Journal articles: 'Functional molecules'

1

Archut, Andreas, and Fritz Vögtle. "Functional cascade molecules." Chemical Society Reviews 27, no. 4 (1998): 233. http://dx.doi.org/10.1039/a827233z.

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Mayo, Kevin H. "Heterologous Interactions with Galectins and Chemokines and Their Functional Consequences." International Journal of Molecular Sciences 24, no. 18 (September 14, 2023): 14083. http://dx.doi.org/10.3390/ijms241814083.

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Extra- and intra-cellular activity occurs under the direction of numerous inter-molecular interactions, and in any tissue or cell, molecules are densely packed, thus promoting those molecular interactions. Galectins and chemokines, the focus of this review, are small, protein effector molecules that mediate various cellular functions—in particular, cell adhesion and migration—as well as cell signaling/activation. In the past, researchers have reported that combinations of these (and other) effector molecules act separately, yet sometimes in concert, but nevertheless physically apart and via their individual cell receptors. This view that each effector molecule functions independently of the other limits our thinking about functional versatility and cooperation, and, in turn, ignores the prospect of physiologically important inter-molecular interactions, especially when both molecules are present or co-expressed in the same cellular environment. This review is focused on such protein-protein interactions with chemokines and galectins, the homo- and hetero-oligomeric structures that they can form, and the functional consequences of those paired interactions.

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Abbaz, Tahar, Amel Bendjeddou, and Didier Villemin. "Molecular structure, NBO analysis, ﬁrst hyper polarizability, and homo-lumo studies of π-extended tetrathiafulvalene (EXTTF) derivatives connected to π-nitro phenyl by density functional method." International Journal of Advanced Chemistry 6, no. 1 (June 5, 2018): 114. http://dx.doi.org/10.14419/ijac.v6i1.11126.

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In these study we have been obtained the structural properties of (exTTF) derivatives 1-4 by using B3LYP/6-31G(d,p) of Density Functional Theory (DFT) utilizing Becke three exchange functional and Lee Yang Paar correlation functional. The calculation of ﬁrst hyperpolarizability shows that the molecules are attractive molecules for future applications in non-linear optics. Molecular electrostatic potential (MEP) at a point in the space around a molecule gives an indication of the net electrostatic effect produced at that point by the total charge distribution of the molecule. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules.

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Simpson, Jeremy C., and Arwyn T. Jones. "Early endocytic Rabs: functional prediction to functional characterization." Biochemical Society Symposia 72 (January 1, 2005): 99–108. http://dx.doi.org/10.1042/bss0720099.

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Endocytic pathways are highly dynamic gateways for molecules to enter cells. Functionality and specificity is in part controlled by a number of small GTPases called Rabs. In defined cellular locations, Rabs mediate multiple functions in membrane trafficking via their specific interaction with organelle membranes and a host of affector and effector molecules. On endocytic pathways, Rabs have been shown to control the formation of vesicles on the plasma membrane and the downstream delivery of internalized molecules to a number of cellular locations. As numerous Rabs are located to endocytic pathways, an internalized molecule may traverse a number of Rab specific substations or subdomains en route to its final destination. Rabs 5, 21 and 22 have all been localized to the early endocytic pathway and have been shown to share a number of characteristics to merit their segregation into a single functional endocytic group. In this review, we compare experiments that describe similarities and differences in endosome morphology and function that is mediated by their expression in cells.

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Maslehat, Sholeh, Soroush Sardari, and Mahboube Ganji Arjenaki. "Frequency and Importance of Six Functional Groups that Play a Role in Drug Discovery." Biosciences, Biotechnology Research Asia 15, no. 3 (September 27, 2018): 541–48. http://dx.doi.org/10.13005/bbra/2659.

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Small molecules are composed of chemical functional groups; they are sets of connected atoms or atom groups that determine properties and reactivity of the parent molecule. DrugBank is a rich source of information that containing molecular data about small molecules, their mechanisms, pharmaceutical interaction and targets. In this study, After collecting data of small drug molecules from DrugBank database and classifying them in different categories based on their mechanism of action, the therapeutic properties of the molecules were recorded. Finally, the functional group from the pharmaceutical structures were elucidated and registered for each group. The functional groups were divided into five distinct groups in drug design, and a correlation between identified functional group to pharmaceutical structure were indicated according to the classified functional groups of small molecule and drug categories; then defined their frequency in categories, at high abundant functional group present in categories reported. The most frequent rings were benzene and cyclohexane; the common acid functionality had been acetate (carboxy-); three most repeated saturated heterocyles are piperidine, piperazine and azetidine; among the unsaturated heterocyles, pyridine, imidazole and indole are noticed; This database, that may be guidance for researchers with the aim at designing new drugs.

