Intermolecular Structure Research Articles

Slow Phase Transition-Induced Scan Rate Dependence of Spin Crossover in a Two-Dimensional Supramolecular Fe(III) Complex

Slow Phase Transition-Induced Scan Rate Dependence of Spin Crossover in a Two-Dimensional Supramolecular Fe(III) Complex

Formation of amorphous and quasi-two-dimensional microcrystalline structures of CO2 in activated carbon pores at low temperatures

Carbon micropores are often used for CO2 capture and storage (CCS) applications. In this study, the intermolecular structure of CO2 molecules adsorbed inside activated carbon with different pore sizes was investigated through in situ X-ray scattering measurements, hybrid reverse Monte Carlo (HRMC), and grand canonical Monte Carlo (GCMC) simulations. Although most of the CO2 molecules in the micropores formed an amorphous structure, some formed a microcrystalline structure at certain pore sizes. To determine the structure and stability of this microcrystalline CO2 structure, a systematic structure analysis technique using computational methods was proposed. A plausible quasi-two-dimensional CO2 crystal structure that reproduced the experimental X-ray scattering results was obtained. The structure was found to be stable below 80 K. This microcrystalline structure, which was a characteristic arrangement formed with the assistance of the intrapore potential, was different from that of the bulk CO2 phases.

3D nanocomposite scaffold of TiO2-nanotube-incorporated carrageenan for wound healing

Three-dimensional (3D) nanocomposite scaffold is an important material for biomedical application owing to their compatibility and effectiveness compared with other types of nanocomposites. In this research, a unique 3D nanocomposite scaffold based on carrageenan biopolymer incorporating titanium dioxide (TiO2) nanotubes (TiO2NTs) was successfully developed. Fourier transform infrared spectroscopy and X-ray powder diffraction were employed to investigate the intermolecular interaction and phase structure of the fabricated 3D TiO2NT-incorporated carrageenan (TiO2NT/CG) nanocomposite scaffold. The ability of 3D TiO2NT/CG nanocomposite scaffold for wound healing was tested in vitro and in vivo. The in vitro study on 3T3 mouse fibroblast cells demonstrated that the number of cells increased up to 190 000 per well. Meanwhile, in vivo studies on Sprague Dawley rat exhibited that a 100% cure rate of wounds was observed after 14 days. These are attributed to the presence of ∼10 nm TiO2NTs that are homogeneously distributed onto the scaffold, as proven by scanning electron microscopy. The TiO2NTs promote wound healing by generating reactive oxygen species to induce the fibroblast growth factor and for the formation of a new extracellular matrix. The interconnected porous structure and rough surface of the 3D titanium dioxide/CG nanocomposite scaffold also support cell proliferation to expedite wound healing, thus offering a good candidate for wound-dressing application.

Intermolecular Dynamics and Structure in Aqueous Lidocaine Hydrochloride Solutions.

We investigated the intermolecular dynamics and static structure in the aqueous solutions of lidocaine hydrochloride (LDHCl) in the concentration range of [LDHCl] = 0-2.00 M using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES), small- and wide-angle X-ray scattering (SWAXS), and dynamic light scattering (DLS). For the fs-RIKES experiments, the concentration dependence of the difference low-frequency spectra of the aqueous LDHCl solutions relative to the neat water, which was mainly due to the intermolecular vibrations, was characterized using an exponential function with a characteristic concentration of ∼1 M. For the SWAXS experiments, we observed a manifestation of an excess scattering component centered within a range of 8-10 nm-1 in the aqueous LDHCl solutions. The results of Fourier inversion and further deconvolution analyses unambiguously demonstrated that lidocaines assemble into a nanometer-sized micelle-like structure with the innermost core (∼0.3 nm) and outer shell (∼0.5 nm), respectively. The DLS experiments also found nanometer-sized aggregates and further indicated evidence of the clusters of the aggregates. The results of viscosities, densities, and surface tensions of the solutions and the quantum chemistry calculations supported the unique features of the microscopic intermolecular interaction and the micelle-like aggregation.

Ion-Triggered Hydrogels Self-Assembled from Statistical Copolypeptides.

