Journal articles: 'Molecules'

1

Vimala, G., J. Haribabu, S. Srividya, R. Karvembu, and A. SubbiahPandi. "Crystal structure ofN-[(4-ethoxyphenyl)carbamothioyl]cyclohexanecarboxamide." Acta Crystallographica Section E Crystallographic Communications 71, no. 11 (October 7, 2015): o820—o821. http://dx.doi.org/10.1107/s205698901501806x.

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The asymmetric unit of the title compound, C16H22N2O2S, contains two crystallographically independent molecules (AandB). In moleculeA, the cyclohexane ring is disordered over two orientations [occupancy ratio 0.841 (10):0.159 (10)]. In each molecule, the central carbonyl thiourea unit is nearly planar (r.m.s. deviations for all non-H atoms of 0.034 Å in moleculeAand 0.094 Å in moleculeB). In both molecules, the cyclohexane ring adopts a chair conformation. The mean plane of the cyclohexane ring makes dihedral angles of 35.8 (4) (moleculeA) and 20.7 (3)° (moleculeB) with that of the benzene ring. Each molecule features an intramolecular N—H...O hydrogen bond, which closes anS(6) ring motif. In the crystal, molecules are linkedviapairs of weak N—H...S interactions, forming inversion dimers with anR22(8) ring motif for both molecules. The crystal structure also features weak C—H...π ring interactions.

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Zhao, Jian-Ping, Rui-Qin Liu, Zhi-Hao Jiang, and Sheng-Di Bai. "Crystal structure ofN′-(2,6-dimethylphenyl)benzenecarboximidamide tetrahydrofuran monosolvate." Acta Crystallographica Section E Crystallographic Communications 71, no. 1 (January 1, 2015): o28—o29. http://dx.doi.org/10.1107/s2056989014026255.

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The asymmetric unit of the title compound, C15H16N2·C4H8O, contains two amidine molecules (AandB) with slightly different conformations and two tetrahydrofuran (THF) solvent molecules. In the amidine molecules, the dimethylphenyl ring and the NH2group lie to the same side of the N=C bond and the dihedral angles between the aromatic rings are 54.25 (7) (moleculeA) and 58.88 (6) ° (moleculeB). In the crystal, N—H...N hydrogen bonds link the amidine molecules into [100]C(4) chains of alternatingAandBmolecules. Both amidine molecules form an N—H...O hydrogen bond to an adjacent THF solvent molecule.

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Szliszka, Ewelina, Zenon P. Czuba, Maciej Domino, Bogdan Mazur, Grzegorz Zydowicz, and Wojciech Krol. "Ethanolic Extract of Propolis (EEP) Enhances the Apoptosis- Inducing Potential of TRAIL in Cancer Cells." Molecules 14, no. 2 (February 13, 2009): 738–54. http://dx.doi.org/10.3390/molecules.

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Zukerman-Schpector, Julio, Ignez Caracelli, Hélio A. Stefani, Olga Gozhina, and Edward R. T. Tiekink. "Crystal structure of 5-(1,3-dithian-2-yl)-2H-1,3-benzodioxole." Acta Crystallographica Section E Crystallographic Communications 71, no. 3 (February 13, 2015): o167—o168. http://dx.doi.org/10.1107/s2056989015002455.

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In the title compound, C11H12O2S2, two independent but virtually superimposable molecules,AandB, comprise the asymmetric unit. In each molecule, the 1,3-dithiane ring has a chair conformation with the 1,4-disposed C atoms being above and below the plane through the remaining four atoms. The substituted benzene ring occupies an equatorial position in each case and forms dihedral angles of 85.62 (9) (moleculeA) and 85.69 (8)° (moleculeB) with the least-squares plane through the 1,3-dithiane ring. The difference between the molecules rests in the conformation of the five-membered 1,3-dioxole ring which is an envelope in moleculeA(the methylene C atom is the flap) and almost planar in moleculeB(r.m.s. deviation = 0.046 Å). In the crystal, molecules ofAself-associate into supramolecular zigzag chains (generated by glide symmetry along thecaxis)viamethylene C—H...π interactions. Molecules ofBform similar chains. The chains pack with no specific directional intermolecular interactions between them.

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Qachchachi, Fatima-Zahrae, Youssef Kandri Rodi, El Mokhtar Essassi, Michael Bodensteiner, and Lahcen El Ammari. "3-(2,3-Dioxoindolin-1-yl)propanenitrile." Acta Crystallographica Section E Structure Reports Online 70, no. 3 (February 26, 2014): o361—o362. http://dx.doi.org/10.1107/s1600536814003985.

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The asymmetric unit of the title compound, C11H8N2O2, contains two independent molecules (AandB). Each molecule is build up from fused five- and six-membered rings with the former linked to a cyanoethyl group. The indoline ring and two carbonyl O atoms of each molecule are nearly coplanar, with the largest deviations from the mean planes being 0.0198 (9) (moleculeA) and 0.0902 (9) Å (moleculeB), each by a carbonyl O atom. The fused ring system is nearly perpendicular to the mean plane passing through the cyanoethyl chains, as indicated by the dihedral angles between them of 69.72 (9) (moleculeA) and 69.15 (9)° (moleculeB). In the crystal, molecules are linked by C—H...O and π–π [intercentroid distance between inversion-related indoline (A) rings = 3.6804 (7) Å] interactions into a double layer that stacks along thea-axis direction.

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Hofierka, Jaroslav, Brian Cunningham, Charlie M. Rawlins, Charles H. Patterson, and Dermot G. Green. "Many-body theory of positron binding to polyatomic molecules." Nature 606, no. 7915 (June 22, 2022): 688–93. http://dx.doi.org/10.1038/s41586-022-04703-3.

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AbstractPositron binding to molecules is key to extremely enhanced positron annihilation and positron-based molecular spectroscopy1. Although positron binding energies have been measured for about 90 polyatomic molecules1–6, an accurate ab initio theoretical description of positron–molecule binding has remained elusive. Of the molecules studied experimentally, ab initio calculations exist for only six; these calculations agree with experiments on polar molecules to at best 25 per cent accuracy and fail to predict binding in nonpolar molecules. The theoretical challenge stems from the need to accurately describe the strong many-body correlations including polarization of the electron cloud, screening of the electron–positron Coulomb interaction and the unique process of virtual-positronium formation (in which a molecular electron temporarily tunnels to the positron)1. Here we develop a many-body theory of positron–molecule interactions that achieves excellent agreement with experiment (to within 1 per cent in cases) and predicts binding in formamide and nucleobases. Our framework quantitatively captures the role of many-body correlations and shows their crucial effect on enhancing binding in polar molecules, enabling binding in nonpolar molecules, and increasing annihilation rates by 2 to 3 orders of magnitude. Our many-body approach can be extended to positron scattering and annihilation γ-ray spectra in molecules and condensed matter, to provide the fundamental insight and predictive capability required to improve materials science diagnostics7,8, develop antimatter-based technologies (including positron traps, beams and positron emission tomography)8–10, and understand positrons in the Galaxy11.

