Molecular Structure Determination Research Articles

Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements.

The Turnpike problem aims to reconstruct a set of one-dimensional points from their unordered pairwise distances. Turnpike arises in biological applications such as molecular structure determination, genomic sequencing, tandem mass spectrometry, and molecular error-correcting codes. Under noisy observation of the distances, the Turnpike problem is NP-hard and can take exponential time and space to solve when using traditional algorithms. To address this, we reframe the noisy Turnpike problem through the lens of optimization, seeking to simultaneously find the unknown point set and a permutation that maximizes similarity to the input distances. Our core contribution is a suite of algorithms that robustly solve this new objective. This includes a bilevel optimization framework that can efficiently solve Turnpike instances with up to 100,000 points. We show that this framework can be extended to scenarios with domain-specific constraints that include duplicated, missing, and partially labeled distances. Using these, we also extend our algorithms to work for points distributed on a circle (the Beltway problem). For small-scale applications that require global optimality, we formulate an integer linear program (ILP) that (i) accepts an objective from a generic family of convex functions and (ii) uses an extended formulation to reduce the number of binary variables. On synthetic and real partial digest data, our bilevel algorithms achieved state-of-the-art scalability across challenging scenarios with performance that matches or exceeds competing baselines. On small-scale instances, our ILP efficiently recovered ground-truth assignments and produced reconstructions that match or exceed our alternating algorithms. Our implementations are available at https://github.com/Kingsford-Group/turnpikesolvermm.

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique "fingerprint" of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. We demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach.

In NMR experiments, residual dipolar couplings (RDCs) in a molecule can be measured by averaging the dipolar couplings (DCs) over the rotational motion of a molecule in an environment that induces a slight anisotropic orientation distribution of the molecule. Since the shape of the anisotropic distribution cannot be measured, it is standard practice to use a particular orientation distribution of the molecule with respect to the magnetic field, in the form of a so-called alignment tensor (AT), to calculate RDC-values for the molecule. Since the same alignment tensor is commonly used to calculate the different RDCs of a molecule, this approach rests on the assumption that the rotational motion of the molecule is decoupled from its internal motions and that the molecule is rigid. The validity of these two assumptions is investigated for a small, simple molecule, using a relatively rigid atomic interaction function or force field and a more flexible one. By simulating the molecule using an orientation-biasing force an anisotropic rotational distribution can be generated, for which RDCs can be obtained. Using these RDCs as target RDCs when applying one of the two approaches of structure refinement based on RDCs, it can be investigated how well the target RDCs are approximated in the RDC restraining and whether the corresponding nonuniform orientation distribution is reproduced. For the relatively rigid version of the molecule, the AT approach reproduces the target RDC-values, although the nonuniform orientation distribution of the angle θab,H between the vector r⃗ab connecting two atoms a and b in the molecule and the vector representing the direction of the magnetic field H⃗ as generated in the orientation-biasing simulation cannot be reproduced in the AT RDC-restraining simulation. For the relatively flexible version of the molecule, the AT approach fails to reproduce both the target RDC values and the nonuniform orientation distribution. For biomolecules with flexible parts, the application of the AT approach is thus not recommended. Instead, a method based on sampling of the rotational and internal degrees of freedom of the molecule should be applied in molecular structure determination or refinement based on measured RDCs.

Benzothiazole-derived Compound with Antitumor Activıiy: Molecular Structure Determination Using Density Functional Theory (Dft) Method

The Gaussian computational chemistry software package was employed to investigate the molecular structure and energetics of benzothiazole, a compound known for its anti-tumor properties. Density functional theory (DFT) calculations were conducted using the Becke, 3-parameter, Lee-Yang-Parr (B3LYP) method, coupled with the LanL2DZ basis set. Molecular structure optimization was carried out to determine the most stable configurations of the benzothiazole compound. Furthermore, thorough analyses of molecular orbital energies, molecular properties, and molecular electrostatic potential surface maps were performed on the optimized molecular system. Our current research suggests that the compound 2-(4-aminophenyl) benzothiazole, containing benzothiazole, maybe a potential drug candidate for free radical species on cells due to its anti-cancer properties.

