Journal articles: 'Significant molecules'

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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 from this that if there are protein molecules, there is an organism’s life and, conversely, there are no proteins — the organism is not viable. Probably, this fact served as an incentive for further study of peptides. So, in the middle of the last century, an opinion appeared among scientists about a new class of chemically active substances-cytomedins (biologically active peptides, regulatory peptides, peptide bioregulators (PB)). These molecules will be discussed in this paper.

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

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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 (September 2004): 1599–620. http://dx.doi.org/10.1016/j.addr.2004.04.002.

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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 (September 1, 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 provides a large surface-to-volume ratio, making it an intensely capable material for biomolecular attachments. The incorporation of Carbon Nanotubes (CNTs) with biological systems forming functional assemblies has shown an explored area of research. Organo-sulfur mainly alkanethiol (CnH2n+1–SH) molecules get adsorbed onto CNTs. This phenomenon has grabbed a lot of attention because Self Assembling Monolayers (SAMs) of organo-sulfur compound acts as an example system for understanding important chemical, physical or biological processes.

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Uday, R. V. Sriram, Rajdip Misra, Annaram Harika, Sandip Dolui, Achintya Saha, Uttam Pal, V. Ravichandiran, and Nakul C. Maiti. "Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease." PLOS ONE 16, no. 9 (September 10, 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 of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.

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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 (September 1, 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 ([Formula: see text] average blinking lifetime). So, a long exposure time allows the time window necessary to detect these elite molecules. The technique involves the detection of fortunate molecules to generate enough statistics for a quality reconstruction of the target protein distribution in a cellular system. Studies show a significant PArticle Resolution Shift (PAR-shift) of about 6 and 11 nm toward single-molecule-limit (far from diffraction-limit) for an exposure time window of 60 and 90 ms, respectively. In addition, a significant decrease in the fraction of fortunate molecules (single molecules with small localization precision) is observed. Specifically, 8.33% and 3.43% molecules are found to emit in 30–60 ms and >60 ms, respectively, when compared to single molecule localization microscopy (SMLM). The long exposure has enabled better visualization of the Dendra2HA molecular cluster, resolving sub-clusters within a large cluster. Thus, the proposed technique leSMLM facilitates a better study of cluster formation in fixed samples. Overall, leSMLM technique offers a spatial resolution improvement of ~ 10 nm compared to traditional SMLM at the cost of marginally poor temporal resolution.

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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 (December 8, 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 particles will be simulated by Moldy. The average potential energy is collected and compared. It discusses how the size of particles affect the average potential energy. Moreover, the trend of potential energy respects to timesteps for each molecule is depicted and compared graphicly by Gnuplot. It discusses how the potential energy changes according to timesteps for different sizes particles. In the end, the result is collected and summarized. It discovers that potential energy increases slowly when particles sizes increase, and the potential energy decreases significantly when particles sizes decrease. In addition, it founds out that molecules with different sizes have a noticeable change initially. Oddly, there is no observation of significant changes in the potential energy of the original molecule. Moreover, the initial decrease for molecules that increase in size is not as significant as that for molecules that decrease in size.

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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 (December 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 LDOS, e.g., devices that respond to changes in either conductance or electroluminescence.

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Chappell, Sarah, Carly Brooke, Richard J. Nichols, Laurence J. Kershaw Cook, Malcolm Halcrow, Jens Ulstrup, and Simon J. Higgins. "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 number of conjugated 1,4-C₆H₄- rings in the structures has been studied, and it is found that the junction conductances vary linearly with molecular length, consistent with a hopping mechanism, whereas there is significant deviation from linearity in plots of log(conductance) vs. length that would be characteristic of tunnelling, and the slopes of the log(conductance)–length plots are much smaller than expected for an oligophenyl system. Moreover, the conductances of molecular junctions involving the redox–active molecules, [M(pyterpy)₂]^2+/3+ (M = Co, Fe) have been studied as a function of electrochemical potential in ionic liquid electrolyte, and the conductance–overpotential relationship is found to fit well with the Kuznetsov–Ulstrup relationship, which is essentially a hopping description.

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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 (January 28, 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 substitution structure (

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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 (September 28, 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 orbital’s and UV-Vis spectra of both the molecules under polar solvents were explored by B3LYP/cc-pVDZ/PCM/EFP1 method. The intramolecular hydrogen atom transpired between hydroxyl to acetyl group in AHM/AHMH molecules from S0→S1 state but not in S0→S3/S0→S2 states even though the S3/S2 states have significant oscillation strengths. This indicates that intramolecular chage transfer (ICT) occurs within the molecules and it confirmed using potential energy surface (PES) scan studies.