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Niemeyer, Jochen, and Noel Pairault. "Chiral Mechanically Interlocked Molecules – Applications of Rotaxanes, Catenanes and Molecular Knots in Stereoselective Chemosensing and Catalysis." Synlett 29, no. 06 (February 26, 2018): 689–98. http://dx.doi.org/10.1055/s-0036-1591934.

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Interlocked molecules, such as rotaxanes, catenanes, and molecular knots, offer conceptually new possibilities for the generation of chiral chemosensors and catalysts. Due to the presence of the mechanical or topological bond, interlocked molecules can be used to design functional systems with unprecedented features, such as switchability and deep binding cavities. In addition, classical elements of chirality can be supplemented with mechanical or topological chirality, which have so far only scarcely been employed as sources of chirality for stereoselective applications. This minireview discusses recent examples in this emerging area, showing that the application of chiral interlocked molecules in sensing and catalysis offers many fascinating opportunities for future research.1 Introduction2 Interlocked Molecules with Chiral Subcomponents2.1 Point Chirality2.2 Axial Chirality3 Mechanically Chiral Interlocked Molecules4 Topologically Chiral Interlocked Molecules5 Outlook

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Valášek, Michal, Marcin Lindner, and Marcel Mayor. "Rigid multipodal platforms for metal surfaces." Beilstein Journal of Nanotechnology 7 (March 8, 2016): 374–405. http://dx.doi.org/10.3762/bjnano.7.34.

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In this review the recent progress in molecular platforms that form rigid and well-defined contact to a metal surface are discussed. Most of the presented examples have at least three anchoring units in order to control the spatial arrangement of the protruding molecular subunit. Another interesting feature is the lateral orientation of these foot structures which, depending on the particular application, is equally important as the spatial arrangement of the molecules. The numerous approaches towards assembling and organizing functional molecules into specific architectures on metal substrates are reviewed here. Particular attention is paid to variations of both, the core structures and the anchoring groups. Furthermore, the analytical methods enabling the investigation of individual molecules as well as monomolecular layers of ordered platform structures are summarized. The presented multipodal platforms bearing several anchoring groups form considerably more stable molecule–metal contacts than corresponding monopodal analogues and exhibit an enlarged separation of the functional molecules due to the increased footprint, as well as restrict tilting of the functional termini with respect to the metal surface. These platforms are thus ideally suited to tune important properties of the molecule–metal interface. On a single-molecule level, several of these platforms enable the control over the arrangement of the protruding rod-type molecular structures (e.g., molecular wires, switches, rotors, sensors) with respect to the surface of the substrate.

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8

Watve, Milind. "How many functional molecules ?" Resonance 2, no. 7 (July 1997): 86–87. http://dx.doi.org/10.1007/bf02838596.

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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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Splitter, Gary A. "Molecular and functional properties of leucocyte surface molecules." Veterinary Immunology and Immunopathology 35 (February 1993): 11–15. http://dx.doi.org/10.1016/0165-2427(93)90127-p.

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11

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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12

Zhu, Zhe, Masahiro Higashi, and Shinji Saito. "Excited states of chlorophyll a and b in solution by time-dependent density functional theory." Journal of Chemical Physics 156, no. 12 (March 28, 2022): 124111. http://dx.doi.org/10.1063/5.0083395.

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The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in the functionals. Here, we optimize the range-separated parameter, μ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of μ for Chl a and Chl b are smaller than the default value of μ and that for bacteriochlorophyll a, indicating the change in the electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of the solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.

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13

Rangel, E., L. F. Magana, L. E. Sansores, and G. J. Vázquez. "Generation of hydrogen peroxide on a pyridine-like nitrogen-nickel doped graphene surface." MRS Proceedings 1451 (2012): 69–74. http://dx.doi.org/10.1557/opl.2012.1335.

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ABSTRACTDensity functional theory and molecular dynamics were used to study the generation of hydrogen peroxide around a nickel atom anchored on a pyridine-like nitrogen-doped graphene (PNG) layer. First, we found that two hydrogen molecules are adsorbed around the nickel atom, with adsorption energy 0.95 eV/molecule. Then we studied the interaction of oxygen molecules with this system at atmospheric pressure and 300 K. It is found that two hydrogen peroxide molecules are formed. However, at 700 K, one hydrogen peroxide molecule, and one water molecule are desorbed. One oxygen atom stays bound to the nickel atom.

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14

Kawagishi, Hirokazu. "Biologically Functional Molecules from Mushrooms." Journal of Synthetic Organic Chemistry, Japan 68, no. 5 (2010): 514–21. http://dx.doi.org/10.5059/yukigoseikyokaishi.68.514.

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Nagatsugi, Fumi, and Kazumitsu Onizuka. "Functional G-Quadruplex Binding Molecules." Chemistry Letters 49, no. 7 (July 5, 2020): 771–80. http://dx.doi.org/10.1246/cl.200214.