Improved detection of magnetic interactions in proteins based on long-lived coherences

Living systems rely on molecular building blocks with low structural symmetry. Therefore, constituent amino acids and nucleotides yield short-lived nuclear magnetic responses to electromagnetic radiation. Magnetic signals are at the basis of molecular imaging, structure determination and interaction studies. In solution state, as the molecular weight of analytes increases, coherences with long lifetimes are needed to yield advantageous through-space magnetisation transfers. Interactions between magnetic nuclei can only be detected provided the lifetimes of spin order are sufficient. In J-coupled pairs of nuclei, long-lived coherences (LLC’s) connect states with different spin-permutation symmetry. Here in, we show sustained LLC’s in protein Lysozyme, weighing 14.3 kDa, with lifetimes twice as long as those of classical magnetisation for the aliphatic protons of glycine residues. We found for the first time that, in a protein of significant molecular weight, LLC’s yield substantial through-space magnetisation transfers: spin-order transfer stemming from LLC’s overcame transfers from classical coherences by factors > 2. Furthermore, in agreement with theory, the permutation symmetry of LLC-based transfers allows mapping interacting atoms in the protein structure with respect to the molecular plane of glycine residues in a stereospecific manner. These findings can extend the scope of liquid-state high-resolution biomolecular spectroscopy.

Benchmarking Guanidinium Organosulfonate Hydrogen-Bonded Frameworks for Structure Determination of Encapsulated Guests.

Single crystal X-ray diffraction (SCXRD) is arguably the most definitive method for molecular structure determination, but it is often challenged by compounds that are liquids or oils at room temperature or do not form crystals adequate for analysis. Our laboratory previously reported a simple, cost-effective, single-step crystallization method based on guanidinium organosulfonate (GS) hydrogen bonded frameworks for structure determination of a wide range of encapsulated guest molecules, including assignment of the absolute configuration of chiral centers. Herein, we expand on those results and report a head-to-head comparison of the GS method with adamantoid "molecular chaperones", which have been reported to be useful hosts for structure determination. Inclusion compounds limited to only two GS hosts are characterized by low R1 values and Flack parameters, infrequent disorder of the host and guest, and manageable disorder when it does exist. The structures of some target molecules that were not included or resolved using the adamantoid chaperones were successfully included and resolved by the GS hosts, and vice versa. Of the 32 guests attempted by the GS method, 31 inclusion compounds afforded successful guest structure solutions, a 97% success rate. The GS hosts and adamantoid chaperones are complementary with respect to guest inclusion, arguing that both should be employed in the arsenal of methods for structure determination. Furthermore, the low cost of organosulfonate host components promises an accessible route to molecular structure determination for a wide range of users.

Application of Laser-Induced Acoustic Desorption for Molecular Rotational Resonance Spectroscopy.

Molecular Rotational Resonance (MRR) spectroscopy is a uniquely precise tool for the determination of molecular structures of volatile compounds in mixtures, as the characteristic rotational transition frequencies of a molecule are extremely sensitive to its 3D structure through the moments of inertia in a three-dimensional coordinate system. This enables identification of the compounds based on just a few parameters that can be calculated, as opposed to, for example, mass spectrometric data, which often require expert analysis of 10-20 different signals and the use of many standards/model compounds. This paper introduces a new sampling technique for MRR, laser-induced acoustic desorption (LIAD), to allow the vaporization of nonvolatile and thermally labile analytes without the need for excessive heating or derivatization. In this proof-of-concept study, LIAD was successfully coupled to an MRR instrument to conduct measurements on seven compounds with differing polarities, molecular weights, and melting and boiling points. Identification of three isomers in a mixture was also successfully performed using LIAD/MRR. Based on these results, LIAD/MRR is demonstrated to provide a powerful approach for the identification of nonvolatile and/or thermally labile analytes with molecular weights up to 600 Da in simple mixtures, which does not require the use of reference compounds. In the future, applications to more complex mixtures, such as those relevant to pharmaceutical research, and quantitative aspects of LIAD/MRR will be reported.

On the performance of composite schemes in determining equilibrium molecular structures.

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, the performance of two different ab initio composite approaches for obtaining equilibrium structures, "energy scheme" and "geometry scheme," is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

Lanthanide Amide Complexes Supported by the Bis‐tris(pyrazolyl)borate Ligand Environment

AbstractSynthesis of primary lanthanide amides in the bis‐hydrotris(1‐pyrazolyl)borate ligand environment has been achieved. Salt metathesis of [Dy(Tp)2(OTf)] 1‐Dy (OTf=CF3SO3) with K(N′′) (N′′=N(SiMe3)2) in toluene yielded the [bis(silyl)]amide [Dy(Tp)2(N′′)] 2‐Dy. Complexes 1‐Ln and 2‐Ln were both used to access primary lanthanide amides, where either metathesis of 1‐Ln with K(NHArCF3) (ArCF3=C6H3(CF3)2‐3,5) or protonolysis of 2‐Ln with H2NArCF3 in toluene yielded [Ln(Tp)2(NHArCF3)] 3‐Ln (Ln=Y, Dy). The synthesis of parent amides was also attempted, but the metathesis of 1‐Y with NaNH2 yielded complicated reaction mixtures, but from which the dimeric parent amide [{Y(Tp)2(μ‐NH2)}2] 4‐Y and an ‘ate’‐salt [{Y(Tp)2(μ2‐OTf)(μ3‐OTf)Na(THF)2}2] 5‐Y were isolated. Full characterisation data are presented for all complexes, including the structure determination.