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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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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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Enisoglu Atalay, Vildan, and Semse Asar. "Determination of the inhibition effect of hesperetin and its derivatives on Candida glabrata by molecular docking method." European Chemistry and Biotechnology Journal, no. 1 (January 2, 2024): 27–38. http://dx.doi.org/10.62063/ecb-15.

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In the study, it was aimed to develop new candidate inhibitor molecules by targeting the AWP1 protein structure of Candida glabrata organism. Hesperetin molecule was taken as a reference and different substituted groups were attached to the determined ends of the molecule to increase the inhibition potential on the protein structure. A total of 100 molecules were designed and after conformer distribution using the Molecular Mechanics/MMFF method for each designed molecule, the area, volume, weight, energy, EHOMO, ELUMO, polarizability, dipole moment, log P values of these molecules were calculated using the Semi Empirical/PM6 method. Molecular docking studies of the optimized molecules were carried out through the Autodock Vina program. After the docking studies, the interactions of the designed molecules with the active site amino acids of the protein structure were analyzed by BIOVIA Discovery Studio Client software in case of possible mutation. As a result of the analysis, five molecules with higher binding energies than other designed molecules and currently used antifungal drugs were recommended.

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Venkatraman, Vishwesh, Jeremiah Gaiser, Daphne Demekas, Amitava Roy, Rui Xiong, and Travis J. Wheeler. "Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)." Pharmaceuticals 17, no. 8 (July 26, 2024): 992. http://dx.doi.org/10.3390/ph17080992.

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Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.

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11

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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12

Caracelli, Ignez, Camila Lury Hino, Julio Zukerman-Schpector, Francisco Carlos Biaggio, and Edward R. T. Tiekink. "Crystal structure of 3-hydroxymethyl-1,2,3,4-tetrahydroisoquinolin-1-one." Acta Crystallographica Section E Crystallographic Communications 71, no. 8 (July 8, 2015): o558—o559. http://dx.doi.org/10.1107/s2056989015012670.

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In the title compound, C10H11NO2, two independent but virtually superimposable molecules,AandB, comprise the asymmetric unit. The heterocyclic ring in each molecule has a screw-boat conformation, and the methylhydroxyl group occupies a position to one side of this ring with N—C—C—O torsion angles of −55.30 (15) (moleculeA) and −55.94 (16)° (moleculeB). In the crystal, O—H...O and N—H...O hydrogen bonding leads to 11-membered {...HNCO...HO...HNC2O} heterosynthons, involving three different molecules, which are edge-shared to generate a supramolecular chain along theaaxis. Interactions of the type C—H...O provide additional stability to the chains, and link these into a three-dimensional architecture.

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13

Shrivastava, Aditya Divyakant, Neil Swainston, Soumitra Samanta, Ivayla Roberts, Marina Wright Muelas, and Douglas B. Kell. "MassGenie: A Transformer-Based Deep Learning Method for Identifying Small Molecules from Their Mass Spectra." Biomolecules 11, no. 12 (November 30, 2021): 1793. http://dx.doi.org/10.3390/biom11121793.

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The ‘inverse problem’ of mass spectrometric molecular identification (‘given a mass spectrum, calculate/predict the 2D structure of the molecule whence it came’) is largely unsolved, and is especially acute in metabolomics where many small molecules remain unidentified. This is largely because the number of experimentally available electrospray mass spectra of small molecules is quite limited. However, the forward problem (‘calculate a small molecule’s likely fragmentation and hence at least some of its mass spectrum from its structure alone’) is much more tractable, because the strengths of different chemical bonds are roughly known. This kind of molecular identification problem may be cast as a language translation problem in which the source language is a list of high-resolution mass spectral peaks and the ‘translation’ a representation (for instance in SMILES) of the molecule. It is thus suitable for attack using the deep neural networks known as transformers. We here present MassGenie, a method that uses a transformer-based deep neural network, trained on ~6 million chemical structures with augmented SMILES encoding and their paired molecular fragments as generated in silico, explicitly including the protonated molecular ion. This architecture (containing some 400 million elements) is used to predict the structure of a molecule from the various fragments that may be expected to be observed when some of its bonds are broken. Despite being given essentially no detailed nor explicit rules about molecular fragmentation methods, isotope patterns, rearrangements, neutral losses, and the like, MassGenie learns the effective properties of the mass spectral fragment and valency space, and can generate candidate molecular structures that are very close or identical to those of the ‘true’ molecules. We also use VAE-Sim, a previously published variational autoencoder, to generate candidate molecules that are ‘similar’ to the top hit. In addition to using the ‘top hits’ directly, we can produce a rank order of these by ‘round-tripping’ candidate molecules and comparing them with the true molecules, where known. As a proof of principle, we confine ourselves to positive electrospray mass spectra from molecules with a molecular mass of 500Da or lower, including those in the last CASMI challenge (for which the results are known), getting 49/93 (53%) precisely correct. The transformer method, applied here for the first time to mass spectral interpretation, works extremely effectively both for mass spectra generated in silico and on experimentally obtained mass spectra from pure compounds. It seems to act as a Las Vegas algorithm, in that it either gives the correct answer or simply states that it cannot find one. The ability to create and to ‘learn’ millions of fragmentation patterns in silico, and therefrom generate candidate structures (that do not have to be in existing libraries) directly, thus opens up entirely the field of de novo small molecule structure prediction from experimental mass spectra.

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Mariyatra, Mahimaidoss Baby, and Helen Stoeckli-Evans. "Crystal structure ofN-(2,2,2-trichloro-1-hydroxyethyl)formamide." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (November 14, 2015): 1501–4. http://dx.doi.org/10.1107/s2056989015020459.

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The title compound, C3H4Cl3NO2, crystallized with two independent molecules (AandB) in the asymmetric unit. The two molecules have the same conformation; the molecular overlap gives weighted and unit-weight r.m.s. fits of 0.047 and 0.043 Å, respectively. The conformation of theN-(hydroxethyl)formamide chains are very similar, as indicated by the C—N(H)—C=O and C—N(H)—C—O(H) torsion angles, which are, respectively, −1.8 (3) and −91.5 (2)° for moleculeA, and −2.1 (3) and −95.7 (2)° for moleculeB. In the crystal, individual molecules are linked by pairs of O—H...O hydrogen bonds, formingA–AandB–Binversion dimers withR22(12) ring motifs. The dimers are linkedviaN—H...O hydrogen bonds, forming alternating layers ofAandBmolecules parallel to thebcplane. Within the layers ofBmolecules, there are weak C—H...Cl hydrogen bonds present.