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Khalilov, Ali N., Victor N. Khrustalev, Tatiana A. Tereshina, Mehmet Akkurt, Rovnag M. Rzayev, Anzurat A. Akobirshoeva, and İbrahim G. Mamedov. "Crystal structure and Hirshfeld surface analysis of 1-(tert-butylamino)-3-mesitylpropan-2-ol hemihydrate." Acta Crystallographica Section E Crystallographic Communications 78, no. 5 (April 28, 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 surface study, H...H interactions are the most significant contributors to the crystal packing (80.3% for molecule A and 84.8% for molecule B).

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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 (February 5, 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 in offering exceptional imaging contrast for dynamic processes in the cell membrane under relatively physiological conditions compared with competing single-molecule techniques. There exist several different complex modes of diffusion, and discriminating these from each other is challenging at the molecular level owing to underlying stochastic behaviour. Analysis is traditionally performed using mean square displacements of tracked particles; however, this generally requires more data points than is typical for single FP tracks owing to photophysical instability. Presented here is a novel approach allowing robust Bayesian ranking of diffusion processes to discriminate multiple complex modes probabilistically. It is a computational approach that biologists can use to understand single-molecule features in live cells.

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Yoshida, Norimasa, Kyoichi Kassai, Hironobu Murase, Yukiko Tanaka, Satoshi Kokura, Hiroshi Ichikawa, Yuji Naito, Takeshi Okanoue, and Toshikazu Yoshikawa. "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 increases in expression of these adhesion molecules. In a fractionation study, approximately 7 kDa fraction showed peak activity. This activity was tolerant to heating and trypsin digestion. These results indicate thatH pyloriwater extract contains water-soluble, low-molecular, nonprotein substances which induce upregulation of adhesion molecules on human umbilical vein endothelial cells, suggesting that products ofH pylorimay elicit gastric mucosal inflammation by promoting expression of endothelial adhesion molecules.

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Ramos Silva, Manuela, Vânia M. Moreira, Cláudia Cardoso, Ana Matos Beja, and 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, no. 3 (February 7, 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 differences in both molecular conformation and supramolecular aggregation between the molecules of the title compounds. The solid-state conformations compared with those obtained theoretically fromab initiomethods for the isolated molecules show large differences, especially in the orientation of the methylimidazole substituent.

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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 (January 1995): 61–71. http://dx.doi.org/10.1016/0198-8859(94)00074-z.

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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 (November 17, 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 determining the binding energies even for isomers with very similar polarizabilities and dipole moments. The possible origins of this dependence are discussed.

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Itami, Kenichiro. "(Invited, Digital Presentation) Molecular Nanocarbon Synthesis and Beyond." ECS Meeting Abstracts MA2022-01, no. 10 (July 7, 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 include: (1) the development of single-step aromatic π-extension (APEX) methods for the rapid and programmable synthesis of nanocarbon molecules (Science 2018, Nature Commun. 2015, Nature Chem. 2015, Nature Commun. 2021); (2) the synthesis of carbon nanorings, nanobelts and pure nanotubes (ACIE 2009, Science 2017, Nature Chem. 2013, Nature Commun. 2018, Nature Commun. 2019, Nature Chem. 2021); and (3) the synthesis of topologically unique nanocarbons such as warped nanographenes, carbon nanocages, all-benzene catenanes, and trefoil knots (Science 2019, Nature Chem. 2013, Nature Catal. 2020). In this talk, most recent beautiful molecular nanocarbons will be presented. We will also describe about our exciting interdisciplinary research conducted at the Institute of Transformative Bio-Molecules (ITbM) in Nagoya University and Institute of Chemistry in Academia Sinica, Taiwan, where we aim at developing game-changing molecules for nanocarbon-based chemical biology. By using our original rapid molecule-assembling catalysts, a number of lead compounds were rapidly discovered.

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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 (January 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 configuration. Molecule-molecule interactions, particularly the interactions of molecular ending functional groups between two adjacent lamellae, such as hydrogen bonds, play a dominant role in determining the molecular packing pattern in a monolayer. These weak interactions may induce or influence molecular chirality. This understanding at the atomic scale allows us to design 2D nanostructured organic materials via precisely manipulating these weak noncovalent interactions. Compared to the self-assembled monolayer formed via weak noncovalent interactions, the structure of directed-assembled monolayer/multilayers formed through strong chemical bonds is significantly dependent on the geometric arrangement and reactivity of active sites on the solid surface. In contrast to the significant role of weak intermolecular interactions in determining molecular packing in a self-assembled monolayer, strong chemical binding between molecules and reactive sites of a substrate plays a major role in determining the molecular packing pattern in a directed-assembly monolayer. Controllable chemical attachment between organic functional groups and reactive sites of the solid surface is crucial for the formation of a highly oriented organic monolayer and the following multilayer.

