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Journal articles on the topic 'Metal-Molecule-Metal structure'

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Author: Grafiati

Published: 14 March 2023

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1

Kučera, Jan, and Axel Groß. "Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction." Beilstein Journal of Nanotechnology 2 (July 12, 2011): 384–93. http://dx.doi.org/10.3762/bjnano.2.44.

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The geometric and electronic structure of the metal–molecule interface in metal/molecule/metal junctions is of great interest since it affects the functionality of such units in possible nanoelectronic devices. We have investigated the interaction between water and a palladium monolayer of a Au(111)/4-mercaptopyridine/Pd junction by means of DFT calculations. A relatively strong bond between water and the palladium monolayer of the Au/Mpy/Pd complex is observed via a one-fold bond between the oxygen atom of the water molecule and a Pd atom. An isolated H2O molecule adsorbs preferentially in a flat-lying geometry on top of a palladium atom that is at the same time also bound to the nitrogen atom of a Mpy molecule of the underlying self-assembled monolayer. The electronic structure of these Pd atoms is considerably modified which is reflected in a reduced local density of states at the Fermi energy. At higher coverages, water can be arranged in a hexagonal ice-like bilayer structure in analogy to water on bulk metal surfaces, but with a much stronger binding which is dominated by O–Pd bonds.

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2

Orpen, A. Guy. "Metal Complex Geometries in Small-Molecule Crystals." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1194–98. http://dx.doi.org/10.1107/s0907444998007744.

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The origins, scope and utility of compilations of metal–ligand and intraligand bond lengths based on the Cambridge Structural Database are discussed. The limitations on the apparent uncertainty of metal–ligand bond lengths derived from crystallographic data and recent evidence of metal-assisted hydrogen bonding involving ligands are reviewed in the light of the transferability of bond-length values from one crystal structure determination.

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3

Maio, U., K. Dolag, B. Ciardi, and L. Tornatore. "Metal and molecule cooling in simulations of structure formation." Monthly Notices of the Royal Astronomical Society 379, no. 3 (August 11, 2007): 963–73. http://dx.doi.org/10.1111/j.1365-2966.2007.12016.x.

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4

Willenbockel, M., D. Lüftner, B. Stadtmüller, G. Koller, C. Kumpf, S. Soubatch, P. Puschnig, M. G. Ramsey, and F. S. Tautz. "The interplay between interface structure, energy level alignment and chemical bonding strength at organic–metal interfaces." Physical Chemistry Chemical Physics 17, no. 3 (2015): 1530–48. http://dx.doi.org/10.1039/c4cp04595e.

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5

Kim, Do-Hyun, Hyoyoung Lee, and Taehyoung Zyoung. "Transport mechanism of self-assembled D-σ-A-thiol monolayers in metal-molecule-metal structure." Synthetic Metals 152, no. 1-3 (September 2005): 293–96. http://dx.doi.org/10.1016/j.synthmet.2005.07.160.

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6

Mondal, Monosij, Maicol A. Ochoa, Maxim Sukharev, and Abraham Nitzan. "Coupling, lifetimes, and “strong coupling” maps for single molecules at plasmonic interfaces." Journal of Chemical Physics 156, no. 15 (April 21, 2022): 154303. http://dx.doi.org/10.1063/5.0077739.

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The interaction between excited states of a molecule and excited states of a metal nanostructure (e.g., plasmons) leads to hybrid states with modified optical properties. When plasmon resonance is swept through molecular transition frequency, an avoided crossing may be observed, which is often regarded as a signature of strong coupling between plasmons and molecules. Such strong coupling is expected to be realized when 2|⟨ U⟩|/ ℏΓ > 1, where ⟨ U⟩ and Γ are the molecule–plasmon coupling and the spectral width of the optical transition, respectively. Because both ⟨ U⟩ and Γ strongly increase with decreasing distance between a molecule and a plasmonic structure, it is not obvious that this condition can be satisfied for any molecule–metal surface distance. In this work, we investigate the behavior of ⟨ U⟩ and Γ for several geometries. Surprisingly, we find that if the only contributions to Γ are lifetime broadenings associated with the radiative and nonradiative relaxation of a single molecular vibronic transition, including effects on molecular radiative and nonradiative lifetimes induced by the metal, the criterion 2|⟨ U⟩|/ ℏΓ > 1 is easily satisfied by many configurations irrespective of the metal–molecule distance. This implies that the Rabi splitting can be observed in such structures if other sources of broadening are suppressed. Additionally, when the molecule–metal surface distance is varied keeping all other molecular and metal parameters constant, this behavior is mitigated due to the spectral shift associated with the same molecule–plasmon interaction, making the observation of Rabi splitting more challenging.

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7

Rojanasuwan, Sunit, Pakorn Prajuabwan, Annop Chanhom, Anuchit Jaruvanawat, Adirek Rangkasikorn, and Jiti Nukeaw. "The Effect of the Central Metal Atom on the Structural Phase Transition of Indium Doped Metal Phthalocyanine." Advanced Materials Research 717 (July 2013): 146–52. http://dx.doi.org/10.4028/www.scientific.net/amr.717.146.