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Turutov, Sally, and Kira Radinsky. "Molecular Optimization Model with Patentability Constraint." Proceedings of the AAAI Conference on Artificial Intelligence 38, no. 1 (March 24, 2024): 257–64. http://dx.doi.org/10.1609/aaai.v38i1.27778.

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In drug development, molecular optimization is a crucial challenge that involves generating novel molecules given a lead molecule as input. The task requires maintaining molecular similarity to the original molecule while simultaneously optimizing multiple chemical attributes. To aid in this process, numerous generative models have been proposed. However, in practical applications, it is crucial for these models not only to generate novel molecules with the above constraints but also to generate molecules that significantly differ from any existing patented compounds. In this work, we present a multi-optimization molecular framework to address this challenge. Our framework trains a model to prioritize both enhanced properties and substantial dissimilarity from patented compounds. By jointly learning continuous representations of optimized and patentable molecules, we ensure that the generated molecules are significantly distant from any patented compounds while improving chemical properties. Through empirical evaluation, we demonstrate the superior performance of our approach compared to state-of-the-art molecular optimization methods both in chemical property optimization and patentability.

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Liébecq, Claude. "‘Molecular’ and ‘molecules’." Trends in Biochemical Sciences 13, no. 3 (March 1988): 84–85. http://dx.doi.org/10.1016/0968-0004(88)90045-x.

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Patil, Siddappa, and Alejandro Bugarin. "Crystal structure of (E)-1,3-dimethyl-2-[3-(3-nitrophenyl)triaz-2-en-1-ylidene]-2,3-dihydro-1H-imidazole." Acta Crystallographica Section E Structure Reports Online 70, no. 10 (September 20, 2014): 224–27. http://dx.doi.org/10.1107/s1600536814020698.

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The title compound, C11H12N6O2, a π-conjugated triazene, crystallized with two independent molecules (AandB) in the asymmetric unit. Both molecules have anEconformation about the –N=N– bond and have slightly twisted overall conformations. In moleculeA, the imidazole ring is inclined to the benzene ring by 8.12 (4)°, while in moleculeBthe two rings are inclined to one another by 7.73 (4)°. In the crystal, the independent molecules are linked to each other by C—H...O hydrogen bonds, forming –A–A–A– and –B–B–B–chains along [100]. The chains are linked by C—H...O and C—H...N hydrogen bonds, forming sheets lying parallel to (001). The sheets are linked by further C—H...N hydrogen bonds and π–π interactions [centroid–centroid distance = 3.5243 (5) Å; involving the imidazole ring of molecule A and the benzene ring of moleculeB], forming a three-dimensional framework structure.

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18

Fayos, Jose. "Space Group Approximation of a Molecular Crystal by Classifying Molecules for Their Electric Potentials and Roughness on Their Inertial Ellipsoid Surface." Advances in Chemistry 2014 (October 16, 2014): 1–9. http://dx.doi.org/10.1155/2014/737480.

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In order to predict the most probable space group where a molecule crystallizes, it is assumed that molecular shape and electric potential distribution on the molecular surface are the main factors or predictors. However, to compare and classify molecules by these two factors seems to be very difficult for in general such different objects. Thus, in order to compare molecules, they are reduced to their inertial ellipsoid in which surface 26 equally spaced points were chosen where a roughness factor and an electric potential due to all atomic charges of the whole molecule are calculated. By this procedure, different molecules encoded by these two predictor vectors can be compared and classified, showing that molecules that crystallize in the same space group have more similar predictor vectors. This result opens the possibility to predict the more probable spatial group associated with a molecule.

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DONG, Z. C., X. L. GUO, Y. WAKAYAMA, and J. G. HOU. "MOLECULAR-SCALE ORGANIC ELECTROLUMINESCENCE FROM TUNNEL JUNCTIONS." Surface Review and Letters 13, no. 02n03 (April 2006): 143–47. http://dx.doi.org/10.1142/s0218625x06008207.

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We report the generation and detection of bipolar organic electroluminescence of porphyrin molecules from a nanoscale junction in an ultrahigh vacuum scanning tunneling microscope (STM). Clear molecular fluorescence from porphyrin molecules near metal substrates has been realized through highly localized electrical excitation of molecules in proximity to a sharp tip apex. The molecular origin of the luminescence, arising from the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) radiative transitions of neutral molecules, is clearly established by the observed well-defined vibrationally resolved fluorescence spectra that match perfectly with conventional photoluminescence data from molecular thin films. The molecules fluoresce at low onset voltages for both bias polarities, presenting an example of bipolar organic electroluminescence at the nanoscale. Such bipolar operation suggests a double-barrier model for electron transport, with hot electron injection into unoccupied states of molecules in both polarities. The optical behavior of molecules in the tunnel junction is also found sensitive to the electronic properties of molecules and energy level alignment at the interface. These results offer new information to the optoelectronic behavior of molecules in a nanoscopic environment and may open up new routes to the development of single-molecule science and molecular scale electronics.

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MAITI, SANTANU K., and S. N. KARMAKAR. "QUANTUM TRANSPORT THROUGH HETEROCYCLIC MOLECULES." International Journal of Modern Physics B 23, no. 02 (January 20, 2009): 177–87. http://dx.doi.org/10.1142/s021797920904970x.

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We explore electron transport properties in molecular wires made of heterocyclic molecules (pyrrole, furan and thiophene) by using the Green's function technique. Parametric calculations are given based on the tight-binding model to describe the electron transport in these wires. It is observed that the transport properties are significantly influenced by (a) the heteroatoms in the heterocyclic molecules and (b) the molecule-to-electrodes coupling strength. Conductance (g) shows sharp resonance peaks associated with the molecular energy levels in the limit of weak molecular coupling, while they get broadened in the strong molecular coupling limit. These resonances get shifted with the change of the heteroatoms in these heterocyclic molecules. All the essential features of the electron transfer through these molecular wires become much more clearly visible from the study of our current-voltage (I-V) characteristics, and they provide several key information in the study of molecular transport.

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Jungclas, Hartmut, Viacheslav V. Komarov, Anna M. Popova, and Lothar Schmidt. "Molecular Interactions in Particular Van der Waals Nanoclusters." Zeitschrift für Naturforschung A 72, no. 1 (January 1, 2017): 17–23. http://dx.doi.org/10.1515/zna-2016-0213.

