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Journal articles on the topic 'Weakly Bound Molecules'

Author: Grafiati

Published: 7 September 2023

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1

Kolganova, E. A., and V. Roudnev. "Weakly Bound Triatomic LiHe2 Molecules." Bulletin of the Russian Academy of Sciences: Physics 84, no. 4 (April 2020): 465–68. http://dx.doi.org/10.3103/s1062873820040140.

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2

Gou, Bingcong, and Fei Wang. "Weakly bound triatomic4He23He and3He24He molecules." International Journal of Quantum Chemistry 101, no. 2 (2004): 169–73. http://dx.doi.org/10.1002/qua.20202.

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3

Yuan, Jianmin, and C. D. Lin. "Weakly bound triatomic He2Li and He2Na molecules." Journal of Physics B: Atomic, Molecular and Optical Physics 31, no. 15 (August 14, 1998): L637—L645. http://dx.doi.org/10.1088/0953-4075/31/15/001.

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4

Borkowski, Mateusz. "Optical clock spectroscopy in weakly bound molecules." Journal of Physics: Conference Series 1289 (July 2019): 012002. http://dx.doi.org/10.1088/1742-6596/1289/1/012002.

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5

Certain, Phillip R., and Nimrod Moiseyev. "Weakly bound, strongly anisotropic van der Waals molecules." Journal of Physical Chemistry 89, no. 14 (July 1985): 2974–75. http://dx.doi.org/10.1021/j100260a003.

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6

Shegelski, Mark R. A., George Jones, Caleb Sample, Mitchell Hawse, and Matthew Reid. "Resonant transmission of weakly bound multi-atomic molecules." Journal of Physics B: Atomic, Molecular and Optical Physics 52, no. 5 (February 6, 2019): 055201. http://dx.doi.org/10.1088/1361-6455/aafa4a.

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7

Cui, Shuxun, Christian Albrecht, Ferdinand Kühner, and Hermann E. Gaub. "Weakly Bound Water Molecules Shorten Single-Stranded DNA." Journal of the American Chemical Society 128, no. 20 (May 2006): 6636–39. http://dx.doi.org/10.1021/ja0582298.

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8

Fedorov, D. V., J. R. Armstrong, N. T. Zinner, and A. S. Jensen. "Weakly Bound States of Polar Molecules in Bilayers." Few-Body Systems 50, no. 1-4 (January 2, 2011): 395–97. http://dx.doi.org/10.1007/s00601-010-0199-0.

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9

Kłos, Jacek, Hui Li, Eite Tiesinga, and Svetlana Kotochigova. "Prospects for assembling ultracold radioactive molecules from laser-cooled atoms." New Journal of Physics 24, no. 2 (February 1, 2022): 025005. http://dx.doi.org/10.1088/1367-2630/ac50ea.

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Abstract Molecules with unstable isotopes often contain heavy and deformed nuclei and thus possess a high sensitivity to parity-violating effects, such as the Schiff moments. Currently the best limits on Schiff moments are set with diamagnetic atoms. Polar molecules with quantum-enhanced sensing capabilities, however, can offer better sensitivity. In this work, we consider the prototypical 223Fr107Ag molecule, as the octupole deformation of the unstable 223Fr francium nucleus amplifies the nuclear Schiff moment of the molecule by two orders of magnitude relative to that of spherical nuclei and as the silver atom has a large electron affinity. To develop a competitive experimental platform based on molecular quantum systems, 223Fr atoms and 107Ag atoms have to be brought together at ultracold temperatures. That is, we explore the prospects of forming 223Fr107Ag from laser-cooled Fr and Ag atoms. We have performed fully relativistic electronic-structure calculations of ground and excited states of FrAg that account for the strong spin-dependent relativistic effects of Fr and the strong ionic bond to Ag. In addition, we predict the nearest-neighbor densities of magnetic-field Feshbach resonances in ultracold 223Fr + 107Ag collisions with coupled-channel calculations. These resonances can be used for magneto-association into ultracold, weakly-bound FrAg. We also determine the conditions for creating 223Fr107Ag molecules in their absolute ground state from these weakly-bound dimers via stimulated Raman adiabatic passage using our calculations of the relativistic transition electric dipole moments.