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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 (May 16, 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 nematic LCs depends. Therefore, we performed all-atom molecular dynamics (MD) simulations for the system composed of both Δ and Λ isomers of a chiral dopant molecule dispersed in a nematic LC and investigated the relationship between the microdynamics of the chiral molecules and their miscibility with the nematic solvent. The miscibility of the chiral dopant molecules with the LC solvent was found to correlate with the diffusion coefficient of the LC solvent. In the system where the chiral dopant molecules with high miscibility were added, the diffusion coefficient of the LC solvents was comparable to that of the system in which the chiral molecule was not doped. Furthermore, it was confirmed that more elongated chiral dopants were more miscible with the nematic solvent consisting of calamitic molecules, and that these dopant molecules did not have a significant effect on the diffusion behavior of the LC molecules.

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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 (January 19, 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 contrastive learning in natural language processing, we propose a contrastive learning framework called CONSMI to learn more comprehensive SMILES representations. This framework leverages different SMILES representations of the same molecule as positive examples and other SMILES representations as negative examples for contrastive learning. The experimental results of generation tasks demonstrate that CONSMI significantly enhances the novelty of generated molecules while maintaining a high validity. Moreover, the generated molecules have similar chemical properties compared to the original dataset. Additionally, we find that CONSMI can achieve favorable results in classifier tasks, such as the compound–protein interaction task.

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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 (May 31, 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 in anR22(8) motif. These dimers are further interconnected by weak N—H...O and C—H...O intermolecular interactions, forming chains along [011].

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Boontham, Pisake, Adrian Robins, Palanichamy Chandran, David Pritchard, Miguel Cámara, Paul Williams, Suebwong Chuthapisith, Alasdair McKechnie, Brian J. Rowlands, and Oleg Eremin. "Significant immunomodulatory effects of Pseudomonas aeruginosa quorum-sensing signal molecules: possible link in human sepsis." Clinical Science 115, no. 11 (November 3, 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 co-stimulatory molecules on dendritic cells; in MLDCRs (mixed lymphocyte dendritic cell reactions), secretion of IL (interleukin)-4 and IL-10 was enhanced, but TNF-α (tumour necrosis factor-α), IFN-γ (interferon-γ) and IL-6 was reduced. Quorum-sensing signal molecules induced apoptosis in dendritic cells and CD4+ cells, but not CD8+ cells. Dendritic cells from patients with sepsis were depleted and ex vivo showed defective expression of co-stimulatory molecules and dysfunctional stimulation of allogeneic T-lymphocytes. Enhanced apoptosis of dendritic cells and differential CD4+ Th1/Th2 (T-helper 1/2) cell apoptotic rate, and modified Th1/Th2 cell cytokine profiles in MLDCRs were also demonstrated in patients with sepsis. The pattern of immunological changes in patients with sepsis mirrors the effects of quorum-sensing signal molecules on responses of immune cells from normal individuals in vitro, suggesting that quorum-sensing signal molecules should be investigated further as a cause of immune dysfunction in sepsis.

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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 (February 14, 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 solutions in a parallelepiped cell of 5.5 × 5.3 × 5.3 nm (one acid molecule per cell) under normal conditions. The time averaging of the obtained distributions is done over 2 ns (after the system thermalization). It is shown that a specific short-range ordering organization of the solvent molecules in the vicinity of the acid molecules has a significant effect on the scattering, which is mainly determined by a relatively large ratio between the effective size of the solvent molecule and the cross-section diameter of the acid molecule. Various approximations to the simulated SLD distributions, based on the cylinder-type symmetry of the acid molecules, are probed to achieve the best consistency with the experimental SANS curves by varying the residual incoherent background.

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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 (May 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 little is known of the function of cell adhesion molecules in these diseases. In this review we summarize the structure, distribution, and function of cell adhesion molecules involved in inflammatory/immune responses. The current knowledge of the distribution of cell adhesion molecules is described and the potential for modulation of cell adhesion molecule function is discussed.

