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12 pages, 27151 KiB

Open AccessArticle

Nature of Linear Spectral Properties and Fast Electronic Relaxations in Green Fluorescent Pyrrolo[3,4-c]Pyridine Derivative

by Nataliia V. Bashmakova, Yevgeniy O. Shaydyuk, Andriy M. Dmytruk, Tomasz Świergosz, Olexiy D. Kachkovsky, Kevin D. Belfield, Mykhailo V. Bondar and Wiktor Kasprzyk

Int. J. Mol. Sci. 2021, 22(11), 5592; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115592 - 25 May 2021

Cited by 7 | Viewed by 2052

Abstract

The electronic nature of 4-hydroxy-1H-pyrrolo[3,4-c]pyridine-1,3,6(2H,5H)-trione (HPPT) was comprehensively investigated in liquid media at room temperature using steady-state and time-resolved femtosecond transient absorption spectroscopic techniques. The analysis of the linear photophysical and photochemical parameters of HPPT, including steady-state absorption, fluorescence and excitation anisotropy spectra, [...] Read more.

The electronic nature of 4-hydroxy-1H-pyrrolo[3,4-c]pyridine-1,3,6(2H,5H)-trione (HPPT) was comprehensively investigated in liquid media at room temperature using steady-state and time-resolved femtosecond transient absorption spectroscopic techniques. The analysis of the linear photophysical and photochemical parameters of HPPT, including steady-state absorption, fluorescence and excitation anisotropy spectra, along with the lifetimes of fluorescence emission and photodecomposition quantum yields, revealed the nature of its large Stokes shift, specific changes in the permanent dipole moments under electronic excitation, weak dipole transitions with partially anisotropic character, and high photostability. Transient absorption spectra of HPPT were obtained with femtosecond resolution and no characteristic solvate relaxation processes in protic (methanol) solvent were revealed. Efficient light amplification (gain) was observed in the fluorescence spectral range of HPPT, but no super-luminescence and lasing phenomena were detected. The electronic structure of HPPT was also analyzed with quantum-chemical calculations using a DFT/B3LYP method and good agreement with experimental data was shown. The development and investigation of new pyrrolo[3,4-c]pyridine derivatives are important due to their promising fluorescent properties and potential for use in physiological applications. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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8 pages, 4823 KiB

Open AccessArticle

Snapshots of the Fragmentation for C₇₀@Single-Walled Carbon Nanotube: Tight-Binding Molecular Dynamics Simulations

by Ji Young Lee, Changhoon Lee, Eiji Osawa, Jong Woan Choi, Jung Chul Sur and Kee Hag Lee

Int. J. Mol. Sci. 2021, 22(8), 3929; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22083929 - 10 Apr 2021

Cited by 4 | Viewed by 1571

Abstract

In previously reported experimental studies, a yield of double-walled carbon nanotubes (DWCNTs) at C₇₀@Single-walled carbon nanotubes (SWCNTs) is higher than C₆₀@SWCNTs due to the higher sensitivity to photolysis of the former. From the perspective of pyrolysis dynamics, we would [...] Read more.

In previously reported experimental studies, a yield of double-walled carbon nanotubes (DWCNTs) at C₇₀@Single-walled carbon nanotubes (SWCNTs) is higher than C₆₀@SWCNTs due to the higher sensitivity to photolysis of the former. From the perspective of pyrolysis dynamics, we would like to understand whether C₇₀@SWCNT is more sensitive to thermal decomposition than C₆₀@SWCNT, and the starting point of DWCNT formation, which can be obtained through the decomposition fragmentation of the nanopeapods, which appears in the early stages. We have studied the fragmentation of C₇₀@SWCNT nanopeapods, using molecular dynamics simulations together with the empirical tight-binding total energy calculation method. We got the snapshots of the fragmentation structure of carbon nano-peapods (CNPs) composed of SWCNT and C₇₀ fullerene molecules and the geometric spatial positioning structure of C₇₀ within the SWCNT as a function of dynamics time (for 2 picoseconds) at the temperatures of 4000 K, 5000 K, and 6000 K. In conclusion, the scenario in which C₇₀@SWCNT transforms to a DWCNT would be followed by the fragmentation of C₇₀, after C₇₀, and the SWCNT have been chemically bonding in the early stages. The relative stability of fullerenes in CNPs could be reversed, compared to the ranking of the relative stability of the encapsulated molecules themselves. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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12 pages, 2725 KiB

Open AccessArticle

A Volumetric Analysis of the ¹H NMR Chemical Shielding in Supramolecular Systems

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2021, 22(7), 3333; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22073333 - 24 Mar 2021

Cited by 2 | Viewed by 2268

Abstract

The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host–guest complexes. Its theoretical counterpart, that is, the ¹H NMR chemical shielding affected by the solvent (¹H CS), may provide important insights into spatial arrangements [...] Read more.