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10

Reisler, Hanna. "Photofragment Spectroscopy and Predissociation Dynamics of Weakly Bound Molecules." Annual Review of Physical Chemistry 60, no. 1 (May 2009): 39–59. http://dx.doi.org/10.1146/annurev.physchem.040808.090441.

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11

Braga, Dario, Fabrizia Grepioni, Emilio Tedesco, and Maria José Calhorda. "Zirconocene Catalysts: Ion-pairs, Zwitterions, or Weakly Bound Molecules?" Zeitschrift für anorganische und allgemeine Chemie 626, no. 2 (February 2000): 462–70. http://dx.doi.org/10.1002/(sici)1521-3749(200002)626:2<462::aid-zaac462>3.0.co;2-a.

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12

Lustig, Christian, and Norbert W. Mitzel. "Crystal Structures of the Supramolecular Aggregates of the Methyl and Chloro Substituted Gallanes MexGaCl3-x." Zeitschrift für Naturforschung B 59, no. 2 (February 1, 2004): 140–47. http://dx.doi.org/10.1515/znb-2004-0204.

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The crystal structures of the complete series of compounds of the general formula MexGaCl3−x have been determined. New polymorphs of GaCl3 and MeGaCl2 were found. All chloro compounds MexGaCl3−x (x = 0, 1, 2) are dimers with Ga2Cl2 four-membered rings. (GaCl3)2 and (MeGaCl2)2 are aggregated into layers with the same aggregation motif (each molecule connected to four neighbouring molecules), (Me2GaCl)2 is associated in a ladder-like structure (each molecule connected to two neighbouring molecules), GaMe3 forms weakly Ga···C bound pseudo-tetramers aggregated into layers by further Ga···C contacts (each molecule has two shorter Ga···C’ and C···Ga’ and two weaker Ga···C’ and C···Ga’ contacts).

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13

Neopane, S., and N. Pantha. "First-Principles Study of Van Der Waals Interactions between Halogen Molecules (Cl2 and I2)." Journal of Nepal Physical Society 5, no. 1 (December 26, 2019): 19–23. http://dx.doi.org/10.3126/jnphyssoc.v5i1.26878.

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Density Functional Theory (DFT) based first-principles calculations have been performed to investigate vander Waals (vdW) interactions in between halogen atoms/molecules —Cl-Cl, I-I, Cl2-Cl2, Cl2-I2, I2-I2—via with and without a non-local exchange-correlation (XC) functional (vdW-DF) using Quantum ESPRESSO codes. The non-polar covalent bond length between atomic halogens (Cl-Cl and I-I) is not observed to be affected by vdW interactions and agrees well with experimental values. The binding energy between theatomic halogens, on the other hand, is slightly corrected by vdW interactions. However, the role of vdW interactions is observed to be crucial to bind molecular halogens. The molecules are weakly bound in the presence of vdW interactions and not correlated (bound) in the absence of them.

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14

Orekhov, M. A. "Coordination Numbers of Bivalent Ions in Organic Solvents." Russian Journal of Physical Chemistry A 95, no. 10 (October 2021): 2059–64. http://dx.doi.org/10.1134/s0036024421100204.

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Abstract Molecular dynamic models are created for properties of bivalent ions in organic solvents. It is shown that molecules of the considered solvents bound to ions via oxygen atoms. A theoretical model is developed that describes the ion coordination number. The coordination number in this model is determined by the ratio between the sizes of the ion and the atom organic molecule bound to it. It is shown that the coordination number depends weakly on the solvent and strongly on the type of ion. A value of 0.13 nm is obtained for the effective size of an oxygen atom bound to a bivalent ion. The constructed theoretical model agrees with the results from molecular dynamic calculations and the available experimental data.