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Rousou, Charis, Josanne de Maar, Boning Qiu, Kim van der Wurff-Jacobs, Marika Ruponen, Arto Urtti, Sabrina Oliveira, et al. "The Effect of Microbubble-Assisted Ultrasound on Molecular Permeability across Cell Barriers." Pharmaceutics 14, no. 3 (February 24, 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 molecules (molecular weight 259 to 376 Da), despite their differences in hydrophilicity (LogD at pH 7.4 from −3.2 to 1.5). The largest molecules (molecular weight 4 and 20 kDa) showed the highest increase in the epithelial permeability (3-7-fold). Simultaneously, USMB enhanced intracellular accumulation of the same molecules. In the case of the clinically relevant anti- C-X-C Chemokine Receptor Type 4 (CXCR4) nanobody (molecular weight 15 kDa), USMB enhanced paracellular permeability by two-fold and increased binding to retinoblastoma cells by five-fold. Consequently, USMB is a potential tool to improve the efficacy and safety of the delivery of drugs to organs protected by tissue barriers, such as the eye and the brain.

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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, and to confirm the validity of the models, we followed the simple dissolution process of a single NaCl molecule. The results reveal approximately 350-fold decrease in real-world runtime when using an implicit solvent model and an elevated temperature, compared to using explicit water molecules and simulating at room temperature. In addition, in a wide range of temperatures, the dissolution times of NaCl are distributed, as expected, exponentially, both in explicit and in implicit solvent models, hence confirming the validity of the simulation approach. Hopefully, our findings will encourage many scientists to take advantage of the recent progress in the molecular dynamics field for various applications.

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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, no. 04 (2009): 635–39. http://dx.doi.org/10.3866/pku.whxb20090405.

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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 (March 26, 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 triclinic space groupP\overline{1} with two molecules in the unit cell. The crystal lattice of compound2reveals C—H...Cl−interactions that are present throughout the entire structure representing head-to-tail contacts between the aromatic (C—H) hydrogens of naphthoquinone and Cl−counter-ions. Compound4stacks with the aid of short interactions between a naphthoquinone O atom of one molecule and the mesityl methyl group of another molecule along theaaxis, leading to a one-dimensional strand that is held together by strong π–η2interactions between the imidazolium backbone and the [AuCl2]−counter-ion. The bond angles defined by the AuIatom and two carbene C atoms [C(carbene)—Au—C(carbene)] in compounds2and4are nearly rectilinear, with an average value of ∼174.1 [2]°. Though2and4share the same cation, they differ in their counter-anion, which alters the crystal lattice of the two compounds. The knowledge gleaned from these studies is expected to be useful in understanding the molecular interactions of2and4under physiological conditions.

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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 (February 17, 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 long short-term memory (LSTM) encoder–decoder structure to generate receptor-specific molecules with novel scaffolds. Remarkably, our model was trained with a molecular assembly accuracy of 98.4%. Leveraging the pre-trained model, we rapidly generated a RET-specific-candidate active-molecule library by transfer learning. Virtual screening based on our molecular generation model was performed, combined with molecular dynamics simulation and binding energy calculation, to discover specific RET inhibitors, and five novel molecules were selected. Further analyses indicated that two of these molecules have good binding affinities and synthesizability, exhibiting high selectivity. Overall, this investigation demonstrates the capacity of our model to generate novel receptor-specific molecules and provides a rapid method to discover potential drugs.

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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 (May 16, 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 for anti-cancer, fungicides, anti-microbials, inhibitors, etc. The structure of the molecules was strategically designed in such a way that their overall structures are the same (central tertiary-amine and peripheral hydroxy groups), except the key functional group (DTC and triazole) in the respective molecules was different. Following synthesis and characterization, the influence of DTC and triazole groups on their bioactivity was compared via interacting with the most abundant proteins present in the blood, including serum albumin, trypsin, haemoglobin, and ribonuclease. From both the experimental and molecular docking studies, it was confirmed that the triazole molecule has a higher binding affinity towards these proteins as compared to the DTC molecule. In summary, two star-shaped DTC- and triazole-based molecules were synthesized and their bioactivity was compared via binding with blood plasma proteins.

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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 (June 1, 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/toxicology screening assays. We used various molecular descriptors (MDL public keys, functional class fingerprints, and pharmacophore fingerprints) and the Tanimoto similarity coefficient. These data were then compared with cross-reactivity data in the package inserts of immunoassays marketed for in vitro diagnostic use. Previously untested compounds that were predicted to have a high probability of cross-reactivity were tested. Results: Molecular similarity calculated using MDL public keys and the Tanimoto similarity coefficient showed a strong and statistically significant separation between cross-reactive and non–cross-reactive compounds. This result was validated experimentally by discovery of additional cross-reactive compounds based on computational predictions. Conclusions: The computational methods employed are amenable toward rapid screening of databases of drugs, metabolites, and endogenous molecules and may be useful for identifying cross-reactive molecules that would be otherwise unsuspected. These methods may also have value in focusing cross-reactivity testing on compounds with high similarity to the target molecule(s) and limiting testing of compounds with low similarity and very low probability of cross-reacting with the assay.