Molecular Gas-Phase Conformational Ensembles.

Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.

Activation and functionalisation of carbon dioxide by bis-tris(pyrazolyl)borate-supported divalent samarium and trivalent lanthanide silylamide complexes.

Synthesis and reactivity with carbon dioxide (CO2) of divalent samarium in the bis-tris(pyrazolyl)borate ligand environment has been reported. In addition, CO2 activation and functionalisation by lanthanide silylamides in the bis-tris(pyrazolyl)borate ligand environment was demonstrated. Reduction of the Sm(III) precursor [Sm(Tp)2(OTf)] (Tp = hydrotris(1-pyrazolyl)borate; OTf = triflate) with KC8 yielded the insoluble Sm(II) multi-metallic coordination polymer [{Sm(Tp)2}n] 1-Sm. Addition of 1,2-dimethoxyethane (DME) to 1-Sm enabled isolation of the monomeric complex [Sm(Tp)2(DME)] 1-Sm(DME). Complex 1-Sm(DME) reduced CO2 to yield the oxalate-bridged dimeric Sm(III) complex [{Sm(Tp)2}2(μ-η2:η2-O2CCO2)] 2-Sm. The reactions of heteroleptic Ln(III) silylamide complexes [Ln(Tp)2(N'')] (Ln = Y, Sm; N'' = N(SiMe3)2) with CO2 yielded monomeric Ln(III) silyloxides [Ln(Tp)2(OSiMe3)] 3-Ln and trimethylsilyl isocyanate (OCNSiMe3). Complexes 3-Ln are the first crystallographically characterised examples of Ln(III)-OSiMe3 bonds accessed via CO2 activation and functionalisation. Full characterisation data are presented for all complexes, including solid-state molecular structure determination by single-crystal X-ray diffraction.

Insights into isotherms, kinetics, and thermodynamics of adsorption of acid blue 113 from an aqueous solution of nutraceutical industrial fennel seed spent

Research studies have been carried out to accentuate Fennel Seed Spent, a by-product of the Nutraceutical Industry, as an inexpensive, recyclable and operational biosorbent for bioremediation of Acid Blue 113 (AB113) in simulated water-dye samples and textile industrial effluent (TIE). The physical process of adhesion of AB113 on the surface of the biosorbent depends on various parameters, such as the initial amount of the dye, amount and expanse of the biosorbent particles, pH of the solution and temperature of the medium. The data obtained was analyzed using three two-parameter and five three-parameter adsorption isotherm models to glean the adsorbent affinities and interaction mechanism of the adsorbate molecules and adsorbent surface. The adsorption feature study is conducted employing models of Weber-Morris, pseudo 1st and 2nd order, diffusion film model, Dumwald-Wagner and Avrami model. The study through 2nd order pseudo and Avrami models produced complementary results for the authentication of experimental data. The thermodynamic features, ΔG0, ΔH0, and ΔS0 of the adsorption process are acclaimed to be almost spontaneous, physical in nature and endothermic in their manifestation. Surface characterization was carried out using Scanner Electron Microscopy, and identification and determination of chemical species and molecular structure was performed using Infrared Spectroscopy (IR). Maximum adsorption evaluated using statistical optimization with different combinations of five independent variables to study the individual as well as combined effects by Fractional Factorial Experimental Design (FFED) was 236.18 mg g−1 under optimized conditions; pH of 2, adsorbent dosage of 0.500 g L−1, and an initial dye concentration of 209.47 mg L−1 for an adsorption time of 126.62 min with orbital shaking of 165 rpm at temperature 49.95 °C.

Structure determination by cryoEM at 100 keV.

Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.