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We investigate the effect of central metal atom on the phthalocyanine (Pc) molecular crystals as intercalated with indium. As dopant, indium has physical interaction with some atom in the ring of Pc molecule and there is charge transfer between indium atom and Pc ring atom. Since In-doped Pc is a hole doping which increase positive charge carriers and the HOMO of ZnPc, CuPc, NiPc and MgPc are localized on the phthalocyanine ring, then, the central metal atom e.g. Zn, Cu, Ni and Mg are not directly involved with the charge transfer between indium dopant and their Pc molecule. The structural phase transition from α phase to β phase of ZnPc upon doping with indium is another evidence for the existing of charge transfer between dopant atom and matrix Pc molecule. A comparative experiment of optical absorption spectrum of each metal Pc reveals that the central metal atom will affect the forming of crystal structure whether will be α phase or β phase as intercalated with indium.

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8

Sartain, Hope T., Richard J. Staples, and Shannon M. Biros. "Crystal structure of pentakis(ethylenediamine-κ2N,N′)lanthanum(III) trichloride–ethylenediamine–dichloromethane (1/1/1)." Acta Crystallographica Section E Structure Reports Online 70, no. 11 (October 29, 2014): 424–26. http://dx.doi.org/10.1107/s1600536814023289.

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We report here the crystal structure of a ten-coordinate lanthanum(III) metal coordinated by five bidentate ethylenediamine ligands, [La(C2H8N2)5]Cl3·C2H8N2·CH2Cl2. One free ethylenediamine molecule and three Cl−anions are also located in the asymmetric unit. The overall structure is held together by an extensive hydrogen-bonding network between the Cl−anions and the NH groups on the metal-bound ethylenediamine ligands. The free ethylenediamine molecule is held in an ordered position by additional hydrogen bonds involving both the chlorides and –NH groups on the metal-bound ligands. One highly disordered molecule of dichloromethane is located on an inversion center; however, all attempts to model this disorder were unsuccessful. The electron density in this space was removed using the BYPASS procedure [van der Sluis & Spek (1990).Acta Cryst.A46, 194–201].

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9

Chu, Yu-Ming, Muhammad Abid, Muhammad Imran Qureshi, Asfand Fahad, and Adnan Aslam. "Irregular topological indices of certain metal organic frameworks." Main Group Metal Chemistry 44, no. 1 (January 1, 2021): 73–81. http://dx.doi.org/10.1515/mgmc-2021-0009.

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Abstract It is interesting to study the molecular topology that provides a base for relationship of physicochemical property of a definite molecule. The topology of a molecule and the irregularity of the structure plays a vital character in shaping properties of the structure like enthalpy and entropy. In this article, we are interested to calculate some irregular topological indices of two classes of metal organic frameworks (MOFs) namely BHT (Butylated hydroxytoluene) based metal (M = Co, Fe, Mn, Cr) organic frameworks (MBHT) and M1TPyP-M2 (TPyP = 5, 10, 15, 20-tetrakis (4-pyridyl) porphyrin and M1, M2, = Fe and Co) MOFs. Also we compare our results graphically.

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10

Pengmanayol, S., and Tanakorn Osotchan. "Optical Properties of Metal Free and Metal Phthalocyanine by Molecular Band Calculation." Advanced Materials Research 55-57 (August 2008): 677–80. http://dx.doi.org/10.4028/www.scientific.net/amr.55-57.677.

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The optical properties of metal-free and metal phthalocyanine were calculated by using density functional theory with various metals including copper, zinc, cobalt, iron and manganese. The polymorphic form of these crystals was employed only for β from. The molecules were optimized with the symmetry of D4h. For the alignments of the molecule in the crystal structures of this polymorphic form which have not been reported in detail, the variation of total energy was examined as a function of the align angles. The align angle at minimum total energy was used for the band calculation. The density functional theory and plane-wave pseudopotential method were used to calculate the energy band structure and electron density of state. The calculated band structures of various metal phthalocyanines can be divided in two groups according to the peak wavelength of the maximum absorption. The first group with the peak wavelength at about 230 nm consists of β-CuPc, β-H2Pc, and β-MnPc while the wavelength of another group for β-CoPc, β-FePc, and β-ZnPc occurs at 350 nm. From the density of state calculation, it indicates that these two transitions originate from the different band and the ratio of the absorption between these states depending on the type of metal in phthalocyanine. The optical absorption was derived to examine the absorption spectra for various metal compositions while the variation in intrinsic electrical conductivity can be estimated from the shape of the band. The phonon and infrared spectra were also determined in order to investigate the vibration mode of molecule in the crystals

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11

Weng, Tingting, Daniel DeBrincat, Vaida Arcisauskaite, and John E. McGrady. "In search of structure–function relationships in transition-metal based rectifiers." Inorg. Chem. Front. 1, no. 6 (2014): 468–77. http://dx.doi.org/10.1039/c4qi00038b.

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12

Komoto, Yuki, Shintaro Fujii, Madoka Iwane, and Manabu Kiguchi. "Single-molecule junctions for molecular electronics." Journal of Materials Chemistry C 4, no. 38 (2016): 8842–58. http://dx.doi.org/10.1039/c6tc03268k.

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13

ZHU, X. "Electronic structure and electron dynamics at molecule?metal interfaces: implications for molecule-based electronics." Surface Science Reports 56, no. 1-2 (November 2004): 1–83. http://dx.doi.org/10.1016/j.surfrep.2004.09.002.

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14

Yuan, Guodong, Felipe Curtolo, Yibing Deng, Tao Wu, Fang Tian, Qun Ma, Yutong Liu, Jinglin Zuo, Guilherme Menegon Arantes, and Peng Zheng. "Highly Dynamic Polynuclear Metal Cluster Revealed in a Single Metallothionein Molecule." Research 2021 (July 14, 2021): 1–11. http://dx.doi.org/10.34133/2021/9756945.