Statistical copolypeptides comprising lysine and tyrosine with unprecedented ion-induced gelation behavior are reported. Copolypeptides are obtained by one-step N-carboxyanhydride (NCA) ring-opening polymerization. The gelation mechanism is studied by in situ SAXS analyses, in addition to optical spectroscopy and transmission electron microscopy (TEM). It is found that the gelation of these statistically polymerized polypeptides is due to the formation of stable intermolecular β-sheet secondary structures induced by the presence of salt ions as well as the aggregation of an α-helix between the copolypeptides. This behavior is unique to the statistical lysine/tyrosine copolypeptides and was not observed in any other amino acid combination or arrangement. Furthermore, the diffusion and mechanical properties of these hydrogels can be tuned through tailoring the polypeptide chain length and ion strength.

The combined effect of humidity and electron beam irradiation on collagen type I - implications for collagen-based devices

Collagen is a biocompatible and bioresorbable material, an excellent active component for the formulation of medical dressings and scaffolds. Its current popularity and the developing methods of producing such medical materials imply the need for methods of controlling and processing collagen used in medicine. One of the basic methods used to sterilize medical devices is radiation sterilization. In this study, we undertook the determination of the influence of humidity, radiation sterilization, and the influence of these factors on the structure of collagen. Spectroscopic tests (EPR, DRS UV–VIS, FTIR), gas chromatography, and thermal methods (TGA, DSC) were used. Humidity appears to affect the amount, and especially the rate, of oxidative damage and the reorganization of oxygen addition products. Despite radiation damage observed by spectral methods, from the point of view of its thermal properties, collagen I remains stable upon irradiation within the dose range up to 50 kGy, probably due to its unique macromolecular and intermolecular structure, containing numerous crosslinks. The high thermal stability of collagen I in response to radiation gives good indications for radiation sterilization of collagen I based medical products. This is in agreement with the observed structural stability of radiation-sterilized collagen scaffolds used in skin wound healing. Nevertheless, oxidative modification was observed, which ultimately introduced new oxygen-containing functional groups in collagen. The result should be considered when designing and sterilizing collagen-based dressing materials and scaffolds.

Intermolecular rovibrational states of the H2O-CO2 and D2O-CO2 van der Waals complexes.

We present quantum five-dimensional bound-state calculations of the fully coupled intermolecular rovibrational states of H2O-CO2 and D2O-CO2 van der Waals (vdW) complexes in the rigid-monomer approximation for the total angular momentum J values of 0, 1, and 2. A rigid-monomer version of the recent ab initio full-dimensional (12D) potential energy surface of H2O-CO2 [Q. Wang and J. M. Bowman, J. Chem. Phys. 147, 161714 (2017)] is employed. This treatment provides for the first time a rigorous and comprehensive description of the intermolecular rovibrational level structure of the two isotopologues that includes the internal-rotation tunneling splittings and their considerable sensitivity to rotational and intermolecular vibrational excitations, as well as the rotational constants of the two vdW complexes. Two approaches are used in the calculations, which differ in the definition of the dimer-fixed (DF) frame and the coordinates associated with them. We demonstrate that with the approach introduced in this work, where the DF frame is fixed to the CO2 moiety, highly accurate results are obtained using significantly smaller basis sets in comparison to those for the alternative approach. In addition, the resulting wavefunctions tend to lend themselves better to physical interpretation and assignment. The H2O-CO2 ground-state internal-rotation tunneling splittings, the rotational transition frequencies, and the rotational constants of both vdW complexes are in excellent agreement with the experimental results. The calculated intermolecular vibrational fundamentals agree well with the scant terahertz spectroscopy data for these complexes in cryogenic neon matrices.

Intermolecular interactions and structure of R5L tau

Tau is a multifunctional protein, most known for its role in the formation and stabilization of microtubules. Its six naturally occurring isoforms differ in the presence or absence of repeat regions in the N-terminus projection domain and C-terminal microtubule-binding region. Irregular tau polymerization correlates highly with the extent and localization of neurodegeneration in frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Mutations in the gene encoding tau have been shown to alter affinity for microtubules as well as kinetics, extent, and morphology of tau aggregation, and the extent of these differences depend on the tau isoform.