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15

Dai, Hai-Lung. "Laser Vibrational Spectroscopy of Transient, Weakly Bound, and Reactive Molecules." Applied Spectroscopy 44, no. 10 (December 1990): 1595–604. http://dx.doi.org/10.1366/0003702904417652.

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16

Suno, Hiroya. "Hyperspherical slow variable discretization method for weakly bound triatomic molecules." Journal of Chemical Physics 134, no. 6 (February 14, 2011): 064318. http://dx.doi.org/10.1063/1.3554329.

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17

Greenberg, Fred H., and Alexander Y. Nazarenko. "Crystal structure of dimethyl 3,4,5,6-tetraphenylcyclohexa-3,5-diene-1,2-dicarboxylate." Acta Crystallographica Section E Crystallographic Communications 72, no. 7 (June 14, 2016): 947–50. http://dx.doi.org/10.1107/s2056989016009403.

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In the title compound, C34H28O4, the cyclohexadiene ring has a screw-boat conformation with a torsion angle between the double bonds being on averageca15° [15.2 (3) and −15.3 (3) in the two independent molecules]. All four phenyl rings in both molecules are arranged in a propeller-like conformation. The two molecules exhibit S,R- andR,S- chirality, respectively, and are connectedviaC—H...O intermolecular interactions. In turn, these weakly bound dimers form the molecular crystal.

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18

Lepers, M., G. Quéméner, E. Luc-Koenig, and O. Dulieu. "Four-body long-range interactions between ultracold weakly-bound diatomic molecules." Journal of Physics B: Atomic, Molecular and Optical Physics 49, no. 1 (November 26, 2015): 014004. http://dx.doi.org/10.1088/0953-4075/49/1/014004.

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19

Devdariani, A. Z., A. K. Belyaev, A. B. Alekseev, H. P. Liebermann, and R. J. Buenker. "Lifetime of weakly bound He(21 S)-Ne molecules. Temperature dependence." Russian Journal of Physical Chemistry B 5, no. 6 (December 2011): 952–55. http://dx.doi.org/10.1134/s1990793111060066.

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20

Huang, Liang-Hui, Peng-Jun Wang, Zheng-Kun Fu, and Jing Zhang. "Radio-frequency spectroscopy of weakly bound molecules in ultracold Fermi gas." Chinese Physics B 23, no. 1 (January 2014): 013402. http://dx.doi.org/10.1088/1674-1056/23/1/013402.

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21

Murray, Craig, Erika L. Derro, Timothy D. Sechler, and Marsha I. Lester. "Weakly Bound Molecules in the Atmosphere: A Case Study of HOOO." Accounts of Chemical Research 42, no. 3 (March 17, 2009): 419–27. http://dx.doi.org/10.1021/ar8001987.

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22

Abdoul-Carime, H., and C. Desfrançois. "Electrons weakly bound to molecules by dipolar, quadrupolar or polarization forces." European Physical Journal D 2, no. 2 (1998): 149. http://dx.doi.org/10.1007/s100530050124.

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23

Braga, Dario, Fabrizia Grepioni, Emilio Tedesco, and Maria Jose Calhorda. "ChemInform Abstract: Zirconocene Catalysts: Ion-Pairs, Zwitterions, or Weakly Bound Molecules?" ChemInform 31, no. 16 (June 9, 2010): no. http://dx.doi.org/10.1002/chin.200016177.

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24

Abdoul-Carime, H., and C. Desfrançois. "Electrons weakly bound to molecules by dipolar, quadrupolar or polarization forces." European Physical Journal D 2, no. 2 (June 1998): 149–56. http://dx.doi.org/10.1007/pl00021568.

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25

Kraevsky, Sergey V., Nikolay A. Barinov, Olga V. Morozova, Vladimir V. Palyulin, Alena V. Kremleva, and Dmitry V. Klinov. "Features of DNA–Montmorillonite Binding Visualized by Atomic Force Microscopy." International Journal of Molecular Sciences 24, no. 12 (June 6, 2023): 9827. http://dx.doi.org/10.3390/ijms24129827.