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Human metallothionein (MT) is a small-size yet efficient metal-binding protein, playing an essential role in metal homeostasis and heavy metal detoxification. MT contains two domains, each forming a polynuclear metal cluster with an exquisite hexatomic ring structure. The apoprotein is intrinsically disordered, which may strongly influence the clusters and the metal-thiolate (M-S) bonds, leading to a highly dynamic structure. However, these features are challenging to identify due to the transient nature of these species. The individual signal from dynamic conformations with different states of the cluster and M-S bond will be averaged and blurred in classic ensemble measurement. To circumvent these problems, we combined a single-molecule approach and multiscale molecular simulations to investigate the rupture mechanism and chemical stability of the metal cluster by a single MT molecule, focusing on the Zn4S11 cluster in the α domain upon unfolding. Unusual multiple unfolding pathways and intermediates are observed for both domains, corresponding to different combinations of M-S bond rupture. None of the pathways is clearly preferred suggesting that unfolding proceeds from the distribution of protein conformational substates with similar M-S bond strengths. Simulations indicate that the metal cluster may rearrange, forming and breaking metal-thiolate bonds even when MT is folded independently of large protein backbone reconfiguration. Thus, a highly dynamic polynuclear metal cluster with multiple conformational states is revealed in MT, responsible for the binding promiscuity and diverse cellular functions of this metal-carrier protein.

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15

Xu, Peng, Mehran Azeem, Muhammad Mubashir Izhar, Syed Mazhar Shah, Muhammad Ahsan Binyamin, and Adnan Aslam. "On Topological Descriptors of Certain Metal-Organic Frameworks." Journal of Chemistry 2020 (November 12, 2020): 1–12. http://dx.doi.org/10.1155/2020/8819008.

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Topological indices are numerical numbers that represent the topology of a molecule and are calculated from the graphical depiction of the molecule. The importance of topological indices is due to their use as descriptors in QSPR/QSAR modeling. QSPRs (quantitative structure-property relationships) and QSARs (quantitative structure-activity relationships) are mathematical correlations between a specified molecular property or biological activity and one or more physicochemical and/or molecular structural properties. In this paper, we give explicit expressions of some degree-based topological indices of two classes of metal-organic frameworks (MOFs), namely, butylated hydroxytoluene- (BHT-) based metal-organic ( M = Co , Fe, Mn, Cr) (MBHT) frameworks and M 1 TPyP − M 2 (TPyP = 5,10,15,20 -tetrakis(4-pyridyl)porphyrin and M 1 , M 2 = Fe and Co) MOFs.

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16

Yonezawa, Tetsu, Toshihiro Tominaga, and Naoki Toshima. "Protecting Structure Analyses of Organic Molecule-protected Nanoscopic Noble Metal Clusters." Polymers for Advanced Technologies 7, no. 8 (August 1996): 645–51. http://dx.doi.org/10.1002/(sici)1099-1581(199608)7:8<645::aid-pat578>3.0.co;2-w.

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17

Rigamonti, Luca, Carri Cotton, Andrea Nava, Heinrich Lang, Tobias Rüffer, Mauro Perfetti, Lorenzo Sorace, et al. "Diamondoid Structure in a Metal-Organic Framework of Fe4Single-Molecule Magnets." Chemistry - A European Journal 22, no. 38 (June 29, 2016): 13705–14. http://dx.doi.org/10.1002/chem.201601383.

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18

Murakoshi, Kei. "(Invited) Room-Temperature Molecule Trapping at Plasmonic Metal Nanostructures." ECS Meeting Abstracts MA2022-01, no. 10 (July 7, 2022): 800. http://dx.doi.org/10.1149/ma2022-0110800mtgabs.

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To control of the motion of individual molecules at room temperature, optical tweezers could be the choice of the methods to realize the desirable selectivity with high resolution in time and space. In this study, we demonstrated plasmonic optical trapping of small molecules at the gap of a single metal nanodimer immersed in an electrolyte solution. In situ electrochemical surface-enhanced Raman scattering measurements proved that the plasmonic structure realized selective molecular condensation leading to the formation of unique mixed molecular phases that were distinct from those under thermodynamic equilibrium in nano scale.

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19

Regulska, E., M. Samsonowicz, R. Świsłocka, and W. Lewandowski. "Theoretical and Experimental Studies on Alkali Metal Phenoxyacetates." Spectroscopy: An International Journal 27 (2012): 321–28. http://dx.doi.org/10.1155/2012/498439.

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Optimized geometrical structures of alkali metal phenoxyacetates were obtained using B3LYP/6-311++G** method. Geometric and magnetic aromaticity indices, dipole moments, and energies were calculated. Atomic charges on the atoms of phenoxyacetic acid molecule and its alkali metal salts were calculated by Mulliken, APT (atomic polar tensor), NPA (natural population analysis), MK (Merz-Singh-Kollman method), and ChelpG (charges from electrostatic potentials using grid-based method) methods. The theoretical wavenumbers and intensities of IR as well as chemical shifts in NMR spectra were obtained and compared with experimental data. The effect of alkali metals on molecular structure of phenoxyacetic acid appears in the shift of selected bands along the series of alkali metal salts. The correlations between chosen bands and some metal parameters, such as electronegativity, ionization energy, and atomic, and ionic radius, have been noticed.

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20

Zheng, Heping, Mahendra Chordia, David Cooper, Ivan Shabalin, Maksymilian Chruszcz, Peter Müller, George Sheldrick, and Wladek Minor. "Check your metal - not every density blob is a water molecule." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1483. http://dx.doi.org/10.1107/s2053273314085167.