Effect of Quadrupole of Nitrogen, as a Probe Molecule for Surface Area Estimation: XRD and HRMC Investigation

Abstract To obtain the properties of nanopores solids, N2 is usually used as probe molecule, however recently, IUPAC recommends using Ar instead. This study used experimental X-ray diffraction (XRD) analysis, Monte Carlo (MC), and hybrid reverse MC (HRMC) simulations to obtain information on the intermolecular structures of adsorbed N2 and Ar. Our results indicate that the quadrupole interaction between N2 molecules is relatively weak, and the N2 gives fairly good assessments as with Ar for porous carbons with low functional groups.

Ohmic vs. conventional heating: Influence of moderate electric fields on properties of egg white protein gels

The present study investigates properties of heat-induced, self-standing gels of globular proteins. Native egg white protein (EWP) with 9,8 wt% protein and 0,395 wt% NaCl content was adjusted to pH = 7,0 and heated from 25 to 85 °C via Ohmic heating (OH) and conventional heating (COV) with respective come-up times (CUT, 240 and 1200 s) and holding times (HOLD, 30 and 900 s). Gels heated under OH showed lower denaturation levels and less water holding capacity. When HOLD was short, the firmness of OH gels exceeded COV gel firmness but deceeded at long HOLD. Similarly, at short HOLD OH samples presented higher hydrophobic interactions whereas at long HOLD COV gels showed more hydrophobic interactions. This correlated with changes of intermolecular beta-sheet structures which increased with HOLD at COV but decreased or remained unchanged during OH. Furthermore, as an SDS-PAGE revealed the main EWP, ovalbumin, did not fully denature when heated via OH, this lead to the assumption that the oscillatory electric field partially interferes the complete denaturation and development of intermolecular beta-sheet structures and hydrophobic interactions during thermal gelation of this protein. Scanning electron microscopy also showed deviances in network structures between OH and COV as COV gels exhibited a denser and OH gels a more open and porous network structure.

Probing aqueous ions with non-local Auger relaxation.

Non-local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non-local autoionization, specifically Intermolecular Coulombic Decay (ICD), of a series of aqueous-phase isoelectronic cations following 1s core-level ionization. In particular, we focus on Na+, Mg2+, and Al3+ ions. We unambiguously identify the ICD contribution to the K-edge Auger spectrum. The different strength of the ion–water interactions is manifested by varying intensities of the respective signals: the ICD signal intensity is greatest for the Al3+ case, weaker for Mg2+, and absent for weakly-solvent-bound Na+. With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non-local decay processes. We assign the ICD signals to decay processes ending in two-hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core-hole-clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2+ and 34 fs for Al3+. Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra- and inter-molecular structure in the liquid phase, simultaneously providing both structural and electronic information.

Long-range DNA interactions: inter-molecular G-quadruplexes and their potential biological relevance.

Guanine-rich DNA sequences are known to fold into secondary structures called G-quadruplexes (G4s), which can form from either individual DNA strands (intra-molecular) or multiple DNA strands (inter-molecular, iG4s). Intra-molecular G4s have been the object of extensive biological investigation due to their enrichment in gene-promoters and telomers. On the other hand, iG4s have never been considered in biological contexts, as the interaction between distal sequences of DNA to form an iG4 in cells was always deemed as highly unlikely. In this feature article, we challenge this dogma by presenting our recent discovery of the first human protein (CSB) displaying astonishing picomolar affinity and binding selectivity for iG4s. These findings suggest potential for iG4 structures to form in cells and highlight the need of further studies to unravel the fundamental biological roles of these inter-molecular DNA structures. Furthermore, we discuss how the potential for formation of iG4s in neuronal cells, triggered by repeat expansions in the C9orf72 gene, can lead to the formation of nucleic-acids based pathological aggregates in neurodegenerative diseases like ALS and FTD. Finally, based on our recent work on short LNA-modified probes, we provide a prespective on how the rational design of G4-selective chemical tools can be leveraged to further elucidate the biological relevance of iG4 structures in the context of ageing-related diseases.