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In the present work, complexes of DNA with nano-clay montmorillonite (Mt) were investigated by means of atomic force microscopy (AFM) under various conditions. In contrast to the integral methods of analysis of the sorption of DNA on clay, AFM allowed us to study this process at the molecular level in detail. DNA molecules in the deionized water were shown to form a 2D fiber network weakly bound to both Mt and mica. The binding sites are mostly along Mt edges. The addition of Mg2+ cations led to the separation of DNA fibers into separate molecules, which bound mainly to the edge joints of the Mt particles according to our reactivity estimations. After the incubation of DNA with Mg2+, the DNA fibers were capable of wrapping around the Mt particles and were weakly bound to the Mt edge surfaces. The reversible sorption of nucleic acids onto the Mt surface allows it to be used for both RNA and DNA isolation for further reverse transcription and polymerase chain reaction (PCR). Our results show that the strongest binding sites for DNA are the edge joints of Mt particles.

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26

He, Xiaodong, Kunpeng Wang, Jun Zhuang, Peng Xu, Xiang Gao, Ruijun Guo, Cheng Sheng, et al. "Coherently forming a single molecule in an optical trap." Science 370, no. 6514 (September 24, 2020): 331–35. http://dx.doi.org/10.1126/science.aba7468.

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Ultracold single molecules have wide-ranging potential applications, such as ultracold chemistry, precision measurements, quantum simulation, and quantum computation. However, given the difficulty of achieving full control of a complex atom-molecule system, the coherent formation of single molecules remains a challenge. Here, we report an alternative route to coherently bind two atoms into a weakly bound molecule at megahertz levels by coupling atomic spins to their two-body relative motion in a strongly focused laser with inherent polarization gradients. The coherent nature is demonstrated by long-lived atom-molecule Rabi oscillations. We further manipulate the motional levels of the molecules and measure the binding energy precisely. This work opens the door to full control of all degrees of freedom in atom-molecule systems.

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27

Dimowa, Louiza, Nadia Petrova, Yana Tzvetanova, Ognyan Petrov, and Iskra Piroeva. "Structural Features and Thermal Behavior of Ion-Exchanged Clinoptilolite from Beli Plast Deposit (Bulgaria)." Minerals 12, no. 12 (December 8, 2022): 1576. http://dx.doi.org/10.3390/min12121576.

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The structural features and the thermal behavior of natural, Na-, Ca-, K-, Mg-, and Cd-exchanged clinoptilolite from the Beli Plast deposit (Bulgaria) were studied. Purified clinoptilolite sample was preliminary prepared and ion-exchanged at 100 °C for six days. DSC-TG analyses were performed for all studied forms. The effects in the DSC curves show differences with temperature due to release of weakly bound H2O molecules and strongly bound ones. The endotherm minima temperatures were between 78 and 115 °C decreasing in the sequence K- < Na- < Natural- < Ca- ≤ Mg- < Cd-clinoptilolite. The hydrate complexes around the exchanged cations also influenced the DSC curves. The cation-coordinating H2O molecules and the non-coordinating ones were determined by XRD structural refinement for all exchanged samples. The H2O molecules of the cation–hydrate complexes are released at higher temperatures than weakly bound ones and affected the DSC curves differently. The structural adjustments made by the Rietveld method, as well as the applied EDS analyzes for the chemical composition of the samples, allowed us to correlate these data to the thermal characteristics of the studied clinoptilolite samples.

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28

Gou Qing-Dong and Li Yong. "Calculations of the binding energies of weakly bound He-He-Ba molecules." Acta Physica Sinica 64, no. 19 (2015): 193102. http://dx.doi.org/10.7498/aps.64.193102.

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29

Belyaev, A. K., A. Z. Devdariani, V. S. Rybak, and I. A. Zlatkin. "Electronic radiative transition in He(21,3S)-Ne weakly bound molecules. Temperature dependence." Journal of Physics: Conference Series 397 (December 6, 2012): 012038. http://dx.doi.org/10.1088/1742-6596/397/1/012038.