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AbstractA method is presented to analyse the interaction energies in a nanocluster, which is consisting of three neutral molecules bound by non-covalent long range Van der Waals forces. One of the molecules (M0) in the nanocluster has a permanent dipole moment, whereas the two other molecules (M1 and M2) are non-polar. Analytical expressions are obtained for the numerical calculation of the dispersion and induction energies of the molecules in the considered nanocluster. The repulsive forces at short intermolecular distances are taken into account by introduction of damping functions. Dispersion and induction energies are calculated for a nanocluster with a definite geometry, in which the polar molecule M0 is a linear hydrocarbon molecule C5H10 and M1 and M2 are pyrene molecules. The calculations are done for fixed distances between the two pyrene molecules. The results show that the induction energies in the considered three-molecular nanocluster are comparable with the dispersion energies. Furthermore, the sum of induction energies in the substructure (M0, M1) of the considered nanocluster is much higher than the sum of induction energies in a two-molecular nanocluster with similar molecules (M0, M1) because of the absence of an electrostatic field in the latter case. This effect can be explained by the essential intermolecular induction in the three-molecular nanocluster.

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Chia, Tze Shyang, and Ching Kheng Quah. "Temperature-induced phase transition of isonicotinamide-malonic acid (2/1) and supramolecular construct analysis of isonicotinamide structures." Zeitschrift für Kristallographie - Crystalline Materials 233, no. 8 (July 26, 2018): 539–54. http://dx.doi.org/10.1515/zkri-2017-2109.

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Abstract The isonicotinamide-malonic acid (2/1) co-crystal salt (2IN·C3) exhibits a first-order displacive structural phase transition from low-temperature triclinic P1̅ crystal structure to high-temperature monoclinic C2/c crystal structure and vice versa at the transition temperatures of 298 (1) and 295 (1) K, respectively, as determined by variable-temperature SCXRD analysis and DSC measurements. The asymmetric unit of 2IN·C3 comprises three malonic acid molecules and six isonicotinamide molecules at the low-temperature phase, and this is reduced to a half-molecule of malonic acid and an isonicotinamide molecule in the high-temperature phase. The carboxyl and pyridinium H atoms are disordered at both phases. The observed phase transition near room temperature is triggered by the molecular displacement of the isonicotinamide molecule and the syn-anti conformational transformation of the malonic acid molecule with deviation angles of 10.4 and 11.7°, respectively, which induced an energy change of 19.1 kJ mol−1 in the molecular cluster comprising a central isonicotinamide molecule and eight neighboring molecules. However, the total interaction energy of the molecular cluster of a central malonic acid molecule and eight neighboring molecules does not change significantly upon the phase transition. The molecules of isonicotinamide structures except IN·IN+·triazole‒ form zero-dimensional finite arrays or one-dimensional chains as the primary supramolecular construct by carboxyl···pyridyl (−35.9 to −56.7 kJ mol−1) and carboxamide···carboxamide (−53.6 to −68.7 kJ mol−1) or carboxyl···carboxamide (−52.6 to −67.1 kJ mol−1) synthons.

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Shamima Shultana, Kazi M Maraz, Arwah Ahmed, Tanzila Sultana, and Ruhul A Khan. "Drug design, discovery and development and their safety or efficacy on human body." GSC Biological and Pharmaceutical Sciences 17, no. 2 (November 30, 2021): 113–22. http://dx.doi.org/10.30574/gscbps.2021.17.2.0330.

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Drug Design, often mentioned as rational drug design or just rational design. It is defined as the study of the shape of molecules in order to determine how they will bind receptors on cells or combine with other molecules. It is based on molecular shape or architecture is an alternative to blindly testing hundreds of molecules to see if one or more of them will bind cellular or molecular targets. The drug is an organic molecule, when it is bind to target site it can either inhibit or activate the function of a bio-molecule which results in therapeutic benefit.

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Wang, Maoning, Jieyi Zhang, Adila Adijiang, Xueyan Zhao, Min Tan, Xiaona Xu, Surong Zhang, et al. "Plasmon-Assisted Trapping of Single Molecules in Nanogap." Materials 16, no. 8 (April 19, 2023): 3230. http://dx.doi.org/10.3390/ma16083230.

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The manipulation of single molecules has attracted extensive attention because of their promising applications in chemical, biological, medical, and materials sciences. Optical trapping of single molecules at room temperature, a critical approach to manipulating the single molecule, still faces great challenges due to the Brownian motions of molecules, weak optical gradient forces of laser, and limited characterization approaches. Here, we put forward localized surface plasmon (LSP)-assisted trapping of single molecules by utilizing scanning tunneling microscope break junction (STM-BJ) techniques, which could provide adjustable plasmonic nanogap and characterize the formation of molecular junction due to plasmonic trapping. We find that the plasmon-assisted trapping of single molecules in the nanogap, revealed by the conductance measurement, strongly depends on the molecular length and the experimental environments, i.e., plasmon could obviously promote the trapping of longer alkane-based molecules but is almost incapable of acting on shorter molecules in solutions. In contrast, the plasmon-assisted trapping of molecules can be ignored when the molecules are self-assembled (SAM) on a substrate independent of the molecular length.

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Vidhyasagar, T., K. Rajeswari, D. Shanthi, M. Kayalvizhi, G. Vasuki, and A. Thiruvalluvar. "Crystal structure of (E)-1-(4′-methoxy-[1,1′-biphenyl]-4-yl)-3-(3-nitrophenyl)prop-2-en-1-one." Acta Crystallographica Section E Crystallographic Communications 71, no. 1 (January 1, 2015): 1–3. http://dx.doi.org/10.1107/s2056989014025110.

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The title compound, C22H17NO4, crystallizes with two independent molecules (AandB) in the asymmetric unit. Each molecule exists as anEisomer with C—C=C—C torsion angles of −175.69 (17) and −178.41 (17)° inAandB, respectively. In moleculeA, the planes of the terminal benzene rings are twisted by an angle of 26.67 (10)°, while the biphenyl unit is non-planar, the dihedral angle between the rings being 30.81 (10)°. The dihedral angle between the nitrophenyl ring and the inner phenyl ring is 6.50 (9)°. The corresponding values in moleculeBare 60.61 (9), 31.07 (8) and 31.05 (9)°. In the crystal, molecules are arranged in a head-to-head manner, with the 3-nitrophenyl groups nearly parallel to one another. TheAandBmolecules are linked to one anotherviaC—H...O hydrogen bonds, forming chains lying parallel to (-320) and enclosingR22(10) andR22(12) ring motifs. The methoxy group in both molecules is positionally disordered with a refined occupancy ratio of 0.979 (4):0.021 (4) for moleculeAand 0.55 (4):0.45 (4) for moleculeB.

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Guo, Xuefeng, Joshua P. Small, Jennifer E. Klare, Yiliang Wang, Meninder S. Purewal, Iris W. Tam, Byung Hee Hong, et al. "Covalently Bridging Gaps in Single-Walled Carbon Nanotubes with Conducting Molecules." Science 311, no. 5759 (January 20, 2006): 356–59. http://dx.doi.org/10.1126/science.1120986.