Molecular structure determination of Nickel(II) isomers bearing bis(thiosemicarbazone) ligands: X-ray, DFT calculations and kinetic groundwork

The formation of isomers can be stimulated by many factors and their properties are often used in the development of new catalysts, optical devices and drugs. Herein, reactions between benzyl-bis(thiosemicarbazones) ligands, so called H2LR (R = Me or Et), were investigated with different NiII starting materials and conditions, affording solids with divergent colors. They were characterized by elemental analysis, FTIR, UV–Vis and 1H NMR spectroscopies, as well as cyclic voltammetry, which revealed distinct products from the respective NiII starting precursors. However, the ESI(+)-MS the products of each ligand presented almost identical m/z patterns, independently from their precursors. Remarkably, the structures of both products were determined by single-crystal X-ray diffraction, showing the formation of two isomers of the type NiIIN2S2, coordinated symmetrically (5–5–5 membered chelate rings) when NiCl2·6H2O or Ni(Ac)2·4H2O were used as precursors or asymmetrically (4–6–5 membered chelate rings) upon reaction with [Ni(acac)2]. Theoretical calculations by DFT were also accomplished to explain the electronic spectra of the two products and to calculate the thermodynamic parameters related to the stability of the two isomers. Finally, a kinetic study was performed to investigate the formation of the asymmetrical and the symmetrical complexes.

Nitro and 4,4′-flourobenzhydryl functionalized bis(imino)pyridine-cobalt complexes for high molecular weight linear polyethylenes

A series of nitro and 4,4′-fluorobenzhydryl functionalized bis(imino)pyridine-cobalt complexes, [2-{(2,6-iPr2-3-NO2-4-((4-F-Ph)2CH)Ph)N=CMe}-6-{(Ar)N=CMe}C5H5N]CoCl2 (where Ar is 2,6-Me2Ph for Co1; 2,6-Et2Ph for Co2; 2,6-iPr2Ph for Co3; 2,4,6-Me3Ph for Co4; 2,6-Et2-4-Me-Ph for Co5; 2,6-iPr2-3-NO2-4-((4-F-Ph)2CH)Ph for Co6) were prepared and investigated for ethylene polymerization. The resultant compounds were characterized by elemental analysis, 1H/13C NMR and FT-IR spectra. The molecular structure determination revealed a distorted square pyramidal geometry for Co3. All prepared complexes demonstrated high catalytic activity for ethylene polymerization (up to 10.7 × 106 g PE (mol of Co)−1 h−1) and produced high-molecular-weight polyethylenes in the level of 105 g mol−1. Structural variations in the catalyst design revealed that the unsymmetrical complexes with sterically less hindrand substituents exhibited comparatively higher polymerization activity, while sterically encumbered symmetrical complexes proved more efficient in enhancing the molecular weight of resultant polyethylenes. Additionally, high-temperature 1H/13C NMR spectra of the produced polyethylenes confirmed their strictly linear microstructure, which is also evident from their high melting temperature (Tm ∼135 °C).

Biphasic NMR of Hyperpolarized Suspensions-Real-Time Monitoring of Solute-to-Solid Conversion to Watch Materials Grow.

Nuclear magnetic resonance (NMR) spectroscopy is a key method for the determination of molecular structures. Due to its intrinsically high (i.e., atomistic) resolution and versatility, it has found numerous applications for investigating gases, liquids, and solids. However, liquid-state NMR has found little application for suspensions of solid particles as the resonances of such systems are excessively broadened, typically beyond the detection threshold. Herein, we propose a route to overcoming this critical limitation by enhancing the signals of particle suspensions by >3.000-fold using dissolution dynamic nuclear polarization (d-DNP) coupled with rapid solid precipitation. For the proof-of-concept series of experiments, we employed calcium phosphate (CaP) as a model system. By d-DNP, we boosted the signals of phosphate 31P spins before rapid CaP precipitation inside the NMR spectrometer, leading to the inclusion of the hyperpolarized phosphate into CaP-nucleated solid particles within milliseconds. With our approach, within only 1 s of acquisition time, we obtained spectra of biphasic systems, i.e., micrometer-sized dilute solid CaP particles coexisting with their solution-state precursors. Thus, this work is a step toward real-time characterization of the solid-solution equilibrium. Finally, integrating the hyperpolarized data with molecular dynamics simulations and electron microscopy enabled us to shed light on the CaP formation mechanism in atomistic detail.

Metal Binding of Alzheimer's Amyloid-β and Its Effect on Peptide Self-Assembly.

