Chemical Bonding in Silicon Carbonyl Complexes.
Ontology highlight
ABSTRACT:
SUBMITTER: Sergeieva T
PROVIDER: S-EPMC8360033 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:DFT calculations have been carried out for coordinatively saturated neutral and charged carbonyl complexes [M(CO) n ] q where M is a metal atom of groups 2-10. The model compounds M(CO)2 (M = Ca, Sr, Ba) and the experimentally observed [Ba(CO)]+ were also studied. The bonding situation has been analyzed with a variety of charge and energy partitioning approaches. It is shown that the Dewar-Chatt-Duncanson model in terms of M ← CO σ-donation and M → CO π-backdonation is a valid approach to explain the M-CO bonds and the trend of the CO stretching frequencies. The carbonyl ligands of the neutral complexes carry a negative charge, and the polarity of the M-CO bonds increases for the less electronegative metals, which is particularly strong for the group 4 and group 2 atoms. The NBO method delivers an unrealistic charge distribution in the carbonyl complexes, while the AIM approach gives physically reasonable partial charges that are consistent with the EDA-NOCV calculations and with the trend of the C-O stretching frequencies. The AdNDP method provides delocalized MOs which are very useful models for the carbonyl complexes. Deep insight into the nature of the metal-CO bonds and quantitative information about the strength of the [M] ← (CO)8 σ-donation and [M(d)] → (CO)8 π-backdonation visualized by the deformation densities are provided by the EDA-NOCV method. The large polarity of the M-CO π orbitals toward the CO end in the alkaline earth octacarbonyls M(CO)8 (M = Ca, Sr, Ba) leads to small values for the delocalization indices δ(M-C) and δ(M···O) and significant overlap between adjacent CO groups, but the origin of the charge migration and the associated red-shift of the C-O stretching frequencies is the [M(d)] → (CO)8 π-backdonation. The heavier alkaline earth metals calcium, strontium and barium use their s/d valence orbitals for covalent bonding. They are therefore to be assigned to the transition metals.
| S-EPMC8395605 | biostudies-literature
Project description:Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand-protein complexes may shed light on rational design of potent ligands in the future.
| S-EPMC8840108 | biostudies-literature
Project description:Several metalloenzymes, including [FeFe]-hydrogenase, employ cofactors wherein multiple metal atoms work together with surrounding ligands that mediate heterolytic and concerted proton-electron transfer (CPET) bond activation steps. Herein, we report a new dinucleating PNNP expanded pincer ligand, which can bind two low-valent iron atoms in close proximity to enable metal-metal cooperativity (MMC). In addition, reversible partial dearomatization of the ligand's naphthyridine core enables both heterolytic metal-ligand cooperativity (MLC) and chemical non-innocence through CPET steps. Thermochemical and computational studies show how a change in ligand binding mode can lower the bond dissociation free energy of ligand C(sp3)-H bonds by ∼25 kcal mol-1. H-atom abstraction enabled trapping of an unstable intermediate, which undergoes facile loss of two carbonyl ligands to form an unusual paramagnetic (S = ) complex containing a mixed-valent iron(0)-iron(i) core bound within a partially dearomatized PNNP ligand. Finally, cyclic voltammetry experiments showed that these diiron complexes show catalytic activity for the electrochemical hydrogen evolution reaction. This work presents the first example of a ligand system that enables MMC, heterolytic MLC and chemical non-innocence, thereby providing important insights and opportunities for the development of bimetallic systems that exploit these features to enable new (catalytic) reactivity.
