Quantitative assessment of intramolecular hydrogen bonds in neutral histidine

Yannacone, Seth; Sethio, Daniel; Kraka, Elfi

doi:10.1007/s00214-020-02631-x

Cited by 20 publications

(14 citation statements)

References 75 publications

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“…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

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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.

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Section: Methodologiesmentioning

confidence: 99%

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

2021

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“…Yannacone et al [ 18 ] established an empirical power law relation between density at a bond critical point and local force constants, of the form ln (k HBOND ) = A ln(ρ BCP ) + B, …”

Section: Resultsmentioning

confidence: 99%

“…Intramolecular hydrogen bonding has a significant effect specifically on conformational preference in systems of importance in biochemistry, as various types of H bonding can occur in various conformations and isomers. The intramolecular H bonds in histidine have been described by Yannacome, Sethlo, and Kraka (YSK) [ 18 ]. To enhance insight into the relative strength of H bonds in context these authors brought together descriptors from Bader’s theory of atoms in molecules (AIM) and the reduced density gradient from analysis of noncovalent interactions (NCI), both of which are described below.…”

Section: Introductionmentioning

confidence: 99%

Focal Point Evaluation of Energies for Tautomers and Isomers for 3-hydroxy-2-butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N)

2021

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The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH.

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“…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 [127]. Thus, local vibration stretching force constants have been used as a unique measure of the intrinsic strength of a chemical bond [86,[128][129][130][131][132][133][134][135][136][137][138][139][140][141] or weak chemical interaction [67][68][69][70][71]81,[142][143][144][145][146][147][148][149][150][151][152][153][154][155][156][157][158][159] based on vibration spectroscopy. We have successfully described bonding in λ 3 iodine bonding in a diverse set of 34 hypervalent iodine compounds [81], in this work we apply LMV and associated local mode stretching vibrational force constants to assess iodine bonding in pincer complexes.…”

Section: Methodsmentioning

confidence: 99%

Halogen Bonding Involving I2 and d8 Transition-Metal Pincer Complexes

et al. 2021

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We systematically investigated iodine–metal and iodine–iodine bonding in van Koten’s pincer complex and 19 modifications changing substituents and/or the transition metal with a PBE0–D3(BJ)/aug–cc–pVTZ/PP(M,I) model chemistry. As a novel tool for the quantitative assessment of the iodine–metal and iodine–iodine bond strength in these complexes we used the local mode analysis, originally introduced by Konkoli and Cremer, complemented with NBO and Bader’s QTAIM analyses. Our study reveals the major electronic effects in the catalytic activity of the M-I-I non-classical three-center bond of the pincer complex, which is involved in the oxidative addition of molecular iodine I2 to the metal center. According to our investigations the charge transfer from the metal to the σ* antibonding orbital of the I-I bond changes the 3c–4e character of the M-I-I three-center bond, which leads to weakening of the iodine I-I bond and strengthening of the metal–iodine M-I bond, facilitating in this way the oxidative addition of I2 to the metal. The charge transfer can be systematically modified by substitution at different places of the pincer complex and by different transition metals, changing the strength of both the M-I and the I2 bonds. We also modeled for the original pincer complex how solvents with different polarity influence the 3c–4e character of the M-I-I bond. Our results provide new guidelines for the design of pincer complexes with specific iodine–metal bond strengths and introduce the local vibrational mode analysis as an efficient tool to assess the bond strength in complexes.

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Quantitative assessment of intramolecular hydrogen bonds in neutral histidine

Cited by 20 publications

References 75 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

Focal Point Evaluation of Energies for Tautomers and Isomers for 3-hydroxy-2-butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N)

Halogen Bonding Involving I2 and d8 Transition-Metal Pincer Complexes

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