A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Verma, Niraj; Tao, Peng; Zou, Wenli; Chen, Xia; Chen, Xin; Freindorf, Marek; Kraka, Elfi

doi:10.3390/s20082358

Cited by 34 publications

(33 citation statements)

References 100 publications

(283 reference statements)

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

“…This forms the basis of the characterization of the normal mode (CNM) procedure [63]. CNM decomposes each normal mode into local mode contributions offering a new, comprehensive way of analyzing IR and Raman spectra, which we successfully applied to assess the usefulness of vibrational Stark effect probes [118]. Recently, the local mode theory was extended for the description of chemical bonding in periodic systems [119,120].…”

Section: Local Vibrational Mode Theorymentioning

confidence: 99%

“…For smaller systems, in particular gas phase molecules, this can be accomplished via the CNM procedure [63,118]. In Fig.…”

Section: Assessment Of Experimental Frequencies As Fec and Co Bond Strength Descriptorsmentioning

confidence: 99%

Critical assessment of the FeC and CO bond strength in carboxymyoglobin: a QM/MM local vibrational mode study

Freindorf

Kraka

2020

J Mol Model

Self Cite

View full text Add to dashboard Cite

The interplay between FeC and CO bonding in carboxymyoglobin (MbCO) and the role of potential hydrogen bonding between the CO moiety and the side chains of the surrounding protein amino acids have been the subject of numerous experimental and theoretical studies. In this work, we present a quantitative measure for the intrinsic FeC and CO bond strength in MbCO, as well as for CO⋯H bonding, based on the local vibrational mode analysis, originally developed by Konkoli and Cremer. We investigated a gas phase model, two models of the wild-type protein, and 17 protein mutations that change the distal polarity of the heme pocket, as well as two protein mutations of the heme porphyrin ring. Based on local mode force constants, we could quantify for the first time the suggested inverse relationship between the CO and FeC bond strength, the strength of CO⋯H bonding, and how it weakens the CO bond. Combined with the natural orbital analysis, we could also confirm the key role of π back donation between Fe and the CO moiety in determining the FeC bond strength. We further clarified that CO and FeC normal modes couple with other protein motions in the protein environment. Therefore, normal mode frequencies/force constants are not suited as bond strength descriptors and instead their local mode counterparts should be used. Our comprehensive results provide new guidelines for the fine-tuning of existing and the design of MbCO models with specific FeC, CO, and CO⋯H bond strengths.

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%

“…i.e., a completely localized normal mode l µ has a C nµ value of 1 (corresponding to 100% if C nµ is given as a percentage). The CNM procedure was recently applied to assess the usefulness of Vibrational Stark Effect probes [102], and to analyze π-hole interactions between aryl (Ar) donors and small molecule acceptors [126]. In this work, CNM is used to interpret exp and theor spectra.…”

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

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Cited by 34 publications

References 100 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

Critical assessment of the FeC and CO bond strength in carboxymyoglobin: a QM/MM local vibrational mode study

Vibrational Analysis of Benziodoxoles and Benziodazolotetrazoles

Contact Info

Product

Resources

About