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Dai, Cheng, Dong Liang, Huiwu Li, Masayuki Sasaki, Ted M. Dawson, and Valina L. Dawson. "Functional Identification of Neuroprotective Molecules." PLoS ONE 5, no. 11 (November 24, 2010): e15008. http://dx.doi.org/10.1371/journal.pone.0015008.

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Karr, R. W., N. L. Reinsmoen, R. C. Gehrz, and E. Celis. "Functional heterogeneity of DPw4 molecules." Human Immunology 23, no. 2 (January 1988): 111. http://dx.doi.org/10.1016/0198-8859(88)90177-2.

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18

ARCHUT, A., and F. VOEGTLE. "ChemInform Abstract: Functional Cascade Molecules." ChemInform 29, no. 39 (June 19, 2010): no. http://dx.doi.org/10.1002/chin.199839322.

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UEDA, Mitsuyoshi. "Molecular Tool Creating Novel and Functional Bio-active Molecules." Kobunshi 50, no. 4 (2001): 254. http://dx.doi.org/10.1295/kobunshi.50.254.

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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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Xiang, Feifei, Tobias Schmitt, Marco Raschmann, and M. Alexander Schneider. "Adsorption and self-assembly of porphyrins on ultrathin CoO films on Ir(100)." Beilstein Journal of Nanotechnology 11 (October 5, 2020): 1516–24. http://dx.doi.org/10.3762/bjnano.11.134.

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Porphyrins represent a versatile class of molecules, the adsorption behavior of which on solid surfaces is of fundamental interest due to a variety of potential applications. We investigate here the molecule–molecule and molecule–substrate interaction of Co-5,15-diphenylporphyrin (Co-DPP) and 2H-tetrakis(p-cyanophenyl)porphyrin (2H-TCNP) on one bilayer (1BL) and two bilayer (2BL) thick cobalt oxide films on Ir(100) by scanning tunneling microscopy (STM) and density functional theory (DFT). The two substrates differ greatly with respect to their structural and potential-energy landscape corrugation with immediate consequences for adsorption and self-assembly of the molecules studied. On both films, an effective electronic decoupling from the metal substrate is achieved. However, on the 1BL film, Co-DPP molecules are sufficiently mobile at 300 K and coalesce to self-assembled molecular islands when cooled to 80 K despite their rather weak intermolecular interaction. In contrast, on the 2BL film, due to the rather flat potential landscape, molecular rotation is thermally activated, which effectively prevents self-assembly. The situation is different for 2H-TCNPP, which, due to the additional functional anchoring groups, does not self-assemble on the 1BL film but forms self-assembled compact islands on the 2BL film. The findings demonstrate the guiding effect of the cobalt oxide films of different thickness and the effect of functional surface anchoring.

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Feng, Simin, Maria Cristina dos Santos, Bruno R. Carvalho, Ruitao Lv, Qing Li, Kazunori Fujisawa, Ana Laura Elías, et al. "Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering." Science Advances 2, no. 7 (July 2016): e1600322. http://dx.doi.org/10.1126/sciadv.1600322.

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As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (EF) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule’s vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10−11M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps.

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FAHRENDORF, SARAH, FRANK MATTHES, DANIEL E. BÜRGLER, CLAUS M. SCHNEIDER, NICOLAE ATODIRESEI, VASILE CACIUC, STEFAN BLÜGEL, CLAIRE BESSON, and PAUL KÖGERLER. "STRUCTURAL INTEGRITY OF SINGLE BIS(PHTHALOCYANINATO)-NEODYMIUM(III) MOLECULES ON METAL SURFACES WITH DIFFERENT REACTIVITY." SPIN 04, no. 02 (June 2014): 1440007. http://dx.doi.org/10.1142/s2010324714400074.

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Magnetic molecules are auspicious candidates to act as functional units in molecular spintronics. Integrating molecules into a device environment providing mechanical support and electrical contacts requires their deposition as intact entities onto substrates. Thermal sublimation is a very clean deposition process that, however, thermally decomposes molecules of insufficient stability leading to the deposition of molecular fragments. Here, we show that the molecule-surface interaction of chemisorbed molecules affects the intramolecular bonding and can lead depending on the surface reactivity to either molecular decomposition or enhanced stability. We study the integrity of single bis(phthalocyaninato)-neodymium(III) molecules ( NdPc 2) deposited by sublimation on differently reactive surfaces, namely Au (111), Cu (100), and two atomic layers of Fe on W (110), on the single molecular level by scanning tunneling microscopy (STM) and spectroscopy. We find a strongly substrate-dependent tendency of the NdPc 2 molecules to decompose into two Pc molecules. Surprisingly, the most reactive Fe / W (110) surface shows the lowest molecular decomposition probability, whereas there are no intact NdPc 2 molecules at all on the least reactive Au (111) surface. We attribute these findings to substrate-dependent partial charge transfer from the substrate to the Pc ligands of the molecule, which strengthens the intramolecular bonding mediated predominantly by electrostatic interaction.