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30

Reche-Tamayo, M., M. Moral, A. J. Pérez-Jiménez, and J. C. Sancho-García. "Theoretical Determination of Interaction and Cohesive Energies of Weakly Bound Cycloparaphenylene Molecules." Journal of Physical Chemistry C 120, no. 39 (September 21, 2016): 22627–34. http://dx.doi.org/10.1021/acs.jpcc.6b05781.

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31

Baizakov, B. B., S. M. Al-Marzoug, U. Al Khawaja, and H. Bahlouli. "Weakly bound solitons and two-soliton molecules in dipolar Bose–Einstein condensates." Journal of Physics B: Atomic, Molecular and Optical Physics 52, no. 9 (April 16, 2019): 095301. http://dx.doi.org/10.1088/1361-6455/ab0e1b.

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32

SHLYAPNIKOV, G. V. "SUPERFLUID REGIMES IN DEGENERATE ATOMIC FERMI GASES." International Journal of Modern Physics B 20, no. 19 (July 30, 2006): 2739–54. http://dx.doi.org/10.1142/s0217979206035242.

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We give a brief overview of recent studies of quantum degenerate regimes in ultracold Fermi gases. The attention is focused on the regime of Bose-Einstein condensation of weakly bound molecules of fermionic atoms, formed at a large positive scattering length for the interspecies atom-atom interaction. We analyze remarkable collisional stability of these molecules and draw prospects for future studies.

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33

Legault, Claude Y., and Julie Prévost. "1-Fluoro-3,3-dimethyl-1,3-dihydro-1λ3-benzo[d][1,2]iodoxole." Acta Crystallographica Section E Structure Reports Online 68, no. 4 (March 31, 2012): o1238. http://dx.doi.org/10.1107/s1600536812012822.

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The asymmetric unit of the title compound, C9H10FIO, contains two independent molecules which are weakly bound by intermolecular O...I interactions [3.046 (4) and 2.947 (4) Å]. The two covalent I—F bonds are slightly longer than the two I—O bonds.

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34

Mihrin, D., and R. Wugt Larsen. "THz spectroscopy of weakly bound cluster molecules in solid para-hydrogen: a sensitive probe of van der Waals interactions." Physical Chemistry Chemical Physics 21, no. 1 (2019): 349–58. http://dx.doi.org/10.1039/c8cp05060k.

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The present work demonstrates that 99.9% enriched solid para-H₂ below 3 K provides an excellent inert and transparent medium for the exploration of large-amplitude intermolecular vibrational motion of weakly bound van der Waals cluster molecules in the THz spectral region.

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35

Odutola, J. A., and F. A. Adekola. "Computation of character tables for the permutation groups of weakly bound polymer molecules." Molecular Physics 60, no. 6 (April 20, 1987): 1395–413. http://dx.doi.org/10.1080/00268978700100911.

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36

Devdariani, A., A. K. Belyaev, A. B. Alekseyev, H. P. Liebermann, and R. J. Buenker. "Ab initio study of the lifetime of weakly bound He(21S)–Ne molecules." Molecular Physics 108, no. 6 (March 20, 2010): 757–62. http://dx.doi.org/10.1080/00268971003610226.

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37

Rabilloud, F., D. Rayane, A. R. Allouche, R. Antoine, M. Aubert-Frécon, M. Broyer, I. Compagnon, and Ph Dugourd. "Permanent Dipole of Metal−Benzene Molecules: Evidence for Long-Range Weakly Bound States?" Journal of Physical Chemistry A 107, no. 51 (December 2003): 11347–53. http://dx.doi.org/10.1021/jp035403a.

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38

Bakalov, D. D., V. S. Melezhik, L. I. Menshikov, and S. I. Vinitsky. "Relativistic effects in the weakly bound states of ddμ and dtμ mesic molecules." Physics Letters B 161, no. 1-3 (October 1985): 5–8. http://dx.doi.org/10.1016/0370-2693(85)90596-9.