ConspectusMetal ions have been identified as key factors modulating the aggregation of amyloid-β peptide (Aβ) implicated in Alzheimer's disease (AD). The presence of elevated levels of metal ions in the amyloid plaques in AD patients supports the notion that the dysfunction of metal homeostasis is connected to the development of AD pathology. Here, recent findings from high- and low-resolution biophysical techniques are put into perspective, providing detailed insights into the molecular structures and dynamics of metal-bound Aβ complexes and the effect of metal ions on the Aβ aggregation process. In particular, the development of theoretical kinetic models deducing different microscopic nucleation events from the macroscopic aggregation behavior has enabled deciphering of the effect of metal ions on specific nucleation processes. In addition to these macroscopic measurements of bulk aggregation to quantify microscopic rates, recent NMR studies have revealed details about the structures and dynamics of metal-Aβ complexes, thereby linking structural events to bulk aggregation. Interestingly, transition-metal ions, such as copper, zinc, and silver ions, form a compact complex with the N-terminal part of monomeric Aβ, respectively, where the metal-bound "folded" state is in dynamic equilibrium with an "unfolded" state. The rates and thermodynamic features of these exchange dynamics have been determined by using NMR relaxation dispersion experiments. Additionally, the application of specifically tailored paramagnetic NMR experiments on the Cu(II)-Aβ complex has been fruitful in obtaining structural constraints within the blind sphere of conventional NMR experiments. This enables the determination of molecular structures of the "folded" Cu(II)-coordinated N-terminal region of Aβ. Furthermore, the discussed transition-metal ions modulate Aβ self-assembly in a concentration-dependent manner, where low metal ion concentrations inhibit Aβ fibril formation, while at high metal ion concentrations other processes occur, resulting in amorphous aggregate formation. Remarkably, the metal-Aβ interaction predominately reduces one specific nucleation step, the fibril-end elongation, whereas primary and surface-catalyzed secondary nucleation mechanisms are less affected. Specific inhibition of fibril-end elongation theoretically predicts an enhanced generation of Aβ oligomers, which is an interesting contribution to understanding metal-Aβ-associated neurotoxic effects. Taken together, the metal binding process creates a metal-bound Aβ complex, which is seemingly inert to aggregation. This process hence efficiently reduces the aggregation-prone peptide pool, which on the macroscopic level is reflected as slower aggregation kinetics. Thus, the specific binding of metals to the Aβ monomer can be linked to the macroscopic inhibitory effect on Aβ bulk aggregation, providing a molecular understanding of the Aβ aggregation mechanism in the presence of metal ions, where the metal ion can be seen as a minimalist agent against Aβ self-assembly. These insights can help to target Aβ aggregation in vivo, where metal ions are key factors modulating the Aβ self-assembly and Aβ-associated neurotoxicity.

Seven Nuclei Cluster of Copper: Synthesis, Structure and Assembly

AbstractThe determination of molecular and assembly structure of small clusters is a key step toward understanding the complicated nanostructures or even bulk materials. We report herein the synthesis, molecular structure, and assembly structure of novel copper clusters with seven nuclei. The clusters, with the total molecular formula of [Cu7Cl6(PPh3)7]+, has been obtained by (PPh3)2CuBH4‐mediated reduction of CuCl2 in one pot. Molecular structure of the clusters has been determined by X‐ray single crystal analysis, revealing a Cu7Cl6 metal core protected by phosphine ligands. Interestingly, the clusters are assembled as dimers in the unit cell, in which the cluster interacts with each other via π⋅⋅π interaction from the phenyl groups of the phosphine ligands. This work not only provides an atomically precise copper cluster that may find applications in future, but also reveals the assembly structure of the cluster at the atomic level thus shedding light on the structural dedication of larger nanostructures.

Hydrogen-bonded frameworks for molecular structure determination

Hydrogen-bonded frameworks for molecular structure determination

Improving protein crystal quality using deep eutectic solvents

Protein crystallization is an essentially important process for its valuable applications in molecular structure determination of proteins, the study of biomolecular interaction mechanism, research and development of special functional crystal materials, theoretical study of crystallization mechanism, industrial production of proteins, and so on. Improving the quality of protein crystals is desirable research because it can provide high-quality samples or products for these studies and applications. Here we report that the utilization of DESs as additives in protein crystallization can significantly affect the crystallization process and effectively improve the crystal quality. We synthesized 9 types of DESs, studied their physicochemical properties, and selected 3 DESs suitable as additives for protein crystallization. Using three model proteins (lysozyme, thaumatin, and proteinase K), we confirmed that DESs can significantly affect the protein crystallization process. Crystals obtained at appropriate concentrations of DESs have higher quality, higher diffraction resolution, and better diffraction data collection. A comparison of the 3D structure of protein molecules showed that the addition of DESs did not affect the molecular structure of the proteins. These results proved that the presence of DESs during protein crystallization can help to improve crystal quality without affecting the structure of proteins, showing that DESs can be employed as a novel class of additives for protein crystallization.