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Zhang, Xin Wei, Cun Li, and Jun Qi Xu. "Study on the Second-Order Nonlinear Optical Properties of [6]Helicenes with Chromophores." Applied Mechanics and Materials 303-306 (February 2013): 2563–66. http://dx.doi.org/10.4028/www.scientific.net/amm.303-306.2563.

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A series of chiral [6]helicenes have been designed using the molecular engineering of organic nonlinear optical materials. The geometries of [6]helicenes 1, 2, 3, 4,5 are optimized using density functional theory (DFT-B3LYP) method at the 6-31g (d, p) basis set level. Based on the obtained stable molecular configuration, we adopt the TDHT/PM3 method and time-dependent density-functional theory (TD-DFT) to calculate the nonlinear optical (NLO) properties and electronic spectra of these molecules. Results show that the static hyperpolarizability βµ alternates between positive value and negative value, whereas it remains positive for the molecues 2 and 3 which have medium magnitudes βµ, 3.4×10-30esu and 9.6×10-30esu respectively. In molecule 5, there exists two competitive charge transfers that reduce the hyperpolarizability β.

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Zhang, Jian Wei, Cai Jiang, Gang Shi, and Da Zhi Jiang. "Diffusion of Epoxy Molecules on the Chemically Modified Graphene: A Molecular Dynamics Simulation Study." Materials Science Forum 817 (April 2015): 803–8. http://dx.doi.org/10.4028/www.scientific.net/msf.817.803.

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Buckypaper based polymer composites provides a new technical approach toward realizing conductive/structural multifunctional composites. Resin infiltration in the buckypaper is critical for the fabrication of buckypaper/polymer composites. To investigate the micro-infusion process of the polymer inside the paper, molecular dynamics (MD) simulations are conducted to study the diffusion behavior of epoxy molecules on the modified graphene and between graphene layers. The graphene molecular structures are constructed to represent the wall structures of the carbon nanotubes. Diffusion coefficients of the epoxy molecules on the graphene modified with different functionalization densities and interlayer distances are calculated. The results indicate that the functional groups increase the interfacial interactions between the epoxy molecules and graphene, however, largely decrease the diffusion speeds of the epoxy molecule. The simulations on the graphene layer systems indicate that, the viscous resistance of the resin is the main factor for retarding the diffusion of the epoxy molecules for the unmodified graphene layers; while for the modified graphene layers, functional groups are the main factor for retarding the resin diffusion

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Misaghi, Shahram, Zhen-Yu J. Sun, Patrick Stern, Rachelle Gaudet, Gerhard Wagner, and Hidde Ploegh. "Structural and Functional Analysis of Human Cytomegalovirus US3 Protein." Journal of Virology 78, no. 1 (January 1, 2004): 413–23. http://dx.doi.org/10.1128/jvi.78.1.413-423.2004.

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ABSTRACT Human cytomegalovirus (HCMV) unique short region 3 (US3) protein, a type I membrane protein, prevents maturation of class I major histocompatibility complex (MHC) molecules by retaining them in the endoplasmic reticulum (ER) and thus helps inhibit antigen presentation to cytotoxic T cells. US3 molecules bind to class I MHC molecules in a transient fashion but retain them very efficiently in the ER nonetheless. The US3 luminal domain is responsible for ER retention of US3 itself, while both the US3 luminal and transmembrane domains are necessary for retaining class I MHC in the ER. We have expressed the luminal domain of US3 molecule in Escherichia coli and analyzed its secondary structure by using nuclear magnetic resonance. We then predicted the US3 tertiary structure by modeling it based on the US2 structure. Unlike the luminal domain of US2, the US3 luminal domain does not obviously interact with class I MHC molecules. The luminal domain of US3 dynamically oligomerizes in vitro and full-length US3 molecules associate with each other in vivo. We present a model depicting how dynamic oligomerization of US3 may enhance its ability to retain class I molecules within the ER.

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Ogata, Makoto. "Functional design of glycan-conjugated molecules using a chemoenzymatic approach." Bioscience, Biotechnology, and Biochemistry 85, no. 5 (February 15, 2021): 1046–55. http://dx.doi.org/10.1093/bbb/zbab024.

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ABSTRACT Carbohydrates play important and diverse roles in the fundamental processes of life. We have established a method for accurately and a large-scale synthesis of functional carbohydrates with diverse properties using a unique enzymatic method. Furthermore, various artificial glycan-conjugated molecules have been developed by adding these synthetic carbohydrates to macromolecules and to middle- and low-molecular-weight molecules with different properties. These glycan-conjugated molecules have biological activities comparable to or higher than those of natural compounds and present unique functions. In this review, several synthetic glycan-conjugated molecules are taken as examples to show design, synthesis, and function.