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Metals play vital roles in both the mechanism and architecture of biological macromolecules, and are the most frequently encountered ligands (i.e. non-solvent heterogeneous chemical atoms) in the determination of macromolecular crystal structures. However, metal coordinating environments in protein structures are not always easy to check in routine validation procedures, resulting in an abundance of misidentified and/or suboptimally modeled metal ions in the Protein Data Bank (PDB). We present a solution to identify these problems in three distinct yet related aspects: (1) coordination chemistry; (2) agreement of experimental B-factors and occupancy; and (3) the composition and motif of the metal binding environment. Due to additional strain introduced by macromolecular backbones, the patterns of coordination of metal binding sites in metal-containing macromolecules are more complex and diverse than those found in inorganic or organometallic chemistry. These complications make a comprehensive library of "permitted" coordination chemistry in protein structures less feasible, and the usage of global parameters such as the bond valence method more practical, in the determination and validation of metal binding environments. Although they are relatively infrequent, there are also cases where the experimental B-factor or occupancy of a metal ion suggests careful examination. We have developed a web-based tool called CheckMyMetal [1](http://csgid.org/csgid/metal_sites/) for the quick validation of metal binding sites. Moreover, the acquired knowledge of the composition and spatial arrangement (motif) of the coordinating atoms around the metal ion may also help in the modeling of metal binding sites in macromolecular structures. All of the studies described herein were performed using the NEIGHBORHOOD SQL database [2], which connects information about all modeled non-solvent heterogeneous chemical motifs in PDB structure by vectors describing all contacts to neighboring residues and atoms. NEIGHBORHOOD has broad applications for the validation and data mining of ligand binding environments in the PDB.

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21

Kučera, Jan, and Axel Groß. "Geometric and electronic structure of Pd/4-aminothiophenol/Au(111) metal–molecule–metal contacts: a periodic DFT study." Physical Chemistry Chemical Physics 12, no. 17 (2010): 4423. http://dx.doi.org/10.1039/b923700c.

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22

Dinpajooh, Mohammadhasan, and Abraham Nitzan. "Heat conduction in polymer chains: Effect of substrate on the thermal conductance." Journal of Chemical Physics 156, no. 14 (April 14, 2022): 144901. http://dx.doi.org/10.1063/5.0087163.

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In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale energy transport. In this work, we use nonequilibrium molecular dynamics simulations to address the effect of stretching on the phononic contribution to the heat conduction of molecular junctions consisting of single long-chain alkanes and various metal leads, such as Ag, Au, Cu, Ni, and Pt. The thermal conductance of such junctions is found to be much smaller than the intrinsic thermal conductance of the polymer and significantly depends on the nature of metal leads as expressed by the metal–molecule coupling and metal vibrational density of states. This behavior is expected and reflects the mismatch of phonon spectra at the metal molecule interfaces. As a function of stretching, we find a behavior similar to what was observed earlier [M. Dinpajooh and A. Nitzan, J. Chem. Phys. 153, 164903 (2020)] for pure polymeric structures. At relatively short electrode distances, where the polyethylene chains are compressed, it is found that the thermal conductances of the molecular junctions remain almost constant as one stretches the polymer chains. At critical electrode distances, the thermal conductances start to increase, reaching the values of the fully extended molecular junctions. Similar behaviors are observed for junctions in which several long-chain alkanes are sandwiched between various metal leads. These findings indicate that this behavior under stretching is an intrinsic property of the polymer chain and not significantly associated with the interfacial structures.

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23

Román-Pérez, J., I. López-Tocón, J. L. Castro, J. F. Arenas, J. Soto, and J. C. Otero. "The electronic structure of metal–molecule hybrids in charged interfaces: surface-enhanced Raman selection rules derived from plasmon-like resonances." Physical Chemistry Chemical Physics 17, no. 4 (2015): 2326–29. http://dx.doi.org/10.1039/c4cp04724a.

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24

Litecká, M., R. Gyepes, Z. Vargová, M. Vilková, M. Almáši, M. Walko, and J. Imrich. "Toxic metal complexes of macrocyclic cyclen molecule – synthesis, structure and complexing properties." Journal of Coordination Chemistry 70, no. 10 (March 28, 2017): 1698–712. http://dx.doi.org/10.1080/00958972.2017.1305493.

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25

Hansen, Christian R., Thomas J. Sørensen, Magni Glyvradal, Jacob Larsen, Sara H. Eisenhardt, Thomas Bjørnholm, Martin M. Nielsen, Robert Feidenhans’l, and Bo W. Laursen. "Structure of the Buried Metal−Molecule Interface in Organic Thin Film Devices." Nano Letters 9, no. 3 (March 11, 2009): 1052–57. http://dx.doi.org/10.1021/nl803393m.

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26

Lei, Haitao, Xialiang Li, Jia Meng, Haoquan Zheng, Wei Zhang, and Rui Cao. "Structure Effects of Metal Corroles on Energy-Related Small Molecule Activation Reactions." ACS Catalysis 9, no. 5 (April 3, 2019): 4320–44. http://dx.doi.org/10.1021/acscatal.9b00310.

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27

Duncan, Michael A. "Infrared spectroscopy to probe structure and dynamics in metal ion-molecule complexes." International Reviews in Physical Chemistry 22, no. 2 (April 2003): 407–35. http://dx.doi.org/10.1080/0144235031000095201.