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Molecular electronics is often limited by the poorly defined nature of the contact between the molecules and the metal surface. We describe a method to wire molecules into gaps in single-walled carbon nanotubes (SWNTs). Precise oxidative cutting of a SWNT produces carboxylic acid–terminated electrodes separated by gaps of ≤10 nanometers. These point contacts react with molecules derivatized with amines to form molecular bridges held in place by amide linkages. These chemical contacts are robust and allow a wide variety of molecules to be tested electrically. In addition to testing molecular wires, we show how to install functionality in the molecular backbone that allows the conductance of the single-molecule bridges to switch with pH.

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Fan, Yang, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, and Tao Qin. "Back translation for molecule generation." Bioinformatics 38, no. 5 (December 7, 2021): 1244–51. http://dx.doi.org/10.1093/bioinformatics/btab817.

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Abstract Motivation Molecule generation, which is to generate new molecules, is an important problem in bioinformatics. Typical tasks include generating molecules with given properties, molecular property improvement (i.e. improving specific properties of an input molecule), retrosynthesis (i.e. predicting the molecules that can be used to synthesize a target molecule), etc. Recently, deep-learning-based methods received more attention for molecule generation. The labeled data of bioinformatics is usually costly to obtain, but there are millions of unlabeled molecules. Inspired by the success of sequence generation in natural language processing with unlabeled data, we would like to explore an effective way of using unlabeled molecules for molecule generation. Results We propose a new method, back translation for molecule generation, which is a simple yet effective semisupervised method. Let X be the source domain, which is the collection of properties, the molecules to be optimized, etc. Let Y be the target domain which is the collection of molecules. In particular, given a main task which is about to learn a mapping from the source domain X to the target domain Y, we first train a reversed model g for the Y to X mapping. After that, we use g to back translate the unlabeled data in Y to X and obtain more synthetic data. Finally, we combine the synthetic data with the labeled data and train a model for the main task. We conduct experiments on molecular property improvement and retrosynthesis, and we achieve state-of-the-art results on four molecule generation tasks and one retrosynthesis benchmark, USPTO-50k. Availability and implementation Our code and data are available at https://github.com/fyabc/BT4MolGen. Supplementary information Supplementary data are available at Bioinformatics online.

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Rajesh, Rajagopal, E. S. Sella, Olivier Blacque, and Kunjanpillai Rajesh. "Crystal structure of a new 2,6-bis(imino)pyridine derivative: (1E,1′E)-1,1′-(pyridine-2,6-diyl)bis[N-(4-chlorophenyl)ethan-1-imine]." Acta Crystallographica Section E Crystallographic Communications 75, no. 2 (January 4, 2019): 115–18. http://dx.doi.org/10.1107/s2056989018017966.

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The asymmetric unit of the title compound, C21H17Cl2N3, contains two crystallographically independent molecules (AandB). Both molecules haveEconfigurations for both imine double bonds with regard to the aryl and pyridine groups. The conformations of the two molecules differ with the 4-chlorophenyl rings being inclined to the central pyridine ring by 77.64 (6) and 86.18 (6)° in moleculeA, and 80.02 (5) and 43.41 (6)° in moleculeB. In the crystal, molecules are linked by a number of C—H...π interactions, forming layers parallel to thebcplane.

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Magrashi, Maryam Ali, and Elham Shafik Aazam. "The co-crystal 4,6-diacetylresorcinol–1-aminopyrene (2/1)." Acta Crystallographica Section E Crystallographic Communications 78, no. 6 (May 31, 2022): 679–81. http://dx.doi.org/10.1107/s2056989022005588.

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The structure of the title molecular complex, C16H11N·2C10H10O4, at 150 K has been determined. The molecules form stacks consisting of aggregates with disordered 1-aminopyrene molecule surrounded by two 4,6-diacetylresorcinol molecules. Neighbouring stacks are linked by hydrogen bonds between the amine H atoms of the 1-aminopyrene molecule with the adjacent carbonyl oxygen atom of the 4,6-diacetylresorcinol molecule.

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Yu, Chang Feng. "A Novel High Precision Analytic Potential Function for Diatomic Molecules." Key Engineering Materials 645-646 (May 2015): 313–18. http://dx.doi.org/10.4028/www.scientific.net/kem.645-646.313.

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A new analytical potential energy functions is presented, the potential energy function is examined by 13 examples of different diatomic molecules or ions——homonuclear ground-state for neutral diatomic molecules, heternuclear ground-state for charged diatomic molecular ion, heternuclear excitation-state neutral diatomic molecules ,heternuclear excited-state for charged diatomic molecular ion, homonuclear excited-state for neutral diatomic molecule , homonuclear excited-state for charged diatomic moleculeetc.. as a consequence, the theoretical values of the vibrational energy level of molecules calculated by the potential energy function are in high-precision consistent with RKR data (Rydberg-Klein-Rees) or experimental data.

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Tondar, Abtin, Sergio Sánchez-Herrero, Asim Kumar Bepari, Amir Bahmani, Laura Calvet Liñán, and David Hervás-Marín. "Virtual Screening of Small Molecules Targeting BCL-2 with Machine Learning, Molecular Docking, and MD Simulation." Biomolecules 14, no. 5 (May 1, 2024): 544. http://dx.doi.org/10.3390/biom14050544.

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This study aimed to identify potential BCL-2 small molecule inhibitors using deep neural networks (DNN) and random forest (RF) algorithms as well as molecular docking and molecular dynamics (MD) simulations to screen a library of small molecules. The RF model classified 61% (2355/3867) of molecules as ‘Active’. Further analysis through molecular docking with Vina identified CHEMBL3940231, CHEMBL3938023, and CHEMBL3947358 as top-scored small molecules with docking scores of −11, −10.9, and 10.8 kcal/mol, respectively. MD simulations validated these compounds’ stability and binding affinity to the BCL-2 protein.

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LIAO, RUIJIN, MENGZHAO ZHU, XIN ZHOU, FUZHOU ZHANG, JIAMING YAN, WENBIN ZHU, and CHAO GU. "MOLECULAR DYNAMICS STUDY OF THE DISRUPTION OF H-BONDS BY WATER MOLECULES AND ITS DIFFUSION BEHAVIOR IN AMORPHOUS CELLULOSE." Modern Physics Letters B 26, no. 14 (May 14, 2012): 1250088. http://dx.doi.org/10.1142/s0217984912500881.