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Johansen, K., G. Stintzing, K. E. Magnusson, T. Sundqvist, F. Jalil, A. Murtaza, S. R. Khan, 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 (October 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 malnutrition there was also a significant decrease in absorption of PEGs observed. In addition, malnourished patients with rotavirus diarrhea showed a pronounced decrease of PEGs in comparison with well‐nourished patients. The ratio between the recovery of a large PEG molecule, 1,074 Da, and a small molecule, 370 Da, was utilized to assess the absorption of large molecules in relation to that of smaller ones. On applying this ratio, it was noted that the intestine in children with Shigella and EPEC infection was relatively more permeable to larger molecules than in healthy controls, while in rotavirus and Salmonella infection it was less permeable to larger molecules. In this study significant differences in the permeability characteristics were observed, suggesting etiology‐specific effects on the mucosal barrier.

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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 (October 14, 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 positive electrostatic potential in the centers of five classical high-energy molecules for geometries extracted from different crystal structures and theoretically optimized geometries. Density functional theory calculations performed at M06/cc-PVDZ level showed that there are significant differences in the values of electrostatic potentials in critical points obtained for different geometries of the same high-energy molecules. The study also showed that there was an excellent agreement in the values of electrostatic potentials calculated for optimized geometry of 1,3,5-trinitrobenzene and geometry of this molecule obtained by neutron diffraction experiments. The results of this study could help researchers in the area of the computational development of high-energy molecules to better design their studies and to avoid the production of erroneous results.

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Joshi, Prakash, and Partha Pratim Mondal. "Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy." Photonics 9, no. 1 (December 24, 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 Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.

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Zhan, Zhuchang, Jingcheng Huang, Sara Seager, Janusz J. Petkowski, and Sukrit Ranjan. "Organic Carbonyls Are Poor Biosignature Gases in Exoplanet Atmospheres but May Generate Significant CO." Astrophysical Journal 930, no. 2 (May 1, 2022): 133. http://dx.doi.org/10.3847/1538-4357/ac64a8.

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Abstract The search for signs of life beyond Earth is a crucial driving motivation of exoplanet science, fueling new work on biosignature gases in habitable exoplanet atmospheres. We study carbonyls, a category of molecules containing the C=O double bond, following our proposal to systematically identify plausible biosignature gas candidates from a list of all small volatile molecules. We rule out carbonyls as biosignature gases due to both their high water solubility and their high photolysis rate, despite their ubiquitous production by life on Earth, their critical importance in Earth’s life biochemistry, and their uniquely identifiable molecular spectral features in mid- to low-resolution spectroscopy. Even in scenarios where life is a large net source of carbonyls, we demonstrate that detection of carbonyls is not possible on even the most ideal habitable exoplanet, because only 10 ppb of carbonyls can accumulate under our most optimistic assumptions. Moreover, high biological fluxes of organic carbon gases, while mathematically possible, are likely biologically unattainable due to the resulting huge waste of carbon—a main building block for life. Our simulations show that photochemical processing of carbonyls leads to generation of CO in quantities that can reengineer the atmosphere, affirming the ambiguity of CO as an antibiosignature. Overall, we find that the expression of a carbonyl-producing biosphere by CO, though potentially detectable by the James Webb Space Telescope, is unable to be uniquely traced back to carbonyls. While carbonyls fail as a bioindicator, by investigating them we have made a significant step toward systematically assessing the biosignature gas potential of all small volatile molecules.

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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 (February 19, 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 applications. In this article, we survey recent progress in investigating light-driven charge transport in MJs, including junctions composed of a single molecule and self-assembled monolayers (SAMs) of molecules, and new opportunities in optical sensing at the single-molecule level. We focus our attention on describing the experimental design, key phenomena, and the underlying mechanisms. Specifically, topics presented include light-assisted charge transport, photoswitch, and photoemission in MJs. Emerging Raman sensing in MJs is also discussed. Finally, outstanding challenges are explored, and future perspectives in the field are provided.

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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 chemical compounds are discussed. The detected significant molecular parameters suggest what possible molecular processes these drugs can take part in and what electronic and informational properties radioprotectors molecules should possess.