| S-EPMC8849050 | biostudies-literature
Project description:Syntheses of the copper and gold complexes [Cu{Fe(CO)5 }2 ][SbF6 ] and [Au{Fe(CO)5 }2 ][HOB{3,5-(CF3 )2 C6 H3 }3 ] containing the homoleptic carbonyl cations [M{Fe(CO)5 }2 ]+ (M=Cu, Au) are reported. Structural data of the rare, trimetallic Cu2 Fe, Ag2 Fe and Au2 Fe complexes [Cu{Fe(CO)5 }2 ][SbF6 ], [Ag{Fe(CO)5 }2 ][SbF6 ] and [Au{Fe(CO)5 }2 ][HOB{3,5-(CF3 )2 C6 H3 }3 ] are also given. The silver and gold cations [M{Fe(CO)5 }2 ]+ (M=Ag, Au) possess a nearly linear Fe-M-Fe' moiety but the Fe-Cu-Fe' in [Cu{Fe(CO)5 }2 ][SbF6 ] exhibits a significant bending angle of 147° due to the strong interaction with the [SbF6 ]- anion. The Fe(CO)5 ligands adopt a distorted square-pyramidal geometry in the cations [M{Fe(CO)5 }2 ]+ , with the basal CO groups inclined towards M. The geometry optimization with DFT methods of the cations [M{Fe(CO)5 }2 ]+ (M=Cu, Ag, Au) gives equilibrium structures with linear Fe-M-Fe' fragments and D2 symmetry for the copper and silver cations and D4d symmetry for the gold cation. There is nearly free rotation of the Fe(CO)5 ligands around the Fe-M-Fe' axis. The calculated bond dissociation energies for the loss of both Fe(CO)5 ligands from the cations [M{Fe(CO)5 }2 ]+ show the order M=Au (De =137.2 kcal mol-1 )>Cu (De =109.0 kcal mol-1 )>Ag (De =92.4 kcal mol-1 ). The QTAIM analysis shows bond paths and bond critical points for the M-Fe linkage but not between M and the CO ligands. The EDA-NOCV calculations suggest that the [Fe(CO)5 ]→M+ ←[Fe(CO)5 ] donation is significantly stronger than the [Fe(CO)5 ]←M+ →[Fe(CO)5 ] backdonation. Inspection of the pairwise orbital interactions identifies four contributions for the charge donation of the Fe(CO)5 ligands into the vacant (n)s and (n)p AOs of M+ and five components for the backdonation from the occupied (n-1)d AOs of M+ into vacant ligand orbitals.
| S-EPMC8252735 | biostudies-literature
Project description:The next generation of microelectromechanical systems (MEMS) requires new materials and platforms that can exploit the intrinsic properties of advanced materials and structures, such as materials with high thermal conductivity, broad optical transmission spectra, piezoelectric properties, and miniaturization potential. Therefore, we need to look beyond standard SiO2-based silicon-on-insulator (SOI) structures to realize ubiquitous MEMS. This work proposes using AlN as an alternative SOI structure due to several inherent material property advantages as well as functional advantages. This work presents the results of reactively sputtered AlN films on a Si handle wafer bonded with a mirror-polished Si device wafer. Wafer bonding was achieved by using hydrophilic wafer bonding processes, which was realized by appropriate polymerization of the prebonding surfaces. Plasma activation of the AlN surface included O2, Ar, SF6, SF6 + Ar, and/or SF6 + O2, which resulted in a change in the chemical and topography state of the surface. Changes in the AlN surface properties included enhanced hydrophilicity, reduced surface roughness, and low nanotopography, components essential for successful hydrophilic direct wafer bonding. Wafer bonding experiments were carried out using promising surface activation methods. The results showed a multilayered bonding interface of Si(Device)/SiO2/ALON/AlN/Si(Handle) with fluorine in the aluminum oxynitride layer from the proceeding AlN surface activation process. More notably, this work provided wafer bonding tensile strength results of the AlN alternative SOI structure that compares with the traditional SiO2 SOI counterpart, making AlN to Si direct bonding an attractive alternative SOI platform.
| S-EPMC8397240 | biostudies-literature
Project description:Synthetic chemists have learned to mimic nature in using hydrogen bonds and other weak interactions to dictate the spatial arrangement of reaction substrates and to stabilize transition states to enable highly efficient and selective reactions. The activation of a catalyst molecule itself by hydrogen-bonding networks, in order to enhance its catalytic activity to achieve a desired reaction outcome, is less explored in organic synthesis, despite being a commonly found phenomenon in nature. Herein, we show our investigation into this underexplored area by studying the promotion of carbonyl-olefin metathesis reactions by hydrogen-bonding-assisted Brønsted acid catalysis, using hexafluoroisopropanol (HFIP) solvent in combination with para-toluenesulfonic acid (pTSA). Our experimental and computational mechanistic studies reveal not only an interesting role of HFIP solvent in assisting pTSA Brønsted acid catalyst, but also insightful knowledge about the current limitations of the carbonyl-olefin metathesis reaction.
| S-EPMC9303705 | biostudies-literature
Project description:Vibrational probes can provide a direct readout of the local electrostatic field in complex molecular environments, such as protein binding sites and enzyme active sites. This information provides an experimental method to explore the underlying physical causes of important biomolecular processes such as binding and catalysis. However, specific chemical interactions such as hydrogen bonds can have complicated effects on vibrational probes and confound simple electrostatic interpretations of their frequency shifts. We employ vibrational Stark spectroscopy along with infrared spectroscopy of carbonyl probes in different solvent environments and in ribonuclease S to understand the sensitivity of carbonyl frequencies to electrostatic fields, including those due to hydrogen bonds. Additionally, we carried out molecular dynamics simulations to calculate ensemble-averaged electric fields in solvents and in ribonuclease S and found excellent correlation between calculated fields and vibrational frequencies. These data enabled the construction of a robust field-frequency calibration curve for the C═O vibration. The present results suggest that carbonyl probes are capable of quantitatively assessing the electrostatics of hydrogen bonding, making them promising for future study of protein function.
