Understanding hydrogen-bonding structures of molecular crystals via electron and NMR nanocrystallography

Guzmán-Afonso, C.; Hong, You lee; Colaux, Henri; Iijima, Hirofumi; Saitow, Akihiro; Fukumura, Takuma; Aoyama, Yoshitaka; Motoki, Shinichi; Oikawa, Tetsuo; Yamazaki, Toshio; Yonekura, Koji; Nishiyama, Yusuke

doi:10.1038/s41467-019-11469-2

Cited by 54 publications

(51 citation statements)

References 51 publications

(45 reference statements)

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“…This type of monitoring is presented here for samarosporin I (a naturally occurring peptaibol comprised of 15 amino acids [16]) on the basis of benchmarking calculations for a set of six triglycines, and for N-Ac-Aib-OH, N-Ac-Leu-OH and Ala-Pro-Gly dihydrate, after their assessment performed for melanostatin (Pro-Leu-Gly-NH 2 hemihydrate [17]). The results directly capture an influence of secondary structural elements upon the NMR parameters (see reference [18] for the most recent review of this topic) and could be important in NMR crystallography [19][20][21][22][23] of oligopeptides and in an interpretation of spectra of their oriented samples [24].…”

Section: Introductionmentioning

confidence: 94%

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

Czernek

Brus

2020

IJMS

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Reliable values of the solid-state NMR (SSNMR) parameters together with precise structural data specific for a given amino acid site in an oligopeptide are needed for the proper interpretation of measurements aiming at an understanding of oligopeptides’ function. The periodic density functional theory (DFT)-based computations of geometries and SSNMR chemical shielding tensors (CSTs) of solids are shown to be accurate enough to support the SSNMR investigations of suitably chosen models of oriented samples of oligopeptides. This finding is based on a thorough comparison between the DFT and experimental data for a set of tripeptides with both 13Cα and 15Namid CSTs available from the single-crystal SSNMR measurements and covering the three most common secondary structural elements of polypeptides. Thus, the ground is laid for a quantitative description of local spectral parameters of crystalline oligopeptides, as demonstrated for the backbone 15Namid nuclei of samarosporin I, which is a pentadecapeptide (composed of five classical and ten nonproteinogenic amino acids) featuring a strong antimicrobial activity.

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Section: Introductionmentioning

confidence: 94%

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

Czernek

Brus

2020

IJMS

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“…Intermolecular hydrogen bonds (H‐bonds) are of paramount importance in supramolecular chemistry, 1,2 crystal engineering 3 and biochemistry 4 . These noncovalent interactions have been intensively studied by various theoretical and experimental techniques 5–8 : ab initio calculations, 9,10 molecular dynamic modeling, 11 quantum mechanics/molecular mechanics calculations, 12 NMR and IR spectroscopy, 13–15 X‐Ray and neutron diffraction 16–18 and thermochemical experiments 19 . Among theoretical approaches, the electron density 7,20–23 and energy decomposition analyses 7,24 are gaining considerable popularity in the studies of H‐bonds in the isolated state, 25,26 solution 27 and solid state 28,29 .…”

Section: Introductionmentioning

confidence: 99%

The explicit role of electron exchange in the hydrogen bonded molecular complexes