The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host–guest complexes. Its theoretical counterpart, that is, the ¹H NMR chemical shielding affected by the solvent (¹H CS), may provide important insights into spatial arrangements of supramolecular systems, and it can also be reliably obtained for challenging cases of an aggregation of aromatic and antiaromatic molecules in solution. This computational analysis is performed for the complex of coronene and an antiaromatic model compound in acetonitrile by employing the GIAO-B3LYP-PCM approach combined with a saturated basis set. Predicted ¹H CS values are used to generate volumetric data, whose properties are thoroughly investigated. The ¹H CS isosurface, corresponding to a value of the proton chemical shift taken from a previous experimental study, is described. The presence of the ¹H CS isosurface should be taken into account in deriving structural information about supramolecular hosts and their encapsulation of small molecules. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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10 pages, 8794 KiB

Open AccessArticle

Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

by V. V. Krishnan, Timothy Bentley, Alina Xiong and Kalyani Maitra

Int. J. Mol. Sci. 2021, 22(3), 1364; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22031364 - 29 Jan 2021

Cited by 3 | Viewed by 1934

Abstract

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, [...] Read more.

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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12 pages, 2101 KiB

Open AccessArticle

Signal Deconvolution and Generative Topographic Mapping Regression for Solid-State NMR of Multi-Component Materials

by Shunji Yamada, Eisuke Chikayama and Jun Kikuchi

Int. J. Mol. Sci. 2021, 22(3), 1086; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22031086 - 22 Jan 2021

Cited by 8 | Viewed by 3265

Abstract

Solid-state nuclear magnetic resonance (ssNMR) spectroscopy provides information on native structures and the dynamics for predicting and designing the physical properties of multi-component solid materials. However, such an analysis is difficult because of the broad and overlapping spectra of these materials. Therefore, signal [...] Read more.

Solid-state nuclear magnetic resonance (ssNMR) spectroscopy provides information on native structures and the dynamics for predicting and designing the physical properties of multi-component solid materials. However, such an analysis is difficult because of the broad and overlapping spectra of these materials. Therefore, signal deconvolution and prediction are great challenges for their ssNMR analysis. We examined signal deconvolution methods using a short-time Fourier transform (STFT) and a non-negative tensor/matrix factorization (NTF, NMF), and methods for predicting NMR signals and physical properties using generative topographic mapping regression (GTMR). We demonstrated the applications for macromolecular samples involved in cellulose degradation, plastics, and microalgae such as Euglena gracilis. During cellulose degradation, ¹³C cross-polarization (CP)–magic angle spinning spectra were separated into signals of cellulose, proteins, and lipids by STFT and NTF. GTMR accurately predicted cellulose degradation for catabolic products such as acetate and CO₂. Using these methods, the ¹H anisotropic spectrum of poly-ε-caprolactone was separated into the signals of crystalline and amorphous solids. Forward prediction and inverse prediction of GTMR were used to compute STFT-processed NMR signals from the physical properties of polylactic acid. These signal deconvolution and prediction methods for ssNMR spectra of macromolecules can resolve the problem of overlapping spectra and support macromolecular characterization and material design. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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13 pages, 1456 KiB

Open AccessArticle

Parametrizing the Spatial Dependence of ¹H NMR Chemical Shifts in π-Stacked Molecular Fragments

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2020, 21(21), 7908; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21217908 - 24 Oct 2020

Cited by 5 | Viewed by 2307

Abstract

Most recently a renewed interest in several areas has arisen in factors governing the ¹H NMR chemical shift (¹H CS) of protons in aromatic systems. Therefore, it is important to describe how ¹H CS values are affected by π-stacking [...] Read more.