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Hydrolysis is an important component of the aging of cellulose, and it severely affects the insulating performance of cellulosic materials. The diffusion behavior of water molecules in amorphous cellulose and their destructive effect on the hydrogen bonding structure of cellulose were investigated by molecular dynamics. The change in the hydrogen bonding structure indicates that water molecules have a considerable effect on the hydrogen bonding structure within cellulose: both intermolecular and intramolecular hydrogen bonds decreased with an increase in ingressive water molecules. Moreover, the stabilities of the cellulose molecules were disrupted when the number of intermolecular hydrogen bonds declined to a certain degree. Both the free volumes of amorphous cells and water molecule-cellulose interaction affect the diffusion of water molecules. The latter, especially the hydrogen bonding interaction between water molecules and cellulose, plays a predominant role in the diffusion behavior of water molecules in the models of which the free volume rarely varies. The diffusion coefficient of water molecules has an excellent correlation with water molecule-cellulose interaction and the average hydrogen bonds between each water molecule and cellulose; however, this relationship was not apparent between the diffusion coefficient and free volume.

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Park, Ki-Min, Hankook Oh, and Youngjin Kang. "2,2′-Bi(9,9-diethylfluorene)." Acta Crystallographica Section E Structure Reports Online 70, no. 2 (January 22, 2014): o185. http://dx.doi.org/10.1107/s1600536814001378.

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The title compound, C34H34, systematic name 9,9,9′,9′-tetraethyl-2,2′-bi(9H-fluorene), crystallized with two crystallographically independent molecules (AandB) in the asymmetric unit. These differ mainly in the orientation of the lateral ethyl chains: in moleculeA, they are both on the same side of the molecule whereas in moleculeB, one diethylfluorene moiety has undergone a 180° rotation such that the two pairs of ethyl residues appear on opposite sides of the molecule. The fluorene ring systems subtend dihedral angles of 31.37 (4) and 43.18 (3)° in moleculesAandB, respectively. Hence the two fluorene moieties are tilted slightly toward one another. This may be due to the presence of intermolecular C—H...π interactions between neighboring molecules. The lateral ethyl chains (excluding H atoms) are also almost planar, with each pair almost perpendicular to the plane of the fluorene system to which they are attached with dihedral angles between the ethyl and fluorene planes in the range 86.04 (8)–89.5 (1)°.

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Grabowski, Sławomir J., and Jesus M. Ugalde. "Ab initio calculations on C6H6···(HF)n clusters — X–H···π hydrogen bond." Canadian Journal of Chemistry 88, no. 8 (August 2010): 769–78. http://dx.doi.org/10.1139/v10-031.

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MP2/6–311++G(d,p) calculations on C6H6···(HF)n clusters were performed and full optimizations were carried out for systems containing up to four HF molecules (n = 4) and calculations on the systems of C6v symmetry were carried out for up to six HF molecules (n = 6). Cooperativity effects were analyzed for these molecular aggregates. It was found that F–H···π and F–H···F hydrogen bonds exist for these complexes and those interactions are enhanced as the number of HF molecules increases. The cooperativity effects cause numerous changes in geometrical, energetic, and topological parameters, the latter ones derived from the quantum theory of atoms in molecules. Various correlations between the analyzed parameters are presented. There are meaningful differences between the molecular graphs for the fully optimized complexes and those for the linear complexes of C6v symmetry (for the latter, the linear chain of HF molecules is attached to a benzene molecule acting as the Lewis base). For the linear complexes, unique bond paths connect the H-attractor of the HF molecule and the ring critical point of the benzene molecule.

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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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Henault, Emilie S., Maria H. Rasmussen, and Jan H. Jensen. "Chemical space exploration: how genetic algorithms find the needle in the haystack." PeerJ Physical Chemistry 2 (July 31, 2020): e11. http://dx.doi.org/10.7717/peerj-pchem.11.

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We explain why search algorithms can find molecules with particular properties in an enormous chemical space (ca 1060 molecules) by considering only a tiny subset (typically 103−6 molecules). Using a very simple example, we show that the number of potential paths that the search algorithms can follow to the target is equally vast. Thus, the probability of randomly finding a molecule that is on one of these paths is quite high and from here a search algorithm can follow the path to the target molecule. A path is defined as a series of molecules that have some non-zero quantifiable similarity (score) with the target molecule and that are increasingly similar to the target molecule. The minimum path length from any point in chemical space to the target corresponds is on the order of 100 steps, where a step is the change of and atom- or bond-type. Thus, a perfect search algorithm should be able to locate a particular molecule in chemical space by screening on the order of 100s of molecules, provided the score changes incrementally. We show that the actual number for a genetic search algorithm is between 100 and several millions, and depending on the target property and its dependence on molecular changes, the molecular representation, and the number of solutions to the search problem.

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Yang, Huan, Jin Cao, Zhen Su, Jun Rui, Bo Zhao, and Jian-Wei Pan. "Creation of an ultracold gas of triatomic molecules from an atom–diatomic molecule mixture." Science 378, no. 6623 (December 2, 2022): 1009–13. http://dx.doi.org/10.1126/science.ade6307.

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In recent years, there has been notable progress in the preparation and control of ultracold gases of diatomic molecules. The next experimental challenge is the production of ultracold polyatomic molecular gases. Here, we report the creation of an ultracold gas of 23 Na 40 K 2 triatomic molecules from a mixture of ground-state sodium-23–potassium-40 ( 23 Na 40 K) molecules and potassium-40 ( 40 K) atoms. The triatomic molecules were created by adiabatic magneto-association through an atom–diatomic molecule Feshbach resonance. We obtained clear evidence for the creation of triatomic molecules by directly detecting them using radio-frequency dissociation. Approximately 4000 triatomic molecules with a high-peak phase-space density of 0.05 could be created. The ultracold triatomic molecules can serve as a launchpad to probe the three-body potential energy surface and may be used to prepare quantum degenerate triatomic molecular gases.

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Sivanathan, M., and B. Karthikeyan. "Computational Studies of Self Assembled 3,5 Bis(Tri Fluoro Methyl) Benzyl Amine Phenyl Alanine Nano Tubes." Materials Science Forum 1070 (October 13, 2022): 105–13. http://dx.doi.org/10.4028/p-ftw4x6.

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In this work 3,5 Bis(Tri fluro methyl)Benzyl amine phenyl alanine a monmer molecule is DFT theoretically optimized to get the structural insight of the molecule. Band gap energy, Mullikan atomic charges, DOS spectral analysis, HOMO - LUMO, Electrostatic surface potential , molecular electrostatic potential and theoretical Raman spectral analysis is computed and compared with the experimental data .Since this molecule shows self assembly similar to peptide molecules it is quite interesting to analyze its structure based on theory and experimental the results suggests the H –boding interactions between the molecules is the key mechanism. The band energy from DOS plots suggests the molecular interactions through π-π .The possibility of the self assembly is explained further from Raman spectral studies that tells the mode specific interaction among the molecules..