2021

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We applied a set of advanced bonding descriptors to establish the hidden electron density features and binding energy characteristics of intermolecular D HÁÁÁA hydrogen bonds (O HÁÁÁO, N HÁÁÁO and S HÁÁÁO) in 150 isolated and solvated molecular complexes. The exchange-correlation and Pauli potentials as well as corresponding local one-electron forces allowed us to explicitly ascertain how electron exchange defines the bonding picture in the proximity of the H-bond critical point. The electron density features of D HÁÁÁA interaction are governed by alterations in the electron localization in the H-bond region displaying itself in the exchange hole. At that, they do not depend on the variations in the exchange hole mobility. The electrostatic interaction mainly defines the energy of H-bonds of different types, whereas the strengthening/weakening of H-bonds in complexes with varying substituents depends on the barrier height of the exchange potential near the bond critical point. Energy variations between H-bonds in isolated and solvated systems are also caused the electron exchange peculiarities as follows from the corresponding potential and the interacting quantum atom analyses complemented by electron delocalization index calculations. Our approach is based on the bonding descriptors associated with the characteristics of the observable electron density and can be recommended for in-depth studies of non-covalent bonding. K E Y W O R D S electron density, hydrogen bond, IQA, potential acting on an electron in a molecule, QM/MM, QTAIM, source function 1 | INTRODUCTION Intermolecular hydrogen bonds (H-bonds) are of paramount importance in supramolecular chemistry, 1,2 crystal engineering 3 and biochemistry. 4 These noncovalent interactions have been intensively studied by various theoretical and experimental techniques 5-8 : ab initio calculations, 9,10 molecular dynamic modeling, 11 quantum mechanics/molecular mechanics calculations, 12 NMR and IR spectroscopy, 13-15 X-Ray and neutron diffraction 16-18 and thermochemical experiments. 19 Among theoretical approaches, the electron density 7,20-23 and energy decomposition analyses 7,24 are gaining considerable popularity in the studies of H-bonds in the isolated state, 25,26 solution 27 and solid state. 28,29 Lest us consider some of them shortly. The non-local density-based descriptors 30-36 carry information about the mutual influence of electrons in spatially remote regions and detect subtle effects in chemical bonding. The source function (SF) 30,31 reveals the role of atoms, defined in terms of QTAIM, 37 in formation of H-bonds. 30 It is successfully used for classification of the H-bonds and other noncovalent interactions 38,39 as well as for identification of molecular parts having the greatest impact on the electron density along the H-bonds. 40 The electron delocalization indices (DI) characterize the extent of electron-pair sharing between atoms 41 and measure the H-bond covalency. 7,42-45

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“…First, ssNMR spectroscopy is applicable to various systems no matter their states, i.e., lacking long-range order or even being a disorder, which are intractable by diffraction techniques. Second, it enables the precise location of the H-atom positions, which is poorly determined by X-ray diffraction (XRD) or electron diffraction (Guzmán-Afonso et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Selective 1H-14N Distance Measurements by 14N Overtone Solid-State NMR Spectroscopy at Fast MAS

Duong

Gan

Nishiyama

2021

Front. Mol. Biosci.

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Accurate distance measurements between proton and nitrogen can provide detailed information on the structures and dynamics of various molecules. The combination of broadband phase-modulated (PM) pulse and rotational-echo saturation-pulse double-resonance (RESPDOR) sequence at fast magic-angle spinning (MAS) has enabled the measurement of multiple 1H-14N distances with high accuracy. However, complications may arise when applying this sequence to systems with multiple inequivalent 14N nuclei, especially a single 1H sitting close to multiple 14N atoms. Due to its broadband characteristics, the PM pulse saturates all 14N atoms; hence, the single 1H simultaneously experiences the RESPDOR effect from multiple 1H-14N couplings. Consequently, no reliable H-N distances are obtained. To overcome the problem, selective 14N saturation is desired, but it is difficult because 14N is an integer quadrupolar nucleus. Alternatively, 14N overtone (OT) NMR spectroscopy can be employed owing to its narrow bandwidth for selectivity. Moreover, owing to the sole presence of two energy levels (m = ± 1), the 14N OT spin dynamics behaves similarly to that of spin-1/2. This allows the interchangeability between RESPDOR and rotational-echo double-resonance (REDOR) since their principles are the same except the degree of 14N OT population transfer; saturation for the former whereas inversion for the latter. As the ideal saturation/inversion is impractical due to the slow and orientation-dependent effective nutation of 14N OT, the working condition is usually an intermediate between REDOR and RESPDOR. The degree of 14N OT population transfer can be determined from the results of protons with short distances to 14N and then can be used to obtain long-distance determination of other protons to the same 14N site. Herein, we combine the 14N OT and REDOR/RESPDOR to explore the feasibility of selective 1H-14N distance measurements. Experimental demonstrations on simple biological compounds of L-tyrosine.HCl, N-acetyl-L-alanine, and L-alanyl-L-alanine were performed at 14.1 T and MAS frequency of 62.5 kHz. The former two consist of a single 14N site, whereas the latter consists of two 14N sites. The experimental optimizations and reliable fittings by the universal curves are described. The extracted 1H-14N distances by OT-REDOR are in good agreement with those determined by PM-RESPDOR and diffraction techniques.

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Understanding hydrogen-bonding structures of molecular crystals via electron and NMR nanocrystallography

Cited by 54 publications

References 51 publications

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

The explicit role of electron exchange in the hydrogen bonded molecular complexes

Selective 1H-14N Distance Measurements by 14N Overtone Solid-State NMR Spectroscopy at Fast MAS

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