Most recently a renewed interest in several areas has arisen in factors governing the ¹H NMR chemical shift (¹H CS) of protons in aromatic systems. Therefore, it is important to describe how ¹H CS values are affected by π-stacking intermolecular interactions. The parametrization of radial and angular dependences of the ¹H CS is proposed, which is based on conventional gauge-independent atomic orbital (GIAO) calculations of explicit molecular fragments. Such a parametrization is exemplified for a benzene dimer with intermonomer vertical and horizontal distances which are in the range of values often found in crystals of organic compounds. Results obtained by the GIAO calculations combined with B3LYP and MP2 methods were compared, and revealed qualitatively the same trends in the ¹H CS data. The parametrization was found to be quantitatively correct for the T-shaped benzene dimers, and its limitations were discussed. Parametrized ¹H CS surfaces should become useful for providing additional restraints in the search of site-specific information through an analysis of structurally induced ¹H CS changes. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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26 pages, 8046 KiB

Open AccessArticle

Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors

by Alexander S. Paramonov, Milita V. Kocharovskaya, Andrey V. Tsarev, Dmitrii S. Kulbatskii, Eugene V. Loktyushov, Mikhail A. Shulepko, Mikhail P. Kirpichnikov, Ekaterina N. Lyukmanova and Zakhar O. Shenkarev

Int. J. Mol. Sci. 2020, 21(19), 7280; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197280 - 01 Oct 2020

Cited by 13 | Viewed by 3063

Abstract

Ly-6/uPAR or three-finger proteins (TFPs) contain a disulfide-stabilized β-structural core and three protruding loops (fingers). In mammals, TFPs have been found in epithelium and the nervous, endocrine, reproductive, and immune systems. Here, using heteronuclear NMR, we determined the three-dimensional (3D) structure and backbone [...] Read more.

Ly-6/uPAR or three-finger proteins (TFPs) contain a disulfide-stabilized β-structural core and three protruding loops (fingers). In mammals, TFPs have been found in epithelium and the nervous, endocrine, reproductive, and immune systems. Here, using heteronuclear NMR, we determined the three-dimensional (3D) structure and backbone dynamics of the epithelial secreted protein SLURP-1 and soluble domains of GPI-anchored TFPs from the brain (Lynx2, Lypd6, Lypd6b) acting on nicotinic acetylcholine receptors (nAChRs). Results were compared with the data about human TFPs Lynx1 and SLURP-2 and snake α-neurotoxins WTX and NTII. Two different topologies of the β-structure were revealed: one large antiparallel β-sheet in Lypd6 and Lypd6b, and two β-sheets in other proteins. α-Helical segments were found in the loops I/III of Lynx2, Lypd6, and Lypd6b. Differences in the surface distribution of charged and hydrophobic groups indicated significant differences in a mode of TFPs/nAChR interactions. TFPs showed significant conformational plasticity: the loops were highly mobile at picosecond-nanosecond timescale, while the β-structural regions demonstrated microsecond-millisecond motions. SLURP-1 had the largest plasticity and characterized by the unordered loops II/III and cis-trans isomerization of the Tyr39-Pro40 bond. In conclusion, plasticity could be an important feature of TFPs adapting their structures for optimal interaction with the different conformational states of nAChRs. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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15 pages, 6018 KiB

Open AccessArticle

Oxidative Photocyclization of Aromatic Schiff Bases in Synthesis of Phenanthridines and Other Aza-PAHs

by Martin Kos, Jaroslav Žádný, Jan Storch, Vladimír Církva, Petra Cuřínová, Jan Sýkora, Ivana Císařová, Febin Kuriakose and Igor. V. Alabugin

Int. J. Mol. Sci. 2020, 21(16), 5868; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21165868 - 15 Aug 2020

Cited by 15 | Viewed by 4177

Abstract

The oxidative photocyclization of aromatic Schiff bases was investigated as a potential method for synthesis of phenanthridine derivatives, biologically active compounds with medical applications. Although it is possible to prepare the desired phenanthridines using such an approach, the reaction has to be performed [...] Read more.