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Mehboob, Muhammad Yasir, Muhammad Usman Khan, Riaz Hussain, Rafia Fatima, Zobia Irshad, and Muhammad Adnan. "Designing of near-infrared sensitive asymmetric small molecular donors for high-efficiency organic solar cells." Journal of Theoretical and Computational Chemistry 19, no. 08 (September 18, 2020): 2050034. http://dx.doi.org/10.1142/s0219633620500340.

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Herein, we have designed four small molecular donors (SMDs) with Donor–Acceptor–Acceptor (D–Á–A) backbone having different acceptor units for highly efficient organic solar cells (OSCs). The specific molecular modeling has been made by replacing the additional acceptor unit (A) of recently synthesized TPA-DAA-MDN molecule (R) by employing different highly efficient acceptor units in order to improve the photovoltaic performances of the molecules. A theoretical approach (DFT and TD-DFT) has been applied to investigate the photophysical, opto-electronic and photovoltaic parameters of the designed molecules (DAA1–DAA4) and compared with the reference molecule (R). The red-shifting absorption of SMDs is the most important factor for highly efficient OSCs. Our all formulated molecules showed a red shifted absorption spectrum and also exhibit near IR sensitivity. Acceptor unit modification of R molecule causes reduction in HOMO-LUMO energy gap; therefore, all designed molecules offer better opto-electronic properties as compared to R molecule. A variety of certain critical factors essential for efficient SMDs like frontier molecular orbitals (FMOs), absorption maxima, dipole moment, exciton binding energy along with transition density matrix, excitation energy, open circuit voltages and charge mobilities of (DAA1–DAA4) and R have also been investigated. Generally, low values of reorganizational energy (hole and electron) offer high charge mobility and our all designed molecules are enriched in this aspect. High open circuit voltage values, low excitation energies, large dipole moment values indicate that our designed SMDs are suitable candidates for high-efficiency OSCs. Furthermore, conceptualized molecules are superior and thus are suggested to experimentalist for out-looking future progresses of highly efficient OSCs devices.

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Efimov, Ilya, Pavel Slepukhin, and Vasiliy Bakulev. "Crystal structure of ethyl 3-(4-chlorophenyl)-5-[(E)-2-(dimethylamino)ethenyl]-1,2-oxazole-4-carboxylate." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (December 1, 2015): o1028. http://dx.doi.org/10.1107/s2056989015023257.

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In the title compound, C16H17ClN2O3, two molecules,AandB, with different conformations, comprise the asymmetric unit. In moleculeA, the C=O group of the ester points away from the benzene ring [C—C—C=O = −170.8 (3)°], whereas in moleculeB, it points back towards the benzene ring [C—C—C=O = 17.9 (4)°]. The dihedral angles betweeen the oxazole and benzene rings also differ somewhat [46.26 (13) for moleculeAand 41.59 (13) for moleculeB]. Each molecule features an intramolecular C—H...O interaction, which closes anS(6) ring. In the crystal, theBmolecules are linked into [001]C(12) chains by weak C—H...Cl interactions.

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Borodin, Dmitriy, Igor Rahinov, Pranav R. Shirhatti, Meng Huang, Alexander Kandratsenka, Daniel J. Auerbach, Tianli Zhong, et al. "Following the microscopic pathway to adsorption through chemisorption and physisorption wells." Science 369, no. 6510 (September 17, 2020): 1461–65. http://dx.doi.org/10.1126/science.abc9581.

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Adsorption involves molecules colliding at the surface of a solid and losing their incidence energy by traversing a dynamical pathway to equilibrium. The interactions responsible for energy loss generally include both chemical bond formation (chemisorption) and nonbonding interactions (physisorption). In this work, we present experiments that revealed a quantitative energy landscape and the microscopic pathways underlying a molecule’s equilibration with a surface in a prototypical system: CO adsorption on Au(111). Although the minimum energy state was physisorbed, initial capture of the gas-phase molecule, dosed with an energetic molecular beam, was into a metastable chemisorption state. Subsequent thermal decay of the chemisorbed state led molecules to the physisorption minimum. We found, through detailed balance, that thermal adsorption into both binding states was important at all temperatures.

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Ortiz-Garcia, José J., and Rebecca C. Quardokus. "Influence of local chemical environment and external perturbations of porphyrins on surfaces." Journal of Vacuum Science & Technology A 41, no. 3 (May 2023): 030801. http://dx.doi.org/10.1116/6.0002401.

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Porphyrins and tetrapyrroles play crucial roles in biological processes such as photosynthesis and molecular transport. These nature-based molecules have found application in artificial systems, such as sensing, catalysis, and 2D/3D networks. They are ideal building blocks due to their chemical diversity, stability, and ability to self-assemble on surfaces. Derivatization of the peripheral positions allows for the rational design of magnetic, catalytic, and photochemical properties. Due to this, porphyrins have been used in a variety of natural and artificial systems such as photodynamic therapies and dye-sensitized solar cells. Recently, much work and attention have focused on using specific porphyrin and molecular relatives for molecular electronics due to their robust nature, functionality, and synthesis. The focus of this review is to summarize the mechanisms that affect the internal structure and properties of the molecules and how changes in the local chemical environment alter the electronic properties of the porphyrin. We review the current state of the literature concerning the intermolecular and surface-adsorbate interactions that dictate self-assembly. We will assess the effects that molecule-molecule and molecule-substrate interactions play on the molecule’s properties and the effects that external forces have on the molecular properties. The goal of this review is to dissect the mechanisms responsible for the unique properties that arise from porphyrinic systems adsorbed on surfaces.

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Gupta, Shivani. "Investigation of anti-microbial activity of imidazol [2, 1-B][1,3,4] thiadiazole by using molecular docking and ADMET studies." Indian Journal of Pharmacy and Pharmacology 9, no. 3 (August 15, 2022): 201–4. http://dx.doi.org/10.18231/j.ijpp.2022.036.

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This report consists of molecular docking based on series of imidazol [2,1-b], , thiadiazole-benzimidazole derivative. Molecular docking is software which gives information about molecular modeling in which molecule fits into target binding sites and predict structure of intermolecular complex. These molecules were investigated by protein ligand binding score, protein ligand interaction and ADME studies. All the target molecules were analyzed against which is a gram positive bacteria found on skin and upper respiratory tract. The protein molecule selected for the analysis was PDB code 4LAE protein ligand. Basically it is a oxidoreductase inhibitor and its structure is based on 7(benzimidazole-1-yl)-2, 4-diaminoquinazolines. Out of all twenty nine compounds five compounds (5B,5G,5H,5N and 5Q) were estimated as most potent molecules as antibacterial agent.

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Levitt, Malcolm H. "Spectroscopy of light-molecule endofullerenes." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 1998 (September 13, 2013): 20120429. http://dx.doi.org/10.1098/rsta.2012.0429.