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V. da Costa, Glauber, Elenilze F. B. Ferreira, Ryan da S. Ramos, Luciane B. da Silva, Ester M. F. de Sá, Alicia K. P. da Silva, Cássio M. Lobato, et al. "Hierarchical Virtual Screening of Potential Insectides Inhibitors of Acetylcholinesterase and Juvenile Hormone from Temephos." Pharmaceuticals 12, no. 2 (April 18, 2019): 61. http://dx.doi.org/10.3390/ph12020061.

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Aedes aegypti (Linnaeus, 1762; Diptera: Culicidae) is the main vector transmitting viral diseases such as dengue fever, dengue haemorrhagic fever, urban yellow fever, zika and chikungunya. Worldwide, especially in the Americas and Brazil, many cases of dengue have been reported in recent years, which have shown significant growth. The main control strategy is the elimination of the vector, carried out through various education programs, to change human habits, but the most usual is biological control, together with environmental management and chemical control. The most commonly insecticide used is temephos (an organophosphorus compound), but Aedes aegypti populations have shown resistance and the product is highly toxic, so we chose it as a template molecule to perform a ligand-based virtual screening in the ChemBrigde (DIVERSet-CL subcollection) database, searching for derivatives with similarity in shape (ROCS) and electrostatic potential (EON). Thus, fourty-five molecules were filtered based on their pharmacokinetic and toxicological properties and 11 molecules were selected by a molecular docking study, including binding affinity and mode of interaction. The L46, L66 and L68 molecules show potential inhibitory activity for both the insect (−9.28, −10.08 and −6.78 Kcal/mol, respectively) and human (−6.05, 6.25 and 7.2 Kcal/mol respectively) enzymes, as well as the juvenile hormone protein (−9.2; −10.96 and −8.16 kcal/mol, respectively), showing a significant difference in comparison to the template molecule temephos. Molecules L46, L66 and L68 interacted with important amino acids at each catalytic site of the enzyme reported in the literature. Thus, the molecules here investigated are potential inhibitors for both the acetylcholinesterase enzymes and juvenile hormone protein–from insect and humans, characterizing them as a potential insecticide against the Aedes aegypti mosquito.

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Kimura, Hiroshi, Yong Tao, Robert G. Roeder, and Peter R. Cook. "Quantitation of RNA Polymerase II and Its Transcription Factors in an HeLa Cell: Little Soluble Holoenzyme but Significant Amounts of Polymerases Attached to the Nuclear Substructure." Molecular and Cellular Biology 19, no. 8 (August 1, 1999): 5383–92. http://dx.doi.org/10.1128/mcb.19.8.5383.

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ABSTRACT Various complexes that contain the core subunits of RNA polymerase II associated with different transcription factors have been isolated from eukaryotes; their precise molecular constitution depends on the purification procedure. We estimated the numbers of various components of such complexes in an HeLa cell by quantitative immunoblotting. The cells were lysed with saponin in a physiological buffer; ∼140,000 unengaged polymerases (mainly of form IIA) were released. Only ∼4,000 of these soluble molecules sedimented in glycerol gradients as holoenzyme-sized complexes. About 180,000 molecules of polymerases (∼110,000 molecules of form IIO) and 10,000 to 30,000 molecules of each of TFIIB, TFIIEα, TFIIEβ, TFIIF-RAP74, TFIIF-RAP30, and TFIIH-MAT1 remained tightly associated with the nuclear substructure. Most proteins and run-on activity were retained when ∼50% of the chromatin was detached with a nuclease, but ∼45,000 molecules of bound TATA binding protein (TBP) were detached. Similar results were obtained after cross-linking living cells with formaldehyde. The results provide little support for the existence of a large pool of soluble holoenzyme; they are consistent with TBP-promoter complexes in nuclease-sensitive chromatin being assembled into preinitiation complexes attached to the underlying structure.

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Wang, Fei, Liang Zhao, Yan Ling Zhang, and Da Lei Jing. "Effect of Adsorption Stress-Induced Change in Neutral Layer Position on Static Behavior of Microcantilever Gas Sensor." Key Engineering Materials 562-565 (July 2013): 268–75. http://dx.doi.org/10.4028/www.scientific.net/kem.562-565.268.