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28

Ye, Lin, Pu Zhao, Molly Meng-Jung Li, Benedict T. W. Lo, Chiu Tang, and Shik Chi Edman Tsang. "Evaluation of the molecular poisoning phenomenon of W sites in ZSM-5 via synchrotron X-ray powder diffraction." Chemical Communications 54, no. 51 (2018): 7014–17. http://dx.doi.org/10.1039/c8cc02904k.

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29

Bergmann, Uwe, Vittal Yachandra, and Junko Yano. "How ultrafast X-ray pulses can reveal hidden secrets of photosynthesis." Biochemist 41, no. 2 (April 1, 2019): 24–29. http://dx.doi.org/10.1042/bio04102024.

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X-ray-based techniques are extremely versatile and can provide information regarding the atomic arrangement of atoms in a molecule and are often the method of choice for exploring the structures of proteins and their ligands. The photosynthetic splitting of water and evolution of molecular oxygen by plants and cyanobacteria is one of the key reactions in nature, which is catalysed by a metal site in a membrane-bound photosynthetic protein complex. In this article, we will describe how X-ray pulse lasers can simultaneously probe the overall atomic structure of the photosynthetic system and the electronic structure of a catalytic metal site under physiological conditions in real time.

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Varughese, Kottayil I. "Conformational Changes of Spo0F along the Phosphotransfer Pathway." Journal of Bacteriology 187, no. 24 (December 15, 2005): 8221–27. http://dx.doi.org/10.1128/jb.187.24.8221-8227.2005.

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ABSTRACT Spo0F is a secondary messenger in the sporulation phosphorelay, and its structure has been characterized crystallographically in the apo-state, in the metal-bound state, and in an interacting state with a phosphotransferase. Additionally, the solution structure of the molecule has been characterized by nuclear magnetic resonance techniques in the unliganded state and in complex with beryllofluoride. Spo0F is a single-domain protein with a well-defined three-dimensional structure, but it is capable of adapting to specific conformations for catching and releasing the phosphoryl moiety. This commentary deals with the conformational fluctuations of the molecule as it moves from an apo-state to a metal-coordinated state, to a phosphorylated state, and then to a phosphoryl-transferring state.

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Pandey, Rajiv K., Swatantra K. Yadav, Chandan Upadhyay, Rajiv Prakash, and Hirdyesh Mishra. "Surface plasmon coupled metal enhanced spectral and charge transport properties of poly(3,3′′′-dialkylquarterthiophene) Langmuir Schaefer films." Nanoscale 7, no. 14 (2015): 6083–92. http://dx.doi.org/10.1039/c5nr00682a.

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32

Thirugnanasambandam, Arunachalam, Selvam Karthik, Gunanithi Artheswari, and Namasivayam Gautham. "DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC)." Acta Crystallographica Section D Structural Biology 72, no. 6 (May 25, 2016): 780–88. http://dx.doi.org/10.1107/s2059798316006306.

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High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals. The decanucleotide d(GCATGCATGC) was previously reported to assume a single-stranded double-fold structure. In one of the two crystal structures described here the decamer assumes both the double-fold conformation and, simultaneously, the more conventional B-type double-helical structure. In the other crystal the sequence assumes the A-type double-helical conformation. These results, taken together with CD spectra, which were recorded as the decamer was titrated against four metal ions and spermine, indicate that the molecule may exist as a mixed population of structures in solution. Small differences in the environmental conditions, such as the concentration of metal ion, may decide which of these crystallizes out. The results also support the idea that it may be possible for DNA to change its structure to suit the binding requirements of proteins or drugs.

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33

Svensson, Lars Anders, Lars Thim, Ole Hvilsted Olsen, and Else Marie Nicolaisen. "Evaluation of the metal binding sites in a recombinant coagulation factor VIII identifies two sites with unique metal binding properties." Biological Chemistry 394, no. 6 (June 1, 2013): 761–65. http://dx.doi.org/10.1515/hsz-2012-0298.

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Abstract Coagulation factor VIII is a glycosylated, non-covalent heterodimer consisting of a heavy chain (A1-A2-B domains) and a light chain (A3-C1-C2 domains). The association of the chains, and the stability and function of the dimer depend on the presence of metal ions. We applied X-ray fluorescence, X-ray crystallographic structure determination with anomalous signals at different wavelengths, and colorimetric measurements to evaluate the metal binding sites in a recombinant factor VIII molecule, turoctocog alfa. We identified a metal binding site in domain A3 dominated by Cu+ binding and a site in domain A1 dominated by Zn2+ binding.

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34

Martin, T. P., M. Heinebrodt, U. Näher, H. Göhlich, T. Lange, and H. Schaber. "FULLERENES DOPED WITH METAL HALIDES." International Journal of Modern Physics B 06, no. 23n24 (December 1992): 3871–77. http://dx.doi.org/10.1142/s021797929200195x.

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The cage-like structure of fullerenes is a challenge to every experimentalist to put something inside—to dope the fullerenes. In fact, the research team that first identified C 60 as a football-like molecule quickly succeeded in trapping metal atoms inside and in shrinking the cage around this atom by photofragmentation. In this paper we report the results of “shrink-wrapping” the fullerenes around metal halide molecules. Of special interest is the critical size (the minimum number of carbon atoms) that can still enclose the dopant. A rough model for the space available inside a carbon cage gives good agreement with the measured shrinking limits.

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35

Han, Xinyi, Jinpeng Xin, Yangrong Yao, Zhihui Liang, Yongfu Qiu, Muqing Chen, and Shangfeng Yang. "Capturing the Long-Sought Dy@C2v(5)-C80 via Benzyl Radical Stabilization." Nanomaterials 12, no. 19 (September 22, 2022): 3291. http://dx.doi.org/10.3390/nano12193291.