The oxidative photocyclization of aromatic Schiff bases was investigated as a potential method for synthesis of phenanthridine derivatives, biologically active compounds with medical applications. Although it is possible to prepare the desired phenanthridines using such an approach, the reaction has to be performed in the presence of acid and TEMPO to increase reaction rate and yield. The reaction kinetics was studied on a series of substituted imines covering the range from electron-withdrawing to electron-donating substituents. It was found that imines with electron-withdrawing substituents react one order of magnitude faster than imines bearing electron-donating groups. The ¹H NMR monitoring of the reaction course showed that a significant part of the Z isomer in the reaction is transformed into E isomer which is more prone to photocyclization. The portion of the Z isomer transformed showed a linear correlation to the Hammett substituent constants. The reaction scope was expanded towards synthesis of larger aromatic systems, namely to the synthesis of strained aromatic systems, e.g., helicenes. In this respect, it was found that the scope of oxidative photocyclization of aromatic imines is limited to the formation of no more than five ortho-fused aromatic rings. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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24 pages, 5533 KiB

Open AccessArticle

Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations

by Katarzyna Bucholc, Aleksandra Skrajna, Kinga Adamska, Xiao-Cui Yang, Krzysztof Krajewski, Jarosław Poznański, Michał Dadlez, Zbigniew Domiński and Igor Zhukov

Int. J. Mol. Sci. 2020, 21(15), 5268; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155268 - 24 Jul 2020

Cited by 5 | Viewed by 2603

Abstract

FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a [...] Read more.

FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a highly homologous domain that interacts with the C-terminal region of NPAT. Structural aspects of the FLASH–NPAT and YARP–NPAT complexes and their role in histone gene expression remain largely unknown. In this study, we used multidimensional NMR spectroscopy and in silico modeling to analyze the C-terminal domain in FLASH and YARP in an unbound form and in a complex with the last 31 amino acids of NPAT. Our results demonstrate that FLASH and YARP domains share the same fold of a triple

α

-helical bundle that resembles the DNA binding domain of Myb transcriptional factors and the SANT domain found in chromatin-modifying and remodeling complexes. The NPAT peptide contains a single

α

-helix that makes multiple contacts with

α

-helices I and III of the FLASH and YARP domains. Surprisingly, in spite of sharing a significant amino acid similarity, each domain likely binds NPAT using a unique network of interactions, yielding two distinct complexes. In silico modeling suggests that both complexes are structurally compatible with DNA binding, raising the possibility that they may function in identifying specific sequences within histone gene clusters, hence initiating the assembly of HLBs and regulating histone gene expression during cell cycle progression. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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14 pages, 2135 KiB

Open AccessArticle

NMR Spectroscopic Studies of Cation Dynamics in Symmetrically-Substituted Imidazolium-Based Ionic Liquid Crystals

by Debashis Majhi, Andrei V. Komolkin and Sergey V. Dvinskikh

Int. J. Mol. Sci. 2020, 21(14), 5024; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21145024 - 16 Jul 2020

Cited by 7 | Viewed by 2206

Abstract

Ionic liquid crystals (ILCs) present a new class of non-molecular soft materials with a unique combination of high ionic conductivity and anisotropy of physicochemical properties. Symmetrically-substituted long-chain imidazolium-based mesogenic ionic liquids exhibiting a smectic liquid crystalline phase were investigated by solid state NMR [...] Read more.

Ionic liquid crystals (ILCs) present a new class of non-molecular soft materials with a unique combination of high ionic conductivity and anisotropy of physicochemical properties. Symmetrically-substituted long-chain imidazolium-based mesogenic ionic liquids exhibiting a smectic liquid crystalline phase were investigated by solid state NMR spectroscopy and computational methods. The aim of the study was to reveal the correlation between cation size and structure, local dynamics, and orientational order in the layered mesophase. The obtained experimental data are consistent with the model of a rod-shaped cation with the two chains aligned in opposite directions outward from the imidazolium core. The alignment of the core plane to the phase director and the restricted conformations of the chain segments were determined and compared to those in single-chain counterparts. The orientational order parameter S~0.5–0.6 of double-chain ionic liquid crystals is higher than that of corresponding single-chain analogues. This is compatible with the enhanced contribution of van der Waals forces to the stabilization of smectic layers. Increased orientational order for the material with Br⁻ counterions, which exhibit a smaller ionic radius and higher ability to form hydrogen bonds as compared to that of BF₄⁻, also indicated a non-negligible influence of electrostatic and hydrogen bonding interactions. The enhanced rod-shape character and higher orientational order of symmetrically-substituted ILCs can offer additional opportunities in the design of self-assembling non-molecular materials. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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13 pages, 2180 KiB

Open AccessArticle

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2020, 21(14), 4907; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21144907 - 11 Jul 2020

Cited by 8 | Viewed by 2660

Abstract

A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its [...] Read more.