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Liang, Zezhou, Lihe Yan, Jinhai Si, Pingping Gong, Xiaoming Li, Deyu Liu, Jianfeng Li, and Xun Hou. "Rational Design and Characterization of Symmetry-Breaking Organic Semiconductors in Polymer Solar Cells: A Theory Insight of the Asymmetric Advantage." Materials 14, no. 21 (November 8, 2021): 6723. http://dx.doi.org/10.3390/ma14216723.

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Asymmetric molecule strategy is considered an effective method to achieve high power conversion efficiency (PCE) of polymer solar cells (PSCs). In this paper, nine oligomers are designed by combining three new electron-deficient units (unitA)—n1, n2, and n3—and three electron-donating units (unitD)—D, E, and F—with their π-conjugation area extended. The relationships between symmetric/asymmetric molecule structure and the performance of the oligomers are investigated using the density functional theory (DFT) and time-dependent density functional theory (TD–DFT) calculations. The results indicate that asymmetry molecule PEn2 has the minimum dihedral angle in the angle between two planes of unitD and unitA among all the molecules, which exhibited the advantages of asymmetric structures in molecular stacking. The relationship of the values of ionization potentials (IP) and electron affinities (EA) along with the unitD/unitA π-extend are revealed. The calculated reorganization energy results also demonstrate that the asymmetric molecules PDn2 and PEn2 could better charge the extraction of the PSCs than other molecules for their lower reorganization energy of 0.180 eV and 0.181 eV, respectively.

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Filonenko, O. V. "Raman Spectroscopy Of Fullerene-Like Molecules Of Silicon Dioxide (SiO2)N(H2O)N/2." Фізика і хімія твердого тіла 17, no. 3 (September 15, 2016): 401–6. http://dx.doi.org/10.15330/pcss.17.3.401-406.

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The Raman spectra of monosilicic, disilicic acid molecules, tetra- and pentasilicic acid molecules with cyclic structure, cage-like okta- and dekasilicic asid molecules, and of fullerene-like molecule (SiO2)N(H2O)N/2 have been calculated using density functional theory method (exchange-correlation functional B3LYP and basis set 6-31G (d, p)) and assignment of frequencies in conformity with the shape fluctuations have been executed.

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Zhang, Shanmeiyu, Yanyan Zhang, Chongchong Wu, Hui Yang, Qiqi Zhang, Fuyi Wang, Jingyi Wang, Ian Gates, and Jinben Wang. "A Facile Strategy to Prepare Small Water Clusters via Interacting with Functional Molecules." International Journal of Molecular Sciences 22, no. 15 (July 31, 2021): 8250. http://dx.doi.org/10.3390/ijms22158250.

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Although small water clusters (SWCs) are important in many research fields, efficient methods of preparing SWCs are still rarely reported, which is mainly due to the lack of related materials and understanding of the molecular interaction mechanisms. In this study, a series of functional molecules were added in water to obtain small water cluster systems. The decreasing rate of the half-peak width in a sodium dodecyl sulfate (SDS)–water system reaches ≈20% at 0.05 mM from 17O nuclear magnetic resonance (NMR) results. Based on density functional theory (DFT) and molecular dynamics (MD) simulation calculation, it can be concluded that functional molecules with stronger negative electrostatic potential (ESP) and higher hydrophilicity have a stronger ability to destroy big water clusters. Notably, the concentrations of our selected molecule systems are one to two magnitudes lower than that of previous reports. This study provides a promising way to optimize aqueous systems in various fields such as oilfield development, protein stability, and metal anti-corrosion.

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Fodor, W. L., S. A. Rollins, E. R. Guilmette, E. Setter, and S. P. Squinto. "A novel bifunctional chimeric complement inhibitor that regulates C3 convertase and formation of the membrane attack complex." Journal of Immunology 155, no. 9 (November 1, 1995): 4135–38. http://dx.doi.org/10.4049/jimmunol.155.9.4135.

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Abstract Human cells express cell surface complement regulatory molecules that inhibit the activity of the C3/C5 convertases (DAF, MCP, CR1) or inhibit the membrane attack complex (CD59). A single molecule that inhibits both the convertase activity and formation of the membrane attack complex has never been characterized. To this end, we have developed two reciprocal chimeric complement inhibitors (CD, NH2-CD59-DAF-GPI; and DC, NH2-DAF-CD59-GPI) that contain the functional domains of decay accelerating factor (DAF; CD55) and CD59. Cell surface expression of the CD and DC chimeric proteins was detected with DAF- and CD59-specific antisera. Cell surface C3d deposition was inhibited on cells expressing the chimeric molecules, thereby indicating that the DAF moiety was functional in both molecules. Conversely, Ab-blocking experiments demonstrated that only the DC molecule retained CD59 function. Therefore, the DC molecule represents a novel potent chimeric bifunctional complement inhibitor that retains the functional domains of two distinct complement regulatory molecules.