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Endohedral metallofullerenes (EMFs) are one type of intriguing metal/carbon hybrid molecule with the molecule configuration of sphere cavity-encapsulating metal ions/metal clusters due to their unique physicochemical properties and corresponding application in the fields of biological materials, single molecule magnet materials and energy conversion materials. Although the EMF family is growing, and versatile EMFs have been successfully synthesized and confirmed using crystal structures, some expected EMF members have not been observed using the conventional fullerene separation and purify strategy. These missing EMFs raise an interesting scientific issue as to whether this is due to the difficulty in separating them from the in situ formed carbon soot. Herein, we successfully captured a long-sought dysprosium-based EMF bearing a C2v(5)-C80 cage (Dy@C2v(5)-C80) in the form of Dy@C2v(5)-C80(CH2Ph)(Ph = −C6H5) from carbon soot containing versatile EMFs using simple benzyl radical functionalization and unambiguously confirmed the molecule structure using single crystal X-ray diffraction characterization. Meanwhile, the crystal structure of Dy@C2v(5)-C80(CH2Ph) showed that a single benzyl group was grafted onto the (5,6,6)-carbon, suggesting the open-shell electronic configuration of Dy@C2v(5)-C80. The theoretical calculations unveiled that the benzyl radical addition enables the modulation of the electronic configuration of Dy@C2v(5)-C80 and the corresponding stabilization of Dy@C2v(5)-C80 in conventional organic solvents. This facile stabilization strategy via benzyl radical addition exhibits the considerable capability to capture these missing EMFs, with the benefit of enriching the endohedral fullerene family.

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36

Smerieri, Marco, Igor Píš, Lara Ferrighi, Silvia Nappini, Angelique Lusuan, Luca Vattuone, Luca Vaghi, et al. "Synthesis of corrugated C-based nanostructures by Br-corannulene oligomerization." Physical Chemistry Chemical Physics 20, no. 41 (2018): 26161–72. http://dx.doi.org/10.1039/c8cp04791j.

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37

Pogonin, Alexander E., Arseniy A. Otlyotov, Yury Minenkov, Alexander S. Semeikin, Yuriy A. Zhabanov, Sergey A. Shlykov, and Georgiy V. Girichev. "Molecular Structure of Nickel Octamethylporphyrin—Rare Experimental Evidence of a Ruffling Effect in Gas Phase." International Journal of Molecular Sciences 23, no. 1 (December 28, 2021): 320. http://dx.doi.org/10.3390/ijms23010320.

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The structure of a free nickel (II) octamethylporphyrin (NiOMP) molecule was determined for the first time through a combined gas-phase electron diffraction (GED) and mass spectrometry (MS) experiment, as well as through quantum chemical (QC) calculations. Density functional theory (DFT) calculations do not provide an unambiguous answer about the planarity or non-planar distortion of the NiOMP skeleton. The GED refinement in such cases is non-trivial. Several approaches to the inverse problem solution were used. The obtained results allow us to argue that the ruffling effect is manifested in the NiOMP molecule. The minimal critical distance between the central atom of the metal and nitrogen atoms of the coordination cavity that provokes ruffling distortion in metal porphyrins is about 1.96 Å.

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38

Zhou, Mingyong, Liang Fu, Fengze Jiang, Bingyan Jiang, and Dietmar Drummer. "Atomistic Investigation on the Wetting Behavior and Interfacial Joining of Polymer-Metal Interface." Polymers 12, no. 8 (July 29, 2020): 1696. http://dx.doi.org/10.3390/polym12081696.

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Polymer-metal hybrid structures can reduce the weight of components while ensuring the structural strength, which in turn save cost and subsequently fuel consumption. The interface strength of polymer-metal hybrid structure is mainly determined by the synergistic effects of interfacial interaction and mechanical interlocking. In this study, the wetting behavior of polypropylene (PP) melt on metal surface was studied by molecular dynamics simulation. Atomistic models with smooth surface and nano-column arrays on Al substrate were constructed. Influences of melt temperature, surface roughness and metal material on the wetting behavior and interfacial joining were analyzed. Afterwards the separation process of injection-molded PP-metal hybrid structure was simulated to analyze joining strength. Results show that the initially sphere-like PP model gradually collapses in the wetting simulation. With a higher temperature, it is easier for molecule chains to spread along the surface. For substrate with rough surface, high density is observed at the bottom or on the upper surface of the column. The contact state is transitioning from Wenzel state to Cassie–Baxter state with the decrease of void fraction. The inner force of injection-molded PP-Fe hybrid structure during the separation process is obviously higher, demonstrating a greater joining strength.

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39

Zhang, Yifei, Kehinde Busari, Changhai Cao, and Gao Li. "Structural Quasi-Isomerism in Au/Ag Nanoclusters." Photochem 2, no. 4 (December 5, 2022): 932–46. http://dx.doi.org/10.3390/photochem2040060.

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Atomically precise metal nanoclusters are a new kind of nanomaterials that appeared in recent years; a pair of isomer nanoclusters have the same metal types, numbers of metal atoms, and surface-protected organic ligands but different metal atom arrangements. This article summarizes the structure features of isomer nanoclusters and concentrates on synthesis methods that could lead to isomer structure. The pairs of isomer inorganic nanoclusters’ conversion to each other and their applications in catalyst and photoluminescence are also discussed. We found that the structure conversions are relevant to their stability. However, with the same molecule formulas, different atom arrangements significantly influence their performance in applications. Finally, the existing challenges and some personal perspectives for this novel field in the nano-science investigation are proposed. We hope this minireview can offer a reference for researchers interested in inorganic isomer nanoclusters.