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The static bending model of microcantilever with monolayer molecules has been established based on energy method, in which the change in neutral layer position caused by adsorption-induced stress is introduced. On this basis, we have analyzed the relationship between the bending curvature radius of a microcantilever with its thickness, Young’s modulus and molecule-molecule distance of adsorbed molecules when it is adsorbed with monolayer water molecules. Additionally, we have investigated the effect of change in neutral layer position on the static behavior of microcantilever sensors. The results show that 1)the bending curvature radius of microcantilever is the linear, quadratic and eight approximation function of its Young’s modulus, thickness and distance of adsorbed molecules, respectively; 2)the predicted error of bending curvature radius caused by the change in neutral layer position slightly increases with decreasing Young’s modulus and thickness, whereas the effect of distance between adsorbed molecules on the error is significant; 3)the change in neutral layer position can cause a significant effect on the sensitivity and surface strain of the microcantilever

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Klepetářová, Blanka, Emanuel Makrlík, Vasily A. Babain, and Václav Kašička. "N,N′-Diethyl-N,N′-diphenylpyridine-2,6-dicarboxamide." Acta Crystallographica Section E Structure Reports Online 68, no. 4 (March 17, 2012): o1099—o1100. http://dx.doi.org/10.1107/s1600536812009026.

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The asymmetric unit of the title compound, C23H23N3O2, contains two molecules in both of which, one amide N atom is in asynposition with respect to the pyridine N atom, while the other amide N atom is in anantiposition (thesyn--anticonformation). There are minor conformational differences between the two molecules, as reflected in the Npyridine—C—C—Namidetorsion angles of −44.9 (3) and 136.0 (2)° for one molecule and 43.5 (3) and −131.1 (2)° for the other molecule. However, the two molecules show significant differences in the orientation of an ethyl group, with corresponding C—C—N—C torsion angles of 86.6 (3)° for one molecule and 79.6 (3)° for the other molecule. In the crystal, molecules are linked by weak C—H...O hydrogen bonds, forming a three-dimensional supramolecular network.

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Ghaderi, Amineh, Wen Zhong, Mohammad Ali Okhovat, Johanna Aschan, Ann Svensson, Birgitta Sander, Johan Schultz, et al. "A ROR1 Small Molecule Inhibitor (KAN0441571C) Induced Significant Apoptosis of Mantle Cell Lymphoma (MCL) Cells." Pharmaceutics 14, no. 10 (October 20, 2022): 2238. http://dx.doi.org/10.3390/pharmaceutics14102238.

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The receptor tyrosine kinase orphan receptor 1 (ROR1) is absent in most normal adult tissues but overexpressed in various malignancies and is of importance for tumor cell survival, proliferation, and metastasis. In this study, we evaluated the apoptotic effects of a novel small molecule inhibitor of ROR1 (KAN0441571C) as well as venetoclax (BCL-2 inhibitor), bendamustine, idelalisib (PI3Kδ inhibitor), everolimus (mTOR inhibitor), and ibrutinib (BTK inhibitor) alone or in combination in human MCL primary cells and cell lines. ROR1 expression was evaluated by flow cytometry and Western blot (WB). Cytotoxicity was analyzed by MTT and apoptosis by Annexin V/PI staining as well as signaling and apoptotic proteins (WB). ROR1 was expressed both in patient-derived MCL cells and human MCL cell lines. KAN0441571C alone induced significant time- and dose-dependent apoptosis of MCL cells. Apoptosis was accompanied by decreased expression of MCL-1 and BCL-2 and cleavage of PARP and caspase 3. ROR1 was dephosphorylated as well as ROR1-associated signaling pathway molecules, including the non-canonical WNT signaling pathway (PI3Kδ/AKT/mTOR). The combination of KAN0441571C and ibrutinib, venetoclax, idelalisib, everolimus, or bendamustine had a synergistic apoptotic effect and significantly prevented phosphorylation of ROR1-associated signaling molecules as compared to KAN0441571C alone. Our results suggest that targeting ROR1 by a small molecule inhibitor, KAN0441571C, should be further evaluated particularly in combination with other targeting drugs as a new therapeutic approach for MCL.

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Hersam, M. C., and R. G. Reifenberger. "Charge Transport through Molecular Junctions." MRS Bulletin 29, no. 6 (June 2004): 385–90. http://dx.doi.org/10.1557/mrs2004.120.

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AbstractIn conventional solid-state electronic devices, junctions and interfaces play a significant if not dominant role in controlling charge transport. Although the emerging field of molecular electronics often focuses on the properties of the molecule in the design and understanding of device behavior, the effects of interfaces and junctions are often of comparable importance. This article explores recent work in the study of metal–molecule–metal and semiconductor–molecule–metal junctions. Specific issues include the mixing of discrete molecular levels with the metal continuum, charge transfer between molecules and semiconductors, electron-stimulated desorption, and resonant tunneling. By acknowledging the consequences of junction/interface effects, realistic prospects and limitations can be identified for molecular electronic devices.