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39

Chen, Shyh-Jong, Cheng Chen, and Yaw-Shun Hong. "Theoretical Study of Weakly Bound Dimers between Hydrogen Fluoride and Some Polar Molecules." Journal of the Chinese Chemical Society 53, no. 4 (August 2006): 783–92. http://dx.doi.org/10.1002/jccs.200600104.

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40

Zhou, Tian, Santanu Malakar, Steven L. Webb, Karsten Krogh-Jespersen, and Alan S. Goldman. "Polar molecules catalyze CO insertion into metal-alkyl bonds through the displacement of an agostic C-H bond." Proceedings of the National Academy of Sciences 116, no. 9 (February 12, 2019): 3419–24. http://dx.doi.org/10.1073/pnas.1816339116.

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The insertion of CO into metal-alkyl bonds is the key C-C bond-forming step in many of the most important organic reactions catalyzed by transition metal complexes. Polar organic molecules (e.g., tetrahydrofuran) have long been known to promote CO insertion reactions, but the mechanism of their action has been the subject of unresolved speculation for over five decades. Comprehensive computational studies [density functional theory (DFT)] on the prototypical system Mn(CO)5(arylmethyl) reveal that the polar molecules do not promote the actual alkyl migration step. Instead, CO insertion (i.e. alkyl migration) occurs rapidly and reversibly to give an acyl complex with a sigma-bound (agostic) C-H bond that is not easily displaced by typical ligands (e.g. phosphines or CO). The agostic C-H bond is displaced much more readily, however, by the polar promoter molecules, even though such species bind only weakly to the metal center and are themselves then easily displaced; the facile kinetics of this process are attributable to a hydrogen bonding-like interaction between the agostic C-H bond and the polar promoter. The role of the promoter is to thereby catalyze isomerization of the agostic product of CO insertion to give an η2-C,O-bound acyl product that is more easily trapped than the agostic species. This ability of such promoters to displace a strongly sigma-bound C-H bond and to subsequently undergo facile displacement themselves is without reported precedent, and could have implications for catalytic reactions beyond carbonylation.

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41

Vattuone, L., L. Savio, and M. Rocca. "Ethylene Adsorption on Clean and Oxygen Covered Flat and Stepped Ag(001)." International Journal of Modern Physics B 17, no. 13 (May 20, 2003): 2497–526. http://dx.doi.org/10.1142/s0217979203018417.

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In the present paper we review our findings on ethylene adsorption on clean and oxygen covered Ag(001) surfaces investigated by dosing the gas with a Supersonic Molecular Beam and analysing the adsorption state either by High Resolution Electron Energy Loss Spectroscopy or by High Resolution X Rays Photoemission Spectroscopy. The final adsorption state depends on the translational and on the internal energy of the gas-phase molecules and on the presence of defects. At low translational energy ethylene either physisorbs or very weakly chemisorbs at flat terrace sites. The physisorption probability is thereby hindered by rotational excitation. A more strongly bound, π bonded, state forms at higher translational energy, the activation barrier being related to the energy needed to form the relevant defect at which chemisorption takes place. A further even more strongly bound state forms only when dosing vibrationally excited molecules from the gas phase.

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42

Furmaniak-Kazmierczak, Emilia, Michael E. Nesheim, and Graham P. Côté. "Coagulation factor Va is an actin filament binding and cross-linking protein." Biochemistry and Cell Biology 73, no. 1-2 (January 1, 1995): 105–12. http://dx.doi.org/10.1139/o95-012.

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Bovine coagulation cofactor factor Va is shown to bind to filaments of skeletal muscle actin with a dissociation constant of 40–50 nM in the presence of 50 mM NaCl. At saturation, approximately one molecule of factor Va was bound for every two actin molecules. The binding of factor Va to F-actin was inhibited by increasing ionic strength, being approximately 20-fold weaker at 150 mM NaCl. Addition of factor Va dramatically increased both the low-speed sedimentation and the low-shear viscosity of actin filament solutions, indicating that factor Va cross-links actin filaments. Factor Va also bound to actin filaments saturated with myosin. The isolated 74-kilodalton light chain of factor Va displayed actin binding and cross-linking properties indistinguishable from those of intact factor Va. The procofactor factor V bound weakly to F-actin, indicating that proteolytic activation is required to uncover the actin binding sites within the light chain domain. Actin filaments had only a slight inhibitory effect on the prothombinase activity of the factor Va – factor Xa – phospholipid complex. Since high concentrations of actin filaments can be exposed to the circulation when cells are damaged, the interaction of factor Va with actin may be of physiological relevance.Key words: blood coagulation, factor V, actin.

