki Nakano, and Norio Yoshida. "QM/MM/3D-RISM study of an electronic structure change of benzimidazole derivative induced by molecular recognition of cucurbit[7]uril." IOP Conference Series: Materials Science and Engineering 1325, no. 1 (2025): 012008. https://doi.org/10.1088/1757-899x/1325/1/012008.

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Abstract The quantum mechanics/molecular mechanics three-dimensional reference interaction site model (QM/MM/3D-RISM) method is a three-layer hybrid approach designed to calculate the electronic structure of complex molecules in solution. In this study, the QM/MM/3D-RISM method was employed to investigate electronic structure changes in ligand molecules upon molecular recognition by the macrocyclic host molecule cucurbit[7]uril (CB7). Thiabendazole (TBZ), a benzimidazole derivative, was selected as the ligand, which is known for its significant alterations in properties such as pKa, solubility

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Krasowski, Matthew D., Mohamed G. Siam, Manisha Iyer, Anthony F. Pizon, Spiros Giannoutsos, and Sean Ekins. "Chemoinformatic Methods for Predicting Interference in Drug of Abuse/Toxicology Immunoassays." Clinical Chemistry 55, no. 6 (2009): 1203–13. http://dx.doi.org/10.1373/clinchem.2008.118638.

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Abstract Background: Immunoassays used for routine drug of abuse (DOA) and toxicology screening may be limited by cross-reacting compounds able to bind to the antibodies in a manner similar to the target molecule(s). To date, there has been little systematic investigation using computational tools to predict cross-reactive compounds. Methods: Commonly used molecular similarity methods enabled calculation of structural similarity for a wide range of compounds (prescription and over-the-counter medications, illicit drugs, and clinically significant metabolites) to the target molecules of DOA/tox

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Kretić, Danijela S., Vesna B. Medaković, and Dušan Ž. Veljković. "How Do Small Differences in Geometries Affect Electrostatic Potentials of High-Energy Molecules? Critical News from Critical Points." Crystals 12, no. 10 (2022): 1455. http://dx.doi.org/10.3390/cryst12101455.

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The computational design of explosives is becoming very popular since it represents a safe and environmentally friendly way of predicting the properties of these molecules. It is known that positive values of electrostatic potential in the central areas of the molecular surface are a good indicator of the sensitivity of high-energy materials towards detonation. The molecular electrostatic potential is routinely calculated for molecules of explosives using both geometries extracted from crystal structures, and computationally optimized geometries. Here we calculated and compared values of posit

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Joshi, Prakash, and Partha Pratim Mondal. "Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy." Photonics 9, no. 1 (2021): 7. http://dx.doi.org/10.3390/photonics9010007.

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Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated He

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Flores, Giancarlo Angeles, Gaia Cusumano, Roberto Venanzoni, and Paola Angelini. "The Glucans Mushrooms: Molecules of Significant Biological and Medicinal Value." Polysaccharides 5, no. 3 (2024): 212–24. http://dx.doi.org/10.3390/polysaccharides5030016.

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Mushroom polysaccharides, key components of fungal cell walls, exhibit various biological properties and hold significant medicinal and industrial value. These polysaccharides are known for their medicinal properties like antitumor, antioxidant, anticancer, immunomodulatory, and antiviral properties. Mushroom polysaccharides, particularly β-glucans, α-glucans, and chitin, have been associated with various health benefits. β-glucans are well studied for their bioactivities, while α-glucans and chitin have gained attention for their prebiotic, antimicrobial, and wound-healing properties. The the

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Aher, Ashwini A, Syed Ubaid Razvi, Satish Eknath Bahekar, and Mirza Shiraz Baig. "The Role of Chirality in Drug Design and Delivery: A Comprehensive Review." Acta Pharma Reports 3, no. 2 (2024): 07–10. https://doi.org/10.51470/apr.2024.03.02.07.

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Chirality is an important concept in pharmaceutical chemistry for drug development; it influences the pharmacokinetics, pharmacodynamics, and efficacy of drugs. Chirality changes the shape of drug molecules and the stereochemistry of molecules because of the presence of their chiral centres, which determine any molecule’s interactions with biological systems, and this interaction results in significant differences in therapeutic outcomes of different enantiomers of a single drug molecule. Chirality also has an impact on drug delivery systems and drug design; we discussed the role and importanc

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Hao, SUN. "Molecular Dynamics Simulation of Significant Roles of Structural Water Molecules in Glycogen Synthase Kinase-3β". Acta Physico-Chimica Sinica 25, № 04 (2009): 635–39. http://dx.doi.org/10.3866/pku.whxb20090405.