A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (¹³C/¹⁵N/¹H) isotropic chemical shifts of (C_O, N_amid, H_amid, H_α) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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11 pages, 1371 KiB

Open AccessArticle

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

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2020, 21(8), 2700; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21082700 - 13 Apr 2020

Cited by 4 | Viewed by 2316

Abstract

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 [...] Read more.

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 ¹³C_α and ¹⁵N_amid 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 ¹⁵N_amid nuclei of samarosporin I, which is a pentadecapeptide (composed of five classical and ten nonproteinogenic amino acids) featuring a strong antimicrobial activity. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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16 pages, 1519 KiB

Open AccessArticle

The Proton Density of States in Confined Water (H₂O)

by Sow-Hsin Chen, Carmelo Corsaro, Francesco Mallamace, Enza Fazio and Domenico Mallamace

Int. J. Mol. Sci. 2019, 20(21), 5373; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20215373 - 29 Oct 2019

Cited by 1 | Viewed by 3091

Abstract

The hydrogen density of states (DOS) in confined water has been probed by inelastic neutron scattering spectra in a wide range of its P–T phase diagram. The liquid–liquid transition and the dynamical crossover from the fragile (super-Arrhenius) to strong (Arrhenius) glass [...] Read more.

The hydrogen density of states (DOS) in confined water has been probed by inelastic neutron scattering spectra in a wide range of its P–T phase diagram. The liquid–liquid transition and the dynamical crossover from the fragile (super-Arrhenius) to strong (Arrhenius) glass forming behavior have been studied, by taking into account the system polymorphism in both the liquid and amorphous solid phases. The interest is focused in the low energy region of the DOS (

E < 10

meV) and the data are discussed in terms of the energy landscape (local minima of the potential energy) approach. In this latest research, we consider a unit scale energy (EC) linked to the water local order governed by the hydrogen bonding (HB). All the measured spectra, scaled according to such energy, evidence a universal power law behavior with different exponents (

γ

) in the strong and fragile glass forming regions, respectively. In the first case, the DOS data obey the Debye squared-frequency law, whereas, in the second one, we obtain a value predicted in terms of the mode-coupling theory (MCT) (

γ ≃ 1.6

). Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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Review

Jump to: Research

29 pages, 1711 KiB

Open AccessReview

A Multi-Scale Study of Water Dynamics under Confinement, Exploiting Numerical Simulations in Relation to NMR Relaxometry, PGSE and NMR Micro-Imaging Experiments: An Application to the Clay/Water Interface

by Patrice Porion and Alfred Delville

Int. J. Mol. Sci. 2020, 21(13), 4697; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21134697 - 30 Jun 2020

Cited by 4 | Viewed by 2786

Abstract

Water mobility within the porous network of dense clay sediments was investigated over a broad dynamical range by using ²H nuclear magnetic resonance spectroscopy. Multi-quanta ²H NMR spectroscopy and relaxation measurements were first performed to identify the contributions of the various [...] Read more.

Water mobility within the porous network of dense clay sediments was investigated over a broad dynamical range by using ²H nuclear magnetic resonance spectroscopy. Multi-quanta ²H NMR spectroscopy and relaxation measurements were first performed to identify the contributions of the various relaxation mechanisms monitoring the time evolution of the nuclear magnetisation of the confined heavy water. Secondly, multi-quanta spin-locking NMR relaxation measurements were then performed over a broad frequency domain, probing the mobility of the confined water molecules on a time-scale varying between microseconds and milliseconds. Thirdly, ¹H NMR pulsed-gradient spin-echo attenuation experiments were performed to quantify water mobility on a time-scale limited by the NMR transverse relaxation time of the confined NMR probe, typically a few milliseconds. Fourthly, the long living quantum state of the magnetisation of quadrupolar nuclei was exploited to probe a two-time correlation function at a time-scale reaching one second. Finally, magnetic resonance imaging measurements allow probing the same dynamical process on time-scales varying between seconds and several hours. In that context, multi-scale modelling is required to interpret these NMR measurements and extract information on the influences of the structural properties of the porous network on the apparent mobility of the diffusing water molecules. That dual experimental and numerical approach appears generalizable to a large variety of porous networks, including zeolites, micelles and synthetic or biological membranes. Full article

(This article belongs to the Special Issue Molecular Structure and Dynamics Probed by Spectroscopic Techniques and Computational Approaches: New Trends by NMR, FTIR, Neutron Scattering and Simulation)

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