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Febriana, Fitri Noor, Vera Khoirunisa, Wun Fui Mark-Lee, and Febdian Rusydi. "Theoretical Study of the Stability of Acetylcholine Based on Molecular Orbital Theory using Density Functional Theory." Indonesian Applied Physics Letters 3, no. 1 (October 31, 2022): 16–19. http://dx.doi.org/10.20473/iapl.v3i1.39777.

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Some molecules in nature have a positive or negative charge. One such molecule is acetylcholine. Acetylcholine is a positively charged molecule that is responsible for Alzheimer's disease. This study evaluated acetylcholine through six simple molecules based on the ionization potential and the HOMO-LUMO gap obtained from the density functional theory calculation. The calculation results showed that the ionization potential and the HOMO-LUMO gap could explain the stability of acetylcholine and the six other molecules. As a result, acetylcholine has the same properties as five other simple molecules. Meanwhile, one other molecule has the opposite properties to acetylcholine.

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Laux, Eva-Maria, Christian Wenger, Frank F. Bier, and Ralph Hölzel. "AC electrokinetic immobilization of organic dye molecules." Analytical and Bioanalytical Chemistry 412, no. 16 (March 3, 2020): 3859–70. http://dx.doi.org/10.1007/s00216-020-02480-4.

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Abstract The application of inhomogeneous AC electric fields for molecular immobilization is a very fast and simple method that does not require any adaptions to the molecule’s functional groups or charges. Here, the method is applied to a completely new category of molecules: small organic fluorescence dyes, whose dimensions amount to only 1 nm or even less. The presented setup and the electric field parameters used allow immobilization of dye molecules on the whole electrode surface as opposed to pure dielectrophoretic applications, where molecules are attracted only to regions of high electric field gradients, i.e., to the electrode tips and edges. In addition to dielectrophoresis and AC electrokinetic flow, molecular scale interactions and electrophoresis at short time scales are discussed as further mechanisms leading to migration and immobilization of the molecules.

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Liang, Suning, Zhi Yang, Xianjun Shao, Yiming Zheng, Qiang Wang, and Zhengyong Huang. "Investigation on Adsorption of Polar Molecules in Vegetable Insulating Oil by Functional Fossil Graphene." Materials 16, no. 9 (April 28, 2023): 3434. http://dx.doi.org/10.3390/ma16093434.

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As a new engineering dielectric, vegetable insulating oil is widely used in electrical equipment. Small polar molecules such as alcohol and acid will be produced during the oil-immersed electrical equipment operation, which seriously affects the safety of equipment. The polar molecule can be removed by using functional fossil graphene materials. However, the structural design and group modification of graphene materials lack a theoretical basis. Therefore, in this paper, molecular dynamics (MD) and quantum mechanics theory (Dmol3) were utilized to study the adsorption kinetics and mechanism of graphene (GE), porous graphene (PGE), porous hydroxy graphene (HPGE), and porous graphene modified by hydroxyl and carboxyl groups (COOH-HPGE) on polar small molecules in vegetable oil. The results show that graphene-based materials can effectively adsorb polar small molecules in vegetable oil, and that the modification of graphene materials with carboxyl and hydroxyl groups improves their adsorption ability for polar small molecules, which is attributed to the conversion of physical adsorption to chemical adsorption by the modification of oxygen-containing groups. This study provides a theoretical basis for the design and preparation of graphene materials with high adsorption properties.

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Bodek, Lukasz, Mads Engelund, Aleksandra Cebrat, and Bartosz Such. "Adsorption behavior of tin phthalocyanine onto the (110) face of rutile TiO2." Beilstein Journal of Nanotechnology 11 (May 26, 2020): 821–28. http://dx.doi.org/10.3762/bjnano.11.67.

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The adsorption behavior of tin phthalocyanine (SnPc) molecules on rutile TiO2(110) was studied by scanning tunneling microscopy (STM). Low-temperature STM measurements of single molecules reveal the coexistence of two conformations of molecules on the TiO2 surface. Density functional theory-based simulations (DFT) indicate that the difference originates from the position of the tin atom protruding from the molecule plane. The irreversible switching of Sn-up molecules into the Sn-down conformation was observed either after sample annealing at 200 °C or as a result of tip-induced manipulation. Room-temperature measurements conducted for a coverage of close to a monolayer showed no tendency for molecular arrangement.

