Intermolecular Structure Research Articles

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.

Tailoring flexibility and dispersity of thermoplastic starch gel by controlling intermolecular structure for improving folding endurance of polylactide

• A biobased starch gel with high thermoplasticity was fabricated via reactive extrusion. • For the first time, we characterized and defined this thermoplastic starch as gel, instead of plastic. • A novel “Soft-Hard” structure provided by tartaric acid endowed TGTPS gel with better flexibility. • TGTPS-1 gel acted as micro/nano-meter toughener and motivated PLA to achieve outstanding folding endurance. Polysaccharide-based gels are green, non-toxic, and sustainable materials with a high absorption capability, which make them suitable for numerous applications. In this study, a novel starch-based thermoplastic gel (TGTPS gel) was facilely fabricated via reactive extrusion with glycerol, starch and tartaric acid. The TGTPS gels exhibited tremendous increase of flexibility and processability, which was attributed to the fact that TA molecules could facilitate hydrolysis of starch chains and enhance gel network slippage as evident from gel permeation chromatography and stress-relaxation measurement. Moreover, combining dynamic mechanical analysis and rheological behavior, we found that a special Soft-Hard Segments structure, varied with the fluctuation of tartaric acid (TA) concentration, was developed between TA molecules, glycerol and starch chains. Additionally, TGTPS gels with 1% TA content (TGTPS-1) could also serve as micro/nano-meter toughener, and motivate PLA to achieve outstanding folding endurance. The double folding resistance was performed on PLA/TGTPS-1 blend, and folding cycle time was improved from 1 time of PLA to over 2000 times of PLA/TGTPS-1 (80/20) blends. Overall, this novel TGTPS gels could be promising alternative to petroleum-based polymers and play a great potential in engineering applications.

Hydrophilization of magnetic nanoparticles with an amphiphilic polymer revisited: Roles of nanoparticle capping density and polymer structure

Amphiphilic comb polymers, like poly(maleic anhydride-alt-1-octadecene) (PMAO), are frequently used to transfer hydrophobic magnetic nanoparticles (NPs) into aqueous media. While it is accepted that the hydrophilization is based on the interdigitation of the hydrocarbon chains from the polymer and the NP capping, the factors that determine the success of such process are still not fully understood. In this paper, some key aspects of the formation of water-soluble NP-PMAO assemblies from oleate-capped iron oxide NPs, not considered in previous works, are discussed thoroughly. We have found that the process is notably hindered when the chemisorbed oleates coverage decreases from 2.9 to 1.5 molecules/nm2, revealing the importance of the capping packing density in the assembly mechanism. Combined results from small-angle x-ray scattering and electron microscopy show that, for polymer concentrations ranging from 10 to 200 monomer units/nm2, the NPs are individually covered by polymer chains, although forming rather planar NP-PMAO assemblies which contain several NPs. Both the minimum polymer concentration needed for a successful hydrophilization (0.7 gPMAO/L) and the geometry of the assemblies suggest that intermolecular structures typical of comb polymers act as templates in the assembly process. Finally, we show that the magnetic properties are modulated by the polymer loading.

The Intermolecular NOE Depends on Isotope Selection: Short Range vs Long Range Behavior.

The nuclear Overhauser effect (NOE) is a powerful tool in molecular structure elucidation, combining the subtle chemical shift of NMR and three-dimensional information independent of chemical connectivity. Its usage for intermolecular studies, however, is fundamentally limited by an unspecific long-ranged interaction behavior. This joint experimental and computational work shows that proper selection of interacting isotopes can overcome these limitations: Isotopes with strongly differing gyromagnetic ratios give rise to short-ranged intermolecular NOEs. In this light, existing NOE experiments need to be re-evaluated and future ones can be designed accordingly. Thus, a new chapter on intermolecular structure elucidation is opened.

Intermolecular hydrogen bond ruptured by graphite with different lamellar number.

Intermolecular hydrogen bonds are formed through the electrostatic attraction between the hydrogen nucleus on a strong polar bond and high electronegative atom with an unshared pair of electrons and a partial negative charge. It affects the physical and chemical properties of substances. Based on this, we presented a physical method to modulate intermolecular hydrogen bonds for not changing the physical–chemical properties of materials. The graphite and graphene are added into the glycerol, respectively, by being used as a viscosity reducer in this paper. The samples are characterized by Raman and 1H-nuclear magnetic resonance. Results show that intermolecular hydrogen bonds are adjusted by graphite or graphene. The rheology of glycerol is reduced to varying degrees. Transmission electron microscopes and computer simulation show that the spatial limiting action of graphite or graphene is the main cause of breaking the intermolecular hydrogen bond network structure. We hope this work reveals the potential interplay between nanomaterials and hydroxyl liquids, which will contribute to the field of solid–liquid coupling lubrication.

Conformations, inter-molecular structure and hydrogen bond dynamics of neutral and cationic poly(vinyl amine) in aqueous solution

ABSTRACT Intermolecular structure, hydration and conformations of Poly(vinylamine) (PVAm) in neutral as well as protonated (cationic) condition as polyelectrolyte in dilute aqueous solution, were studied via single-chain atomistic molecular dynamics simulations in explicit solvent. A parametric study of atomic partial charges was carried out at different values of degree-of-ionisation (f) of the amine group. A modification of generic GROMOS force-field is developed. The unusual non-monotonic behaviour of radius-of-gyration with an increase in f is captured, in agreement with experimental results of intrinsic viscosity. Cooperative solvation of PVAm chain occurs with an increase in f as assisted by counter-ion condensation. Three different regimes of the variation of radius-of-gyration of PVAm with change in f are identified. Changes in polymer-water hydrogen bonding is not the dominant effect for the behaviour of chain-size variation. The non-monotonous expansion of PVAm is attributed to the complex interplay between hydrogen bonding and intermolecular structure of polymer chain, water and counter-ions, all of which provide a cooperative solvation of the chain. With an increase in f at the higher range, the formation of ion pairs produces salt-bridges and bends in the chain, as well as ion-pair–ion-pair repulsion extending the chain at complete ionisation.

Enhanced water transport through short nanochannels by regulating the direction of hydrostatic pressure

Molecular dynamics simulations are carried out to study the transport properties of water molecules across 1.34 nm long single-walled carbon nanotubes (SWCNTs) under hydrostatic pressure with different directions. It is found that when the deflection angle φ between the hydrostatic pressure and the tube-axis direction changes from 0° to 90°, the net flux shows significant differences. It is interesting to note that the maximum flux is counter-intuitively obtained at φ=45°, which is about three times that of at φ=0°. This enhancement is mainly attributed to the excellent intermolecular structure, the orientation distribution, and the filling rate of in-tube water at φ=45°. Yet, it is worth noting that with the increase of the length of the SWCNT, the anomalous effect will gradually weaken until it almost disappears. Our work is of great significance for the practical application of high-efficiency nanofiltration membranes under pressure gradients.