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40

Pranowo, Harno Dwi, Tuti Hartati Siregar, and Mudasir Mudasir. "THEORETICAL STUDY OF THE EFFECT OF WATER MOLECULE ADDITION ON THE CONFORMATION OF SUBSTITUTED DIBENZO-18-CROWN-6 ETHER IN ITS COMPLEXATION WITH Na⁺ CATION USING SEMI EMPIRICAL METHOD MNDO/d." Indonesian Journal of Chemistry 3, no. 2 (June 8, 2010): 111–17. http://dx.doi.org/10.22146/ijc.21894.

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The effect of water molecule addition into modeling structure of complex of substituted dibenzo-18-crown-6 ether with metal ion Na+ was studied. The aim of this research is to find information about geometrical conformation of substituted DB18C6 and its selectivity to complex/coordinate metal ion Na+ in the presence of water molecule. In this research semi empirical method was used for calculation. To find the best conformation, trial and error experiments were conducted using semi empirical method available in HyperChem 6.0, finally MNDO/d method was selected. The result of geometry optimization showed that addition of water molecule improve the stability of the conformation of substituted DB18C6 and increase the selectivity of this compound to complex metal ion Na+. The presence of electron-withdrawing substituents decreased the binding energy while that of electron-donating one increase the binding energy (value of DE more negative). Cavity radii of DB18C6 in the presence of water molecule extended from 2.3 Å to 2.6 Å. This figure is almost similar to that of experimental data. Keywords: Crown ether, molecular modelling, semiempirical method

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41

Fleck, Michel, Vahram V. Ghazaryan, and Aram M. Petrosyan. "Diaquaiodidotetrasarcosinepotassium: an overview of sarcosine metal halogenide structures." Acta Crystallographica Section C Crystal Structure Communications 69, no. 1 (December 13, 2012): 11–16. http://dx.doi.org/10.1107/s0108270112048597.

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The monoclinic crystal structure of tetrasarcosine potassium iodide dihydrate {orcatena-poly[[potassium-tetra-μ-sarcosine-κ4O:O′;κ4O:O] iodide dihydrate]}, {[K(C3H7NO2)4]I·2H2O}nor Sar4·KI·2H2O (space groupC2/c), comprises two crystallographically different sarcosine molecules and one water molecule on general positions, and one K+cation and one I−anion located on twofold axes. The irregular eight-coordinated K+polyhedra are connected into infinite chains along [001]viasarcosine molecules. This compound is the first sarcosine metal halogenide salt with a 4:1 ratio. A short overview of other sarcosine metal halogenide salts is presented and relationships to similar glycine salts are discussed.

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42

Huang, Mingzhu, Jianqiao Dong, Zhiye Wang, Yunchuan Li, Lei Yu, Yichong Liu, Gongming Qian, and Shuai Chang. "Revealing the electronic structure of organic emitting semiconductors at the single-molecule level." Chemical Communications 56, no. 94 (2020): 14789–92. http://dx.doi.org/10.1039/d0cc05602b.

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Single-molecule conductance measurements of OLED molecules show that the holes injected from metal electrode can be suppressed by adding electron-withdrawing arms, benefiting the electron–hole balance of OLED devices whose holes are excessive.

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43

Yang, Jing, John H. Enemark, and Martin L. Kirk. "Metal–Dithiolene Bonding Contributions to Pyranopterin Molybdenum Enzyme Reactivity." Inorganics 8, no. 3 (March 5, 2020): 19. http://dx.doi.org/10.3390/inorganics8030019.

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Here we highlight past work on metal–dithiolene interactions and how the unique electronic structure of the metal–dithiolene unit contributes to both the oxidative and reductive half reactions in pyranopterin molybdenum and tungsten enzymes. The metallodithiolene electronic structures detailed here were interrogated using multiple ground and excited state spectroscopic probes on the enzymes and their small molecule analogs. The spectroscopic results have been interpreted in the context of bonding and spectroscopic calculations, and the pseudo-Jahn–Teller effect. The dithiolene is a unique ligand with respect to its redox active nature, electronic synergy with the pyranopterin component of the molybdenum cofactor, and the ability to undergo chelate ring distortions that control covalency, reduction potential, and reactivity in pyranopterin molybdenum and tungsten enzymes.

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44

Meier, B., C. Michel, M. Saran, J. Hüttermann, F. Parak, and G. Rotilio. "Kinetic and spectroscopic studies on a superoxide dismutase from Propionibacterium shermanii that is active with iron or manganese: pH-dependence." Biochemical Journal 310, no. 3 (September 15, 1995): 945–50. http://dx.doi.org/10.1042/bj3100945.

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Kinetic studies were performed on the superoxide dismutases isolated from the anaerobic bacterium Propionibacterium shermanii as active enzymes with either iron or manganese, which were naturally incorporated into the same molecule depending on the metal supply. Both the Fe- and Mn- forms showed decreasing activity with increasing pH. This suggests the protonation of some groups near the metal, possibly a metal-bound water molecule. Thus the kinetic behaviour of this superoxide dismutase is much more dependent on the protein structure than on the metal incorporated into the active site. The secondary structures of both forms were not influenced by variations in pH, whereas the EPR spectra of the Fe-superoxide dismutase changed as a function of pH. The EPR spectra apparently consist of two overlapping species. Steady-state experiments proved that all iron-containing species show catalytic activity, but the species predominating in the alkaline pH range displays a lower reaction rate. The Michaelis constant and maximal turnover number for the Fe-superoxide dismutase were determined polarographically as Km = 0.54 mmol/l and Vmax. = 2000 mol.s-1 at pH 9.5. These data indicate that, in anaerobic bacteria under physiological conditions, the superoxide dismutase is not saturable with O2-. and the catalytic activity is similar to that of metal-specific Fe- or Mn-superoxide dismutases from aerobic organisms.