Realizing Ultrahigh Energy Density in Polymer Dielectric Film by Intermolecular Structure Design

Realizing Ultrahigh Energy Density in Polymer Dielectric Film by Intermolecular Structure Design

Preparation of nanocellulose from cotton fibers in deep eutectic solvent (DES) and its application in paper

The bond strength and stability of the intermolecular network structure of cellulose play a decisive role in the tensile strength and rupture resistance of paper. In this work, the surface morphology, the chemical composition, and the crystal structure of nanocellulose prepared from cotton fibers were characterized by scanning electron microscopy (SEM) analysis, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) to prepare cotton fiber nanocellulose by green solvent deep-eutectic solvent pretreatment combined with the ultrasonic method. Nanocellulose of different morphology and structure was used as a papermaking additive to explore its effect on the strength performance of the paper. The results show that the burst resistance index of the paper handsheets could be increased by 6.1% and 9.8%. The burst resistance index improved as the added amount of the NFC was increased.

Cockayne Syndrome B Protein Selectively Resolves and Interact with Intermolecular DNA G-Quadruplex Structures.

Guanine-rich DNA can fold into secondary structures known as G-quadruplexes (G4s). G4s can form from a single DNA strand (intramolecular) or from multiple DNA strands (intermolecular), but studies on their biological functions have been often limited to intramolecular G4s, owing to the low probability of intermolecular G4s to form within genomic DNA. Herein, we report the first example of an endogenous protein, Cockayne Syndrome B (CSB), that can bind selectively with picomolar affinity toward intermolecular G4s formed within rDNA while displaying negligible binding toward intramolecular structures. We observed that CSB can selectively resolve intermolecular over intramolecular G4s, demonstrating that its selectivity toward intermolecular structures is also reflected at the resolvase level. Immunostaining of G4s with the antibody BG4 in CSB-impaired cells (CS1AN) revealed that G4-staining in the nucleolus of these cells can be abrogated by transfection of viable CSB, suggesting that intermolecular G4s can be formed within rDNA and act as binding substrate for CSB. Given that loss of function of CSB elicits premature aging phenotypes, our findings indicate that the interaction between CSB and intermolecular G4s in rDNA could be of relevance to maintain cellular homeostasis.

Investigation of polar crystalline materials containing hydrochlorothiazide: electron density distribution and optical properties

The polar hydrochlorothiazide polymorph (I) (systematic name: 6-chloro-1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide, C7H8ClN3O4S2) and, recently designed by us, the polar 2-aminopyridine hydrochlorothiazide water <1/1/1> (C7H8ClN3O4S2·C5H6N2·H2O), (II), have been investigated. The crystal structures of both materials were determined using the single-crystal X-ray diffraction technique. The intermolecular interactions in (I) and (II) were studied in detail via topological electron-density analysis. The obtained results showed hydrogen bonds with a character intermediate between closed-shell and shared-shell in both crystal structures. The most important hydrogen bonds in (I) are formed between sulfonamide groups, whereas in (II), water molecules play a crucial role as they interconnect 2-aminopyridine and hydrochlorothiazide molecules. Calculations of the optical properties revealed that both materials exhibit large linear birefringence, twice that of calcite. The theoretically predicted second harmonic generation efficiency is four times and five times larger than that of KH2PO4 for (I) and (II), respectively. The information gathered on intermolecular interactions and structure–property correlations was used to identify the best strategies for the future design of new functional materials of this kind.

Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA

During the origin of life, encapsulation of RNA inside vesicles is believed to have been a defining feature of the earliest cells (protocells). The confined biophysical environment provided by membrane encapsulation differs from that of bulk solution and has been shown to increase activity as well as evolutionary rate for functional RNA. However, the structural basis of the effect on RNA has not been clear. Here, we studied how encapsulation of the hairpin ribozyme inside model protocells affects ribozyme kinetics, ribozyme folding into the active conformation, and cleavage and ligation activities. We further examined the effect of encapsulation on the folding of a stem-loop RNA structure and on the formation of a triplex structure in a pH-sensitive DNA switch. The results indicate that encapsulation promotes RNA-RNA association, both intermolecular and intramolecular, and also stabilizes tertiary folding, including the docked conformation characteristic of the active hairpin ribozyme and the triplex structure. The effects of encapsulation were sufficient to rescue the activity of folding-deficient mutants of the hairpin ribozyme. Stabilization of multiple modes of nucleic acid folding and interaction thus enhanced the activity of encapsulated nucleic acids. Increased association between RNA molecules may facilitate the formation of more complex structures and cooperative interactions. These effects could promote the emergence of biological functions in an "RNA world" and may have utility in the construction of minimal synthetic cells.

Tunable aggregation-induced emission, solid-state fluorescence, and mechanochromic behaviors of tetraphenylethene-based luminophores by slight modulation of substituent structure

Herein, we report the synthesis of two AIE-active tetraphenylethene-derived luminogens with diethylamino (TPEDA) or pyrrolidino group (TPEPL) as terminal substituents, and systematically investigate the influence of diethylamino and pyrrolidino groups as terminal substituents on their photophysical properties and mechanochromic behavior. Single-crystal structural analyses verified that the free alkyl chains of the diethylamino groups were beneficial to loosen the intermolecular stacking. They exhibited distinct luminescence behaviors in the aggregated state. Compared with TPEDA, TPEPL displayed a long-wavelength solid-state fluorescence due to the more extended π-conjugation system across its intermolecular packing structure. However, TPEDA exhibited mechanochromic behavior that manifested in a larger red-shift (25 ​nm), which was attributed to its looser stacking mode. The work not only presents a better understanding of structure-property relationship, but also offers a new method for modulating intermolecular stacking and developing mechanochromic materials.

FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice.

Studying aging is important to further understand the molecular mechanisms underlying this physiological process and, ideally, to identify a panel of aging biomarkers. Animals, in particular mice, are often used in aging studies, since they mimic important features of human aging, age quickly, and are easy to manipulate. The present work describes the use of Fourier Transform Infrared (FTIR) spectroscopy to identify an age-related spectroscopic profile of the cardiac and skeletal muscle tissues of C57BL/6J female mice. We acquired ATR-FTIR spectra of cardiac and skeletal muscle at four different ages: 6; 12; 17 and 24 months (10 samples at each age) and analyzed the data using multivariate statistical tools (PCA and PLS) and peak intensity analyses. The results suggest deep changes in protein secondary structure in 24-month-old mice compared to both tissues in 6-month-old mice. Oligomeric structures decreased with age in both tissues, while intermolecular β-sheet structures increased with aging in cardiac muscle but not in skeletal muscle. Despite FTIR spectroscopy being unable to identify the proteins responsible for these conformational changes, this study gives insights into the potential of FTIR to monitor the aging process and identify an age-specific spectroscopic signature.

Structure, chain dynamics and mechanical properties of poly(vinyl alcohol)/phytic acid composites

The global micro- and nano-plastic issue has greatly triggered the development of advanced biodegradable polymeric materials. The creation of biodegradable polyvinyl alcohol (PVA)/phytic acid (PhyAc) composite represents a sustainable solution. However, it remains unclear how PhyAc molecules affect intermolecular hydrogen-bonding (H-bonding), structure, chain dynamics and mechanical properties of PVA so far. Herein, we explore structure, chain dynamics and mechanical properties of PVA/PhyAc composite by combining molecular dynamics simulation and experimental. The number of PVA-PhyAc H-bonds per PhyAc molecule and that of total H-bonds show different PhyAc content dependence. The PVA composite with 1.9 wt% of PhyAc shows a lower free volume and a smaller diffusion coefficient. Meanwhile, the glass transition temperature (Tg) of PVA reaches the maximum value at ca. 1.25 wt% of PhyAc. Interestingly, 10 wt% PhyAc endows PVA with the highest tensile strength in addition to a good antibacterial capability. This work reveals how small molecules affect structure and mechanical properties of polymers and contributes to expanding practical applications of PVA/PhyAc in industry.