| S-EPMC3762491 | biostudies-literature
Project description:Heteronuclear calcium-iron carbonyl cation complexes in the form of [CaFe(CO)n ]+ (n=5-12) are produced in the gas phase. Infrared photodissociation spectroscopy in conjunction with quantum chemical calculations confirm that the n=10 complex is the coordination saturated ion where a Fe(CO)4 fragment is bonded with a Ca(CO)6 fragment through two side-on bridging carbonyl ligands. Bonding analysis indicates that it is best described by the bonding interactions between a [Ca(CO)6 ]2+ dication and an [Fe(CO)4 ]- anion forming a Fe→Ca d-d dative bond in the [(CO)6 Ca-Fe(CO)4 ]+ structure, which enriches the pool of experimentally observed complexes of calcium that mimic transition metal compounds. The molecule is the first example of a heteronuclear carbonyl complex featuring a d-d bond between calcium and a transition metal.
| S-EPMC8251804 | biostudies-literature
Project description:Abiraterone acetate (AbirAc) is the most used steroidal therapeutic agent for treatment of prostate cancer. The mainly hydrophobic molecular surface of AbirAc results in its poor solubility and plays an important role for retention of abiraterone in the cavity of the receptor formed by peptide chains and heme fragments. In order to evaluate the hydrolytic stability of AbirAc, to modify its solubility by formation of new solid forms and to model bonding of this medication with the heme, a series of d-metal complexes with AbirAc was obtained. AbirAc remains stable in water, acetonitrile, tetrahydrofuran, and ethanol, and readily interacts with dications as a terminal ligand to create discrete complexes, including [FePC(AbirAc)2] and [ZnTPP(AbirAc)] (H2PC = phthalocyanine and H2TPP = 5,10,15,20-tetraphenylporphyrine) models for ligand-receptor bonding. In reactions with silver(I) nitrate, AbirAc acts as a bridge ligand. Energies of chemical bonding between AbirAc and these cations vary from 97 to 235 kJ mol-1 and exceed those between metal atoms and water molecules. This can be indicative of the ability of abiraterone to replace solvent molecules in the coordination sphere of biometals in living cells, although the model [ZnTPP] complex remains stable in CDCl3, CD2Cl2, and 1,1,2,2-tetrachloroethane-d2 solvents and decomposes in polar dimethylsulfoxide-d6 and methanol-d4 solvents, as follows from the 1H DOSY spectra. Dynamics of its behavior in 1,1,2,2-tetrachloroethane-d2 were studied by ROESY and NMR spectra.
| S-EPMC10535913 | biostudies-literature
Project description:Virtually all organosulfur compounds react with Fe(0) carbonyls to give the title complexes. These reactions are reviewed in light of major advances over the past few decades, spurred by interest in Fe2(?-SR)2(CO)x centers at the active sites of the [FeFe]-hydrogenase enzymes. The most useful synthetic route to Fe2(?-SR)2(CO)6 involves the reaction of thiols with Fe2(CO)9 and Fe3(CO)12. Such reactions can proceed via mono-, di-, and triiron intermediates. The reactivity of Fe(0) carbonyls toward thiols is highly chemoselective, and the resulting dithiolato complexes are fairly rugged. Thus, many complexes tolerate further synthetic elaboration directed at the organic substituents. A second major route involves alkylation of Fe2(?-S2)(CO)6, Fe2(?-SH)2(CO)6, and Li2Fe2(?-S)2(CO)6. This approach is especially useful for azadithiolates Fe2[(?-SCH2)2NR](CO)6. Elaborate complexes arise via addition of the FeSH group to electrophilic alkenes, alkynes, and carbonyls. Although the first example of Fe2(?-SR)2(CO)6 was prepared from ferrous reagents, ferrous compounds are infrequently used, although the Fe(II)(SR)2 + Fe(0) condensation reaction is promising. Almost invariably low-yielding, the reaction of Fe3(CO)12, S8, and a variety of unsaturated substrates results in C-H activation, affording otherwise inaccessible derivatives. Thiones and related C?S-containing reagents are highly reactive toward Fe(0), often giving complexes derived from substituted methanedithiolates and C-H activation.
| S-EPMC4933964 | biostudies-literature