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36

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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Mörschel, Philipp, and Martin U. Schmidt. "Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry." Acta Crystallographica Section A Foundations and Advances 71, no. 1 (January 1, 2015): 26–35. http://dx.doi.org/10.1107/s2053273314018907.

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A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12–15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit,e.g.structures withZ′ = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

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Tarachiwin, Lucksanaporn, Jitladda T. Sakdapipanich, and Yasuyuki Tanaka. "Relationship between Particle Size and Molecular Weight of Rubber from Hevea Brasiliensis." Rubber Chemistry and Technology 78, no. 4 (September 1, 2005): 694–704. http://dx.doi.org/10.5254/1.3547907.

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Abstract Rubber particles with different mean diameters obtained from fresh natural rubber latex (FL-latex) were separated by high-speed centrifugation. The small rubber particles (SRP), having mean diameter less than 250 nm, were found to be composed of both low and high number-average molecular-weight (Mn) rubber molecules; while larger rubber particles (LRP), with mean diameter larger than 250 nm, mainly consisted of low Mn rubber molecules. The content of longchain fatty acid ester are mainly due to functional groups such as phospholipids were less in SRP than that of LRP. This indicates clearly that LRP contains mainly rubber molecules which were terminated to form a functional terminal group containing fatty acid ester groups. The high molecular-weight rubber in SRP, containing lower amounts of ester groups, is presumed to be mainly linear molecules having no chain-end group to form branch-points. On the other hand, the low molecular-weight rubber molecules with high ester content in the LRP are presumably terminated with the functional group containing fatty acid esters to form long-chain branching. The molecular-weight of rubber in LRP increased with increasing particle sizes. This suggests that the LRP was derived from the aggregation and/or association of functional groups at ω- and α-terminal end groups.

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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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40

Joly, E., L. Leong, W. J. Coadwell, C. Clarkson, and G. W. Butcher. "The rat MHC haplotype RT1c expresses two classical class I molecules." Journal of Immunology 157, no. 4 (August 15, 1996): 1551–58. http://dx.doi.org/10.4049/jimmunol.157.4.1551.

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Abstract Cloning and characterization of classical MHC class I coding sequences of the laboratory rat Rattus norvegicus has been reported so far for only four haplotypes, RT1a, RT1(1), RT1n, and RT1u. In all four cases, only one RT1.A classical class I molecule was found. Here we report that, in contrast, the RT1c haplotype expresses two different classical class I molecules. Using recombinant rat strains, we find that allotypic serologic determinants carried by the two molecules map to the RT1.A region, and so we have named them RT1.A1c and RT1.A2c. Multiple clones of functional cDNAs for each of these two molecules were isolated using a recently developed PCR-based expression-cloning method. Using a panel of 20 RT1.Ac-reactive mAb, we find that six recognize RT1.A1c, seven recognize RT1.A2c, and seven recognize both. We also show that both molecules are recognized and distinguished by primary alloreactive cytotoxic T lymphocytes, and that they correspond to identifiable and distinct molecular species in cells that express RT1c naturally. These data all concur to demonstrate that the RT1.Ac region carries two different loci, each of which encodes a functional classical class I molecule.

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SERİN, Sümeyya, and Öznur DOĞAN ULU. "Quantum Chemical Benchmark Study on Valdecoxib, a Potent and Selective Inhibitor of COX-2, and its Hydroxylated Derivative." Cumhuriyet Science Journal 43, no. 2 (June 29, 2022): 221–31. http://dx.doi.org/10.17776/csj.1086277.

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In this work, quantum chemical calculations were performed on valdecoxib (VLB), a highly selective and potent COX-2 inhibitor, and its hydroxylated derivative (1H-VLB), an active metabolite. The geometry optimizations and frequency calculations were carried out by using density functional theory (DFT)/B3LYP functional with the 6-311++G (d, p) basis set. To define water phase behaviors, calculations were renewed by using universal SMD solvation model for both molecules. Structural and thermodynamic parameters, FT-IR analysis, Mulliken population analysis (MPA), frontier molecular orbital (FMO) analysis, natural bond orbital (NBO) analysis, and electrostatic surface properties were investigated in detail. Quantum chemical reactivity identifiers were calculated separately for both vacuum and water environment in order to evaluate the bioactivity tendency of both mentioned compounds. When the bioactivity of VLB and 1H-VLB molecules were compared based on quantum chemical reactivity identifiers, it was observed that the VLB molecule was more active. Moreover, drug-likeness properties of studied molecules were predicted by means of Molinspiration cheminformatics software. Molecular lipophilicity potential (MLP) maps that exhibit the accumulative lipophilic contributions of each atom in studied molecules were visualized.

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Markwick, Phineus R. L., and J. Andrew McCammon. "Studying functional dynamics in bio-molecules using accelerated molecular dynamics." Physical Chemistry Chemical Physics 13, no. 45 (2011): 20053. http://dx.doi.org/10.1039/c1cp22100k.

