New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study

Makoś, Małgorzata Z.; Freindorf, Marek; Sethio, Daniel; Kraka, Elfi

doi:10.1007/s00214-019-2463-9

Cited by 35 publications

(26 citation statements)

References 129 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…They are of high sensitivity to electronic structure differences (e.g., caused by changing a substituent) and directly reflect the intrinsic strength of a bond or weak chemical interaction as shown by Zou and Cremer [ 76 ]. Thus, local vibration stretching force constants have been utilized as a unique measure of the intrinsic strength of a chemical bond [ 69 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 ] or weak chemical interaction [ 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 ] based on vibration spectroscopy.…”

Section: Methodologiesmentioning

confidence: 99%

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

2021

Self Cite

View full text Add to dashboard Cite

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N–H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O–H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C–H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C–H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N–H⋯N bond and the C–H⋯O bonds, and at the same time decreases the strength of the N–H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

show abstract

Section: Methodologiesmentioning

confidence: 99%

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…244 Topological analyses based on NBO were also used to revisit the nature and strength of the hydride and dihydrogen interaction with the iron center in the [Ni-Fe] enzyme. 245…”

Section: Geometric Structuresmentioning

confidence: 99%

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Orio

Pantazis

2021

Chem. Commun.

View full text Add to dashboard Cite

show abstract

“…The latter are highly sensitive to electronic structure differences (e.g., caused by changing a substituent) and directly reflect the intrinsic strength of a bond or weak chemical interaction, as has been shown by Zou and Cremer [92]. Thus, LVM stretching force constants have been utilized as a unique measure of the intrinsic strength of chemical bonds [38,39,48,[93][94][95][96][97][98][99][100][101][102][103][104] and weak chemical interactions [19,40, based on vibrational spectroscopy. LVM theory has previously been applied for the description of bonding in a diverse set of 34 HVI compounds, the majority of which are λ 3 -iodanes [19].…”

Section: Computational and Experimental Methodsmentioning

confidence: 99%

Vibrational Analysis of Benziodoxoles and Benziodazolotetrazoles

Yannacone¹,

Sayala²,

Freindorf³

et al. 2021

Physchem

Self Cite

View full text Add to dashboard Cite

Tetrazoles are well known for their high positive enthalpy of formation which makes them attractive as propellants, explosives, and energetic materials. As a step towards a deeper understanding of the stability of benziodazolotetrazole (BIAT)-based materials compared to their benziodoxole (BIO) counterparts, we investigated in this work electronic structure features and bonding properties of two monovalent iodine precursors: 2-iodobenzoic acid and 5-(2-iodophenyl)tetrazole and eight hypervalent iodine (III) compounds: I-hydroxybenzidoxolone, I-methoxybenziodoxolone, I-ethoxybenziodoxolone, I-iso-propoxybenziodoxolone and the corresponding I-hydroxyben ziodazolotetrazole, I-methoxybenziodazolotetrazole, I-ethoxybenziodazolotetrazole and I-iso- propoxybenziodazolotetrazole. As an efficient tool for the interpretation of the experimental IR spectra and for the quantitative assessment of the I−C, I−N, and I−O bond strengths in these compounds reflecting substituent effects, we used the local vibrational mode analysis, originally introduced by Konkoli and Cremer, complemented by electron density and natural bond orbital analyses. Based on the hypothesis that stronger bonds correlate with increased stability, we predict that, for both series, i.e., substituted benziodoxoles and benziodazolotetrazoles, the stability increases as follows: I-iso-propoxy < I-ethoxy < I-methoxy < I-hydroxy. In particular, the I−N bonds in the benziodazolotetrazoles could be identified as the so-called trigger bonds being responsible for the initiation of explosive decomposition in benziodazolotetrazoles. The new insight gained by this work will allow for the design of new benziodazolotetrazole materials with controlled performance or stability based on the modulation of the iodine bonds with its three ligands. The local mode analysis can serve as an effective tool to monitor the bond strengths, in particular to identify potential trigger bonds. We hope that this article will foster future collaboration between the experimental and computational community being engaged in vibrational spectroscopy.

show abstract

New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study

Cited by 35 publications

References 129 publications

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Vibrational Analysis of Benziodoxoles and Benziodazolotetrazoles

Contact Info

Product

Resources

About