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Xin, Zhaorui, Zhiheng Ding, Zhongjuan Li, and Yue Zhang. "41.1: Invited Paper: Design of Organic Electroluminescence Material via High‐Throughput Screening For OLED Applications." SID Symposium Digest of Technical Papers 54, S1 (April 2023): 280–86. http://dx.doi.org/10.1002/sdtp.16282.

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The hot exciton mechanism has joined TTA and TADF as one of the three fundamental theories widely recognized for overcoming the spin statistics constraint in FOLEDs. Although there has been many research and application of hot exciton materials in OLED, the relationship between the molecular structure and its performance of hot exciton material is still unclear. In this work, we performed a high-throughput quantum chemistry calculation for screening hot exciton materials. Ten thousand different molecules are calculated for the electronic donor or acceptor for hot exciton material molecule. Ten hot exciton material molecules were designed based on predicted properties, while other molecular properties were also analyzed. This research represents a significant opportunity to enhance our comprehension of the interplay between material structure and performance and could potentially accelerate the design of hot exciton materials.

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

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Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.

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Hall, Adam R. "Solid-State Nanopores: From Fabrication to Application." Microscopy Today 20, no. 5 (September 2012): 24–29. http://dx.doi.org/10.1017/s1551929512000703.

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There are relatively few technologies for measurement at the single-molecule scale. Fluorescent imaging, for example, can be used to directly visualize molecules and their interactions, but diffraction limitations and labeling requirements may push the system from its native state. Although recent advances in super-resolution imaging have been able to break this resolution barrier, important challenges remain. Atomic force microscopy (AFM) is capable of imaging molecules at high resolution and at high speed. However, AFM imaging is a surface technique, requiring sample preparation and some immobilization. Other technologies such as optical tweezers and magnetic tweezers are capable of molecular manipulation and spectroscopy to great effect but require a significant apparatus and have limited inherent analytical capabilities.

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Mushir, Ayed F., Mohsin K. Al-Khaykaneea, and Rawaa M. Obaida. "Influence of Central-Metallic Atoms of Molecular Junction on Electrical and Thermal Transport." NeuroQuantology 20, no. 5 (May 9, 2022): 343–48. http://dx.doi.org/10.14704/nq.2022.20.5.nq22179.

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Molecular structures of a series of metal-complexes molecules of bipyrimdine have interesting features in various applications such as industrial and scientific. The transition through metal complexes at molecular structures has a significant role in the metal-bridges interactions. Hence, the bipyrimdine's complex molecules were used to show the effect of the metal atoms on the electronics, electrical, and thermoelectric properties and to identify the π-conjugated system in all attempts before/ or after replaced one carbon with nitrogen atoms in one or two the pyridine rings. SIESTA code, and GOLLUM code programs were used in our calculations. The results showed that the energy gap decreased significantly with the type of metal atoms, which appear in electronic applications at various LUMO-HOMO energy gaps. The electrical and thermal results have confirmed the effect of metal-complexes center atoms in the transmission and Seebeck coefficients. From the position of the Fermi energy (E-EF=0 eV), the conductance and the thermopower values are determined, and thus the specificity figure of merit ZTe was computed. Therefore, we found the ZTe be a high value for bipyridine molecule about 1.7, which is several order of magnitude higher than of the set molecules. Whereas a low value of ZTe for Cr-metal-molecule.

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Wilkinson, Trevor C. I. "Discovery of functional monoclonal antibodies targeting G-protein-coupled receptors and ion channels." Biochemical Society Transactions 44, no. 3 (June 9, 2016): 831–37. http://dx.doi.org/10.1042/bst20160028.

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The development of recombinant antibody therapeutics is a significant area of growth in the pharmaceutical industry with almost 50 approved monoclonal antibodies on the market in the US and Europe. Despite this growth, however, certain classes of important molecular targets have remained intractable to therapeutic antibodies due to complexity of the target molecules. These complex target molecules include G-protein-coupled receptors and ion channels which represent a large potential target class for therapeutic intervention with monoclonal antibodies. Although these targets have typically been addressed by small molecule approaches, the exquisite specificity of antibodies provides a significant opportunity to provide selective modulation of these target proteins. Given this opportunity, substantial effort has been applied to address the technical challenges of targeting these complex membrane proteins with monoclonal antibodies. In this review recent progress made in the strategies for discovery of functional monoclonal antibodies for these challenging membrane protein targets is addressed.

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Trimdale, Aija, Anatoly Mishnev, and Agris Bērziņš. "Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases." Pharmaceutics 13, no. 5 (May 16, 2021): 734. http://dx.doi.org/10.3390/pharmaceutics13050734.

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The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

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Journal articles on the topic 'Significant molecules'

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