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Molecular endofullerenes are supramolecular systems consisting of fullerene cages encapsulating small molecules. Although most early examples consist of encapsulated metal clusters, recently developed synthetic routes have provided endofullerenes with non-metallic guest molecules in high purity and macroscopic quantities. The encapsulated light molecule behaves as a confined quantum rotor, displaying rotational quantization as well as translational quantization, and a rich coupling between the translational and rotational degrees of freedom. Furthermore, many encapsulated molecules display spin isomerism. Spectroscopies such as inelastic neutron scattering, nuclear magnetic resonance and infrared spectroscopy may be used to obtain information on the quantized energy level structure and spin isomerism of the guest molecules. It is also possible to study the influence of the guest molecules on the cages, and to explore the communication between the guest molecules and the molecular environment outside the cage.

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Liu, Yuezhou, Panpan Chen, Bingbing Shi, Tianyu Jiao, Huaqiang Ju, Peiren Liu, and Feihe Huang. "Cocrystallization with a clip-type molecule catcher: a new method to determine structures of liquid molecules." Organic Chemistry Frontiers 7, no. 5 (2020): 742–46. http://dx.doi.org/10.1039/c9qo01526d.

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In order to measure the precise structure of liquid molecules by X-ray single-crystal diffraction, we report a new and easy method using a glycoluril-derived molecular clip as a molecule catcher to form cocrystals with liquid molecules.

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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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Liu, Ya-Ling, Pei Zou, Hao Wu, Min-Hao Xie, and Shi-Neng Luo. "3,4,6-Tri-O-acetyl-1,2-O-[1-(exo-ethoxy)ethylidene]-β-D-mannopyranose 0.11-hydrate." Acta Crystallographica Section C Crystal Structure Communications 68, no. 9 (August 1, 2012): o338—o340. http://dx.doi.org/10.1107/s0108270112032076.

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The title compound, C16H24O10·0.11H2O, is a key intermediate in the synthesis of 2-deoxy-2-[18F]fluoro-D-glucose (18F-FDG), which is the most widely used molecular-imaging probe for positron emission tomography (PET). The crystal structure has two independent molecules (AandB) in the asymmetric unit, with closely comparable geometries. The pyranose ring adopts a4C1conformation [Cremer–Pople puckering parameters:Q= 0.553 (2) Å, θ = 16.2 (2)° and ϕ = 290.4 (8)° for moleculeA, andQ= 0.529 (2) Å, θ =15.3 (3)° and ϕ = 268.2 (9)° for moleculeB], and the dioxolane ring adopts an envelope conformation. The chiral centre in the dioxolane ring, introduced during the synthesis of the compound, has anRconfiguration, with the ethoxy groupexoto the mannopyranose ring. The asymmetric unit also contains one water molecule with a refined site-occupancy factor of 0.222 (8), which bridges between moleculesAandB viaO—H...O hydrogen bonds.

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48

Petrov, Victor, and Marta Avilova. "Theoretical Investigations of the Interaction of Gaseous Pollutants Molecules with the Polyacrylonitrile Surface." Chemosensors 6, no. 3 (September 13, 2018): 39. http://dx.doi.org/10.3390/chemosensors6030039.

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This work presents theoretical studies of the interaction of molecules of several gaseous pollutants with polyacrylonitrile (PAN) surface in the presence of a water and/or oxygen molecule. For this purpose, a PAN cluster model has been proposed by the methods of quantum chemical calculations and molecular modeling. The energy-favorable positions, in which the gas molecules are located relative to the surface of the PAN cluster, are determined and the thermodynamic and the following geometric parameters of the systems are calculated: “PAN cluster − oxygen molecule”, “PAN cluster − oxygen molecule − gas molecule”, “PAN cluster − water molecule − molecule of oxygen”, and “PAN cluster − a molecule of water − an oxygen molecule − a gas molecule”. It is concluded that PAN in atmospheric air in the presence of oxygen molecules is sensitive to carbon oxide (IV), sulfur (IV) oxide, chlorine, hydrogen sulfide and carbon oxide (II). In an anoxic environment, PAN films will show selective sensitivity to chlorine. The presence of water molecules in the investigated air should not affect the gas sensitivity of PAN films.

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49

Chen, Zhiwei, and Graeme J. Moxey. "Crystal structure of (E)-1-(4-tert-butylphenyl)-2-(4-iodophenyl)ethene." Acta Crystallographica Section E Crystallographic Communications 71, no. 5 (April 15, 2015): o309—o310. http://dx.doi.org/10.1107/s2056989015007185.

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The title compound, C18H19I, crystallized with two independent molecules (AandB) in the asymmetric unit. Both molecules have anEconformation about the bridging C=C bond. They differ in the orientation of the two benzene rings; the dihedral angle being 12.3 (5)° in moleculeA, but only 1.0 (6)° in moleculeB. In the crystal, the individual molecules are linked by C—I...π interactions forming zigzagAand zigzagBchains propagating along [001]. The structure was refined as an inversion twin [Flack parameter = 0.48 (2)].

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50

Asiri, Abdullah M., Hassan M. Faidallah, Khalid A. Alamry, Seik Weng Ng, and Edward R. T. Tiekink. "A second monoclinic polymorph for 3-amino-1-(4-methoxyphenyl)-9,10-dihydrophenanthrene-2,4-dicarbonitrile." Acta Crystallographica Section E Structure Reports Online 68, no. 4 (March 24, 2012): o1157—o1158. http://dx.doi.org/10.1107/s1600536812011798.

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The title compound, C23H17N3O, has been previously described in a monoclinicP21/cpolymorph withZ= 4 [Asiri, Al-Youbi, Faidallah, Ng & Tiekink (2011).Acta Cryst. E67, o2449]. In the new monoclinicP21/nform, withZ= 8, there are two independent molecules,AandB, in the asymmetric unit. In both molecules, the cyclohexa-1,3-diene ring has a screw-boat conformation, whereas it is a distorted half-chair in the original polymorph. There is a fold in each molecule, as indicated by the dihedral angle between the benzene rings of the 1,2-dihydronaphthalene and aniline residues of 33.19 (10)° (moleculeA) and 30.6 (10)° (moleculeB). The methoxybenzene ring is twisted out of the plane of the aniline residue to which it is connected [dihedral angles = 49.22 (10) and 73.27 (10)°, inAandBrespectively]. In the crystal, the two independent molecules self-associateviaN—H...N hydrogen bonds, generating a 12-membered {...HNC3N}2synthon. These are connected into a supramolecular tape in the (-101) plane by N—H...O(methoxy) interactions. In theP21/cpolymorph, supramolecular layers are formed by N—H...N and N—H...O interactions.

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Journal articles on the topic 'Molecules'

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