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43

Casida, Mark E., Henry Chermette, and Denis Jacquemin. "Time-dependent density-functional theory for molecules and molecular solids." Journal of Molecular Structure: THEOCHEM 914, no. 1-3 (November 2009): 1–2. http://dx.doi.org/10.1016/j.theochem.2009.08.013.

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Casida, Mark E. "Time-dependent density-functional theory for molecules and molecular solids." Journal of Molecular Structure: THEOCHEM 914, no. 1-3 (November 2009): 3–18. http://dx.doi.org/10.1016/j.theochem.2009.08.018.

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45

Hanington, Patrick C., Lesley J. Brennan, Miodrag Belosevic, and B. Andrew Keddie. "Molecular and functional characterization of granulin-like molecules of insects." Insect Biochemistry and Molecular Biology 38, no. 5 (May 2008): 596–603. http://dx.doi.org/10.1016/j.ibmb.2008.02.002.

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46

Mishra, Mirtunjai, Narinder Kumar, Khem Thapa, B. S. Rawat, Reena Dhyani, Devendra Singh, and Devesh Kumar. "Physical, chemical, optical and insulating properties of alkyl benzoic acid derivatives liquid crystal due to extension alkyl chain (CNH2N+1) length: A DFT study." Kragujevac Journal of Science, no. 45 (2023): 21–28. http://dx.doi.org/10.5937/kgjsci2345021m.

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The aim of this paper was to analyze the structure, vibrations and to do global analyses of molecules of p-n-alkyl benzoic acid (nBAC). The energy, IR, and Homo-Lumo optimised parameters were calculated using a density functional method. The global reactivity descriptors of molecules, including electro-negativity, electron affinity, ionisation potential, global softness, chemical potential, and energy gaps is further shown by band gap value drops. It offers important details on the stability of nBAC molecules (n=4,5,6,7,8,9). It has been demonstrated that the molecular series displays the energy of an isolated molecule as the length of the alkyl chain rises. The molecular series is useful for insulating applications since it also has a high band gap.

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Chen, Xiao-Ming. "Crystal Engineering and Applications of Functional Metal-Organic Frameworks." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C16. http://dx.doi.org/10.1107/s2053273314099835.

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As a new kind of molecular materials composed of metal ions (or clusters) and organic bridging ligands that are interconnected by coordination bonds, porous metal-organic frameworks (MOFs) have many useful characteristics, such as high crystallinity, high porosity, structural diversity, designable frameworks, framework flexibility, as well as unique and modifiable organic pore surface. Therefore, they exhibit very promising potential applications in molecular adsorption/separation, catalysis, and sensors, etc. For example, they can be used for selective adsorption and separation of different gas molecules, such as CO2 and N2, capture of CO2 [2], sensing of small organic molecules and gas molecules, such as O2 and CO2, as well as catalysts and devices for solid-phase microextraction. In this presentation, the design and synthesis, unique pore surface, interesting functionalities will be presented by selected examples, in particular those of metal-azolate frameworks (MAFs) and a few devices useful for practical applications, from our group [1-3]. This work was supported by MoST (973 project) and NSFC.

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Matilla-Cuenca, Leticia, Alejandro Toledo-Arana, and Jaione Valle. "Anti-Biofilm Molecules Targeting Functional Amyloids." Antibiotics 10, no. 7 (June 29, 2021): 795. http://dx.doi.org/10.3390/antibiotics10070795.

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The choice of an effective therapeutic strategy in the treatment of biofilm-related infections is a significant issue. Amyloids, which have been historically related to human diseases, are now considered to be prevailing structural components of the biofilm matrix in a wide range of bacteria. This assumption creates the potential for an exciting research area, in which functional amyloids are considered to be attractive targets for drug development to dissemble biofilm structures. The present review describes the best-characterized bacterial functional amyloids and focuses on anti-biofilm agents that target intrinsic and facultative amyloids. This study provides a better understanding of the different modes of actions of the anti-amyloid molecules to inhibit biofilm formation. This information can be further exploited to improve the therapeutic strategies to combat biofilm-related infections.

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DANTZIG, J. A., T. Y. LIU, and Y. E. GOLDMAN. "Functional Studies of Individual Myosin Molecules." Annals of the New York Academy of Sciences 1080, no. 1 (October 1, 2006): 1–18. http://dx.doi.org/10.1196/annals.1380.002.

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TANAKA, Hiroyuki. "Functional Molecules in Allergic Bronchial Asthma." YAKUGAKU ZASSHI 122, no. 9 (September 1, 2002): 637–42. http://dx.doi.org/10.1248/yakushi.122.637.

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Journal articles on the topic 'Functional molecules'

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