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45

Kosionis, Spyridon, and Emmanuel Paspalakis. "Four-Wave Mixing in Asymmetric Double Quantum Dot Molecule–Metal Nanoparticle Assemblies." Materials Proceedings 4, no. 1 (November 11, 2020): 89. http://dx.doi.org/10.3390/iocn2020-07843.

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In this study, the four-wave mixing (FWM) spectrum of a strongly pumped hybrid structure is theoretically examined. The hybrid structure consists of an asymmetric double semiconductor quantum dot (SQD) molecule and a spherical metal nanoparticle (MNP), which are coupled together via long-range Coulomb interaction. Having as a starting point the Hamiltonian of the system, in the dipole and the rotating-wave approximations, we derive a set of nonlinear density matrix equations, which are numerically solved, in the steady-state limit, and then the FWM coefficient is calculated within a range of values of the pump–probe field detuning. The spectral response of the FWM coefficient is investigated, for different values of the pump-field detuning, the electron-tunneling rate, and the energy gap between the upper states in the energy-level scheme of the double SQD molecule, while the interparticle distance between the two components of the structure is modified.

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46

La Gatta, Salvatore, Linda Leone, Ornella Maglio, Maria De Fenza, Flavia Nastri, Vincenzo Pavone, Marco Chino, and Angela Lombardi. "Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach." Molecules 26, no. 17 (August 28, 2021): 5221. http://dx.doi.org/10.3390/molecules26175221.

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Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

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Liu, Yu, Shan Shan Zhang, Da Jun Song, Tian Zhu Yang, Hong Xiao Tian, and Jian Gao. "Structure Studies on Order Assemblage of Manganese^II Isovanillin Complexes." Applied Mechanics and Materials 618 (August 2014): 193–97. http://dx.doi.org/10.4028/www.scientific.net/amm.618.193.

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The ManganeseII Isovanillin complex [Mn2(C8H7O3)4(H2O)2], Diaqua-tetra (isovanillinato-O,O')-bis (manganeseII),the MnII atom is coordinated by three isovanillinate anions and one water molecule in a distorted trigonal bipyramidal configuration with five-coordinations geometry. And one isovanillinate ligand chelates to the MnII atom through its methyl and hydroxy O atoms, the other two isovanillinate ligand chelates to the MnII atom only through its hydroxy O atoms. The same as another MnII atom. So we get a Binuclear MnII metal complexe. The fact clearly suggests not so much significant contribution from the electrostatic interaction in the Mn-O bonding in Binuclear MnII metal complexes as we gotten in mononuclear MnII metal complexes. Adjacent complex link to each other via hydrogen bonds forming the three-dimensional supramolecular structure.

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48

Harding, Marjorie M. "The geometry of metal–ligand interactions relevant to proteins." Acta Crystallographica Section D Biological Crystallography 55, no. 8 (August 1, 1999): 1432–43. http://dx.doi.org/10.1107/s0907444999007374.

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Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from `small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor ≤ 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal–donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using ∼4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal–donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained refinement with low-resolution data.

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Gerile, Naren, Li Hong Bao, Jin Kang Zhang, Ying Zhang, Xiao Tian, Ta Na Bao, and Ojiyed Tegus. "Effect of Moisture Content on the Diverse Structure State of the Octanoyl Alanine Metal (Mg, Ca) Complexes." Solid State Phenomena 288 (March 2019): 1–8. http://dx.doi.org/10.4028/www.scientific.net/ssp.288.1.

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Octanoyl alanine ligands and metal ions (Mg2+, Ca2+) form metal complexes of octanoyl alanine through chemical coordination bonds [1]. According to the acid base reaction and the Lewis acid-base theory[2], the molecule or ion of the central atom or ion (collectively called the central atom) and the ligand (called ligand) around it, completely or partially by the coordination bond to form metal complex. These octanoyl alanine complexes are soluble in water and easily ionize into internal coordination ions and external ions, while the ligands and central atoms do not ionize in the inner boundary. The octanoyl alanine magnesium and calcium complexes belongs to the amino acid metal complexes, which can be widely used in daily life, industrial production and life science in the future application. Recently, with the rapid development of amino acid metal complexes [3-7], it is not only associated with inorganic compounds and organometallic compounds, but also overlaps with the chemistry, coordination catalysis and molecular biology of the current chemical frontiers [8-10]. In this paper, [C10H20NCO3]2M type metal complexes prepared by combining octanoyl alanine ligand with metal ions containing functional group COOH, the influence of water content on the DSC curve and surface morphology of metal complexes was studied, and the information of the diversified structure state of the materials complex can be obtained.

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50

Yang, Yanna, Shuxia Wang, Zhen Zhang, Yingzhou Huang, Guo Chen, Hua Wei, and Weijia Wen. "Selective plasmon driven surface catalysis in metal triangular nanoplate-molecule-film sandwich structure." Chemical Physics Letters 639 (October 2015): 47–51. http://dx.doi.org/10.1016/j.cplett.2015.09.004.

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