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43

Stevenson, K. P., J. D. Close, P. L. Muiño, and R. O. Watts. "Potential Energy Surfaces for Unsaturated Hydrocarbons from Crossed Molecular Beams." Australian Journal of Physics 50, no. 3 (1997): 683. http://dx.doi.org/10.1071/p96079.

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The total differential scattering cross sections for several important unsaturated hydrocarbon molecules with common atmospheric gases were measured in a crossed molecular beam apparatus. The experiments show quantum interferences which relate to potential energy surface parameters, such as the well depth and radial minimum. The damping of the quantum features, over contributions from experimental resolutions, provides information on the angular and radial anisotropies present in the potential energy surfaces. We have investigated two areas: (1) the role of the probe partner in determining the interaction strength for a given hydrocarbon target, and (2) the effect of increasing the overall length of the hydrocarbon molecule for a fixed probe. By comparing results for a class of scattering systems, we can identify chemical and physical trends that determine the van der Waals potential energy surfaces of larger molecules. We expect these results to aid in the prediction and interpretation of complementary experimental measurements on the high resolution infrared spectroscopy of weakly bound complexes.

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44

Robl, Christian. "Komplexe mit aromatischen Carbonsäuren, IV. Ca2[C6H2(COO)4]·6H2O - Eine neue Schichtstruktur/ Complexes with Aromatic Carboxylic Acids, IV. Ca2[C6H2(COO)4]·6H2O - A Novel Layer Structure." Zeitschrift für Naturforschung B 43, no. 8 (August 1, 1988): 993–97. http://dx.doi.org/10.1515/znb-1988-0813.

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AbstractSingle crystals of Ca2[C6H2(COO)4]·6H2O were grown in aqueous silica gel. Ca2+ has CN 6+2. The coordination polyhedron is formed by three water molecules and five oxygen atoms of carboxylate groups. Six oxygen atoms are closely bound (235,9-243,9 pm), the two remaining coordination partners are considerably more remote from Ca2+ (268,2 and 273,8 pm). COO- groups chelate Ca2+ in an asymmetric manner, but the C -O bond lengths do not differ markedly (125,2-126,3 pm). The connection of Ca2+ with [C6H2(COO)4]4- leads to rigid layers. Adjacent layers are interlinked by hydrogen bonds. Those oxygen atoms which are weakly bound to Ca2+ are favoured as proton acceptors in hydrogen bonds. The COO groups are tilted differently against the C6-ring plane. One is approximately coplanar, but the other is oriented almost perpendicularly.

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45

Varadwaj, Pradeep R. "Does Oxygen Feature Chalcogen Bonding?" Molecules 24, no. 17 (August 30, 2019): 3166. http://dx.doi.org/10.3390/molecules24173166.

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Using the second-order Møller–Plesset perturbation theory (MP2), together with Dunning’s all-electron correlation consistent basis set aug-cc-pVTZ, we show that the covalently bound oxygen atom present in a series of 21 prototypical monomer molecules examined does conceive a positive (or a negative) σ-hole. A σ-hole, in general, is an electron density-deficient region on a bound atom M along the outer extension of the R–M covalent bond, where R is the reminder part of the molecule, and M is the main group atom covalently bonded to R. We have also examined some exemplar 1:1 binary complexes that are formed between five randomly chosen monomers of the above series and the nitrogen- and oxygen-containing Lewis bases in N2, PN, NH3, and OH2. We show that the O-centered positive σ-hole in the selected monomers has the ability to form the chalcogen bonding interaction, and this is when the σ-hole on O is placed in the close proximity of the negative site in the partner molecule. Although the interaction energy and the various other 12 characteristics revealed from this study indicate the presence of any weakly bound interaction between the monomers in the six complexes, our result is strongly inconsistent with the general view that oxygen does not form a chalcogen-bonded interaction.