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Zhu, Jie, Ganyu Xia, Dejian Shen, Yangtao Li, Baosheng Jin, and Shengxing Wu. "Selection of Representative Asphaltene Molecules in an Asphalt Molecular Model Based on Quantum Chemistry and Statistical Analysis." Molecules 29, no. 24 (2024): 6015. https://doi.org/10.3390/molecules29246015.

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Asphaltenes, as the most complex and strongly polar component among the four components of asphalt, have a significant impact on the macroscopic physicochemical properties of asphalt. Currently, the vast variety of molecular structures used to characterize asphaltenes increases the construction complexity of asphalt molecular models. To construct a more realistic asphalt molecular model and reduce the construction difficulty, this investigation obtains the molecular morphology, molecular polarity, and infrared spectrum indicators of 21 asphaltene molecules through quantum chemical calculations

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Tang, Chaolong, Mehrdad Shiri, Haixin Zhang, Ridwan Tobi Ayinla, and Kun Wang. "Light-Driven Charge Transport and Optical Sensing in Molecular Junctions." Nanomaterials 12, no. 4 (2022): 698. http://dx.doi.org/10.3390/nano12040698.

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Probing charge and energy transport in molecular junctions (MJs) has not only enabled a fundamental understanding of quantum transport at the atomic and molecular scale, but it also holds significant promise for the development of molecular-scale electronic devices. Recent years have witnessed a rapidly growing interest in understanding light-matter interactions in illuminated MJs. These studies have profoundly deepened our knowledge of the structure–property relations of various molecular materials and paved critical pathways towards utilizing single molecules in future optoelectronics applic

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Johansen, K., G. Stintzing, K. E. Magnusson, et al. "Intestinal Permeability Assessed with Polyethylene Glycols in Children with Diarrhea Due to Rotavirus and Common Bacterial Pathogens in a Developing Community." Journal of Pediatric Gastroenterology and Nutrition 9, no. 3 (1989): 307–13. http://dx.doi.org/10.1002/j.1536-4801.1989.tb09875.x.

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Intestinal permeability was assessed with different‐sized polyethylene glycols (PEG 400 and PEG 1,000) in small children with acute diarrhea. All children with acute diarrhea absorbed and excreted less PEG of all molecular sizes into the urine when compared with healthy control children (p < 0.001). Children with acute rotavius infection excreted significantly less PEG of all sizes than children with Shigella, Salmonella, and enteropathogenic Escherichia coli (EPEC) infection (p < 0.001–0.01), suggesting a more severe mucosal lesion caused by rotavirus. In patients with severe malnutriti

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Tüzün, Burak. "Investigation of the Activity of Benzenesulfonamide Derivative Molecules Against Gastric Cancer Proteins with Gaussian Calculations and Docking Analysis." Cumhuriyet Science Journal 46, no. 2 (2025): 338–47. https://doi.org/10.17776/csj.1665644.

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While gastric cancer poses a significant problem in terms of global health with its high mortality rates, the limitations in current treatment methods necessitate the identification of new molecular targets and potential drug candidates. Benzenesulfonamide derivatives are among the compounds that have attracted attention in recent years due to their structural diversity and biological activity potential. In the study, the electronic properties, orbital distributions and thermodynamic stabilities of benzenesulfonamide derivative molecules were calculated using the Gaussian program; thus, the re

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V. K., Mukhomorov. "Simulation of the Radioprotective Action of Mercaptoethylamine Derivatives and its Analogues with their Quantum-Chemical and Information Features." MOLECULAR SCIENCES AND APPLICATIONS 2 (December 31, 2022): 121–48. http://dx.doi.org/10.37394/232023.2022.2.14.

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Quantum chemistry, condensed matter physics and applied information theory methods are used to reveal the relationship between the molecular structure of radiation injury modifiers and their radioprotective activity in the series of aminothiols and their analogues. Significant electronic and informational parameters of molecules, which are associated with the radioprotective effect of drugs, were determined by statistical analysis methods. Based on the identified significant molecular parameters, possible mechanisms of the biochemical and biophysical radioprotective action of the analyzed chem

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