Bare Molecular Anions of Unsaturated Hydrocarbons: Density Functional Charge and Spin Distributions Based on Their Single Crystal Structures

1998 ◽  
Vol 63 (8) ◽  
pp. 1245-1263 ◽  
Author(s):  
Zdeněk Havlas ◽  
Hans Bock
Keyword(s):  
Alkali Metal ◽  
Conformational Changes ◽  
Density Functional ◽  
Structural Data ◽  
Radical Anions ◽  
Spin Distribution ◽  
Open Chain ◽  
Charge Localization ◽  
Jahn Teller ◽  
Spin Populations

Bare π-hydrocarbon radical anions M•, dianions M− as well as even a radical trianion M• can be crystallized as alkali metal salts, [M(•)−n][Me+solv]n if the solvent-shared contact ion multiples, [M(•)−n..(Me+)n]solv, present in aprotic solution after the reduction at an alkali metal mirror can be separated by advantageous cation solvation. Altogether 22 π-hydrocarbon anions M(•)−n comprising polycyclic cata- as well as peri-annelated six-membered ring compounds, polyphenyls, those with nonalternant polycyclic skeletal topology, open chain and organosilicon derivatives have been characterized by low-temperature X-ray crystallographic analyses. Based on the structural data determined, their charge and spin populations have been approximated by density functional calculations including natural bond orbital analyses (DFT/NBO). Although in general the total (σ + π) charges at individual C centers of the hydrocarbon skeletons cannot be correlated neither with the structural data nor with the spin distribution, numerous interesting details as well as some useful rules are provided. They concern, for instance, central C-C bond elongation and peripheral C-C bond shortening, preferred charge localization patterns, effects of conformational changes in the π-radical anions crystallized or Jahn-Teller distortions of formally degenerate molecular radical anion states.

Die Reduktion von Triphenylphosphan-Derivaten zu ihren Radikalanionen und zum Dibenzophosphol-Radikaldianion [1] / The Reduction of Triphenylphosphane Derivatives to their Radical Anions and to the Radical Dianion of Dibenzophosphole [1]

1982 ◽  
Vol 37 (11) ◽  
pp. 1382-1387 ◽  
Author(s):  
Wolfgang Kaim ◽  
Peter Hänel ◽  
Hans Bock
Keyword(s):  
Low Temperature ◽  
Alkali Metal ◽  
Ring Closure ◽  
Metal Reduction ◽  
Paramagnetic Species ◽  
Radical Anions ◽  
Spin Distribution ◽  
Pyramidal Geometry ◽  
Mercury Cathode ◽  
Electron Reduction

Triphenylphosphane 1, its oxide 2 and sulfide 3 undergo one-electron reduction at a mercury cathode in DMF to yield the corresponding radical anions. ESE analysis of the paramagnetic species is facilitated by deuteration and suggests a pyramidal geometry of the radicals. Reduction with potassium metal in DME at low temperature yields also radical anions for 2 and 3. The phosphane 1, however, reacts under phenyl cleavage and potassiumphenyl-assisted ring closure to the dianion of 5H-dibenzophosphole 4. This radical 4· ⊖⊖ is also obtainod by alkali metal reduction of P-phenyldibenzophosphole o, and its spin distribution is compared to iso-.-π-electronic radicals containing CH, N, O, S, or Se links instead of the phosphorus atom.

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

scholarly journals Effect of vacancy defects on the electronic transport properties of an Ag–ZnO–Pt sandwich structure

2021 ◽  
Vol 20 (2) ◽  
pp. 798-804
Author(s):  
G. R. Berdiyorov ◽  
F. Boltayev ◽  
G. Eshonqulov ◽  
H. Hamoudi
Keyword(s):  
Transport Properties ◽  
Electronic Transport ◽  
Density Functional ◽  
Practical Importance ◽  
Functional Formalism ◽  
Vacancy Defects ◽  
Electronic Transport Properties ◽  
Charge Localization ◽  
Metal Insulator Metal ◽  
Current Rectification

AbstractThe effect of zinc and oxygen vacancy defects on the electronic transport properties of Ag(100)–ZnO(100)–Pt(100) sandwich structures is studied using density functional theory in combination with the nonequilibrium Green’s functional formalism. Defect-free systems show clear current rectification due to voltage dependent charge localization in the system as revealed in our transmission eigenstates analysis. Regardless of the location, oxygen vacancies result in enhanced current in the system, whereas Zn vacancy defects reduce the charge transport across the junction. The current rectification becomes less pronounced in the presence of both types of vacancy defects. Our findings can be of practical importance for developing metal-insulator-metal diodes.

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions

2012 ◽  
Vol 137 (20) ◽  
pp. 205101 ◽  
Author(s):  
Yeon Jae Ko ◽  
Piotr Storoniak ◽  
Haopeng Wang ◽  
Kit H. Bowen ◽  
Janusz Rak
Keyword(s):  
Density Functional Theory ◽  
Photoelectron Spectroscopy ◽  
Density Functional ◽  
Radical Anions ◽  
Functional Theory

scholarly journals Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2217 ◽  
Author(s):  
Ryota Kirikoshi ◽  
Noriyoshi Manabe ◽  
Ohgi Takahashi
Keyword(s):  
Conformational Changes ◽  
Density Functional ◽  
Cyclic Peptide ◽  
Density Functional Theory Method ◽  
Proton Exchange ◽  
Computational Method ◽  
Side Chain ◽  
Tetrahedral Intermediate ◽  
Rate Determining Step ◽  
Proton Source

Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH2CO–NGRC]–NH2. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH3 molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH3 molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate.

scholarly journals Nucleus-independent chemical shift profiles along the intrinsic distortion path for Jahn-Teller active molecules. Study on cyclopentadienyl radical and cobaltocene

2015 ◽  
Vol 80 (7) ◽  
pp. 877-888 ◽  
Author(s):  
Ljubica Andjelkovic ◽  
Marko Peric ◽  
Matija Zlatar ◽  
Maja Gruden-Pavlovic
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
High Symmetry ◽  
Functional Theory ◽  
Aromatic Character ◽  
Nucleus Independent Chemical Shift ◽  
Jahn Teller ◽  
Cyclopentadienyl Radical ◽  
Cyclopentadienyl Anion ◽  
Low Symmetry

The aromatic/antiaromatic behavior of the cyclopentadienyl anion (Cp-), bis(?5-cyclopentadienyl)iron(II) (Fe(Cp)2), as well as of the Jahn-Teller (JT) active cyclopentadienyl radical (Cp?) and bis(?5-cyclopentadienyl)cobalt(II) (Co(Cp)2) has been investigated using Density Functional Theory (DFT) calculations of the Nuclear Independent Chemical Shifts (NICS). According to the NICS values, pentagon ring in Fe(Cp)2 is more aromatic than isolated Cp-. The NICS parameters have been scanned along the Intrinsic Distortion Path (IDP) for Cp? and Co(Cp)2 showing antiaromaticity, which decreases with increasing deviation from high symmetry D5h to low symmetry (LS) C2v. Changes in the NICS values along the IDP revealed that Co(Cp)2 in the LS nuclear arrangement has aromatic character, in contrast to the case of Cp?

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