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Kamar, Ramsey I., Edward J. Banigan, Aykut Erbas, Rebecca D. Giuntoli, Monica Olvera de la Cruz, Reid C. Johnson, and John F. Marko. "Facilitated dissociation of transcription factors from single DNA binding sites." Proceedings of the National Academy of Sciences 114, no. 16 (March 31, 2017): E3251—E3257. http://dx.doi.org/10.1073/pnas.1701884114.

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The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate ∼1×104 M−1s−1, establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.

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Brown, David F. R., Mark N. Gibbs, and David C. Clary. "Combiningabinitiocomputations, neural networks, and diffusion Monte Carlo: An efficient method to treat weakly bound molecules." Journal of Chemical Physics 105, no. 17 (November 1996): 7597–604. http://dx.doi.org/10.1063/1.472596.

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Aubert-Frécon, M., F. Rabilloud, A. R. Allouche, D. Rayane, R. Antoine, M. Broyer, and Ph Dugourd. "Existence of weakly bound states for metal–benzene molecules confirmed from a long-range model." Chemical Physics Letters 405, no. 4-6 (April 2005): 422–24. http://dx.doi.org/10.1016/j.cplett.2005.02.071.

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Friedrich, Břetislav, Manish Gupta, and Dudley Herschbach. "Probing Weakly-Bound Species with Nonresonant Light: Dissociation of He2Induced by Rotational Hybridization." Collection of Czechoslovak Chemical Communications 63, no. 8 (1998): 1089–93. http://dx.doi.org/10.1135/cccc19981089.

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A field-dependent value of angular momentum can be imparted to a 4He2 cluster by the interaction of its anisotropic polarizability with a nonresonant laser field. In this way a centrifugal term is introduced that can be tuned to a critical value sufficient to overcome the potential that binds the dimer. Due to its dependence on the internuclear distance and laser intensity, the critical angular momentum for dissociation is attained at different internuclear separations for different pulsed-laser intensities. As a result, the dependence of the dissociation probability on the laser intensity offers a means to map the potential and/or the polarizability anisotropy. A comparison with experiment thus could provide a test of either. The technique is applicable to other molecules in bound states close to the dissociation limit.

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Ritschel, Thomas, Lutz Zülicke, and Philip J. Kuntz. "Cationic Van-der-Waals Complexes: Theoretical Study of Ar2H+ Structure and Stability." Zeitschrift für Physikalische Chemie 218, no. 4 (April 1, 2004): 377–90. http://dx.doi.org/10.1524/zpch.218.4.377.29196.

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AbstractThe electronic and geometric structure, stability and molecular properties of the cationic van-der-Waals complex Ar2H+ in its ground electronic state are studied by means of two ab-initio quantum-chemical approaches: conventional configuration interaction (multi-reference and coupled-cluster methods) and a diatomics-in-molecules model with ab-initio input data. To ensure consistency between the two approaches, one and the same one-electron atomic basis set (aug-cc-pVTZ by Dunning) is employed in both. The topography of the ground-state potential-energy surface is examined with respect to the nature of the binding and the stability of structures corresponding to stationary points. In accordance with most earlier theoretical work, there are two local minima at linear arrangements: a strongly bound centro-symmetric moiety, (Ar–H–Ar)+, and a weakly bound van-der-Waals complex, Ar···ArH+. These are separated by a low barrier. Only the centro-symmetric molecule is significantly stable (De = 0.68eV) against fragmentation into Ar + ArH+ and should have structural and dynamical relevance. A fairly simple diatomics-in-molecules model taking into account only the few lowest electronic fragment states yields a qualitatively correct description of the ground state but shows quantitative deviations from the more accurate configuration-interaction data in detail. Nevertheless, it should provide a good starting point for the treatment of larger complexes ArnH+ with n > 2.

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