Pairs Of Molecules Research Articles

Self-assembled properties of water cuboids

Although liquid water and ice are characterised by predominantly tetrahedral coordination, small water clusters often exhibit a cubic structural motif. In this article, the stability of hydrogen-bonded water nanostructures in the form of n 1×n 2×n 3 cuboids is investigated. The requirement for complete hydrogen bonding imposes a strong constraint on their structure. The equations of the donor–acceptor balance are derived, from which all possible forms of completely hydrogen-bonded cuboids are deduced. The flexible non-additive AMOEBA potential is used for geometric optimisation of the set of configurations with different directions of hydrogen (H-) bonds. It has been established that the majority of completely hydrogen-bonded structures are formed by one layer of fused cubes. The lowest energy configurations of the, in fact, bilayer structures are formed by trans-configurations of transverse pairs of molecules, although some H-bonds are broken in this case. It is noted that the structure of the cuboids may result from the assembly of short nanotubes and smaller cuboids. On the other hand, unrealised H-bonds at the corners of the cuboids make it possible to assemble larger bilayer structures.

A Gravitational-like Relationship of Dispersion Interactions is Exhibited by 40 Pairs of Molecules and Noble Gas Atoms.

We present computational results of many-body dispersion (MBD) interactions for 40 pairs of molecular and atomic species: hydrocarbons, silanes, corresponding fluorinated derivatives, pairs which have multiple H---H contacts between the molecules, as well as pairs having π-π interactions, and pairs of noble gases. The calculations reveal that the MBD stabilization energy (EDISP,MBD) obeys a global relationship, which is gravitational-like. It is proportional to the product of the masses of the two molecules (M1M2) and inversely proportional to the corresponding distances between the molecular centers-of-mass (RCOM-COM) or the H---H distances of the atoms mediating the interactions of the two molecules (RH-H). This relationship reflects the interactions of instantaneous dipoles, which are formed by the ensemble of bonds/atoms in the interacting molecules. Using the D4-corrected dispersion energy (EDISP,D4), which accounts for three-body interactions, we find that the EDISP,MBD and EDISP,D4 data sets are strongly correlated. Based on valence-bond modeling, the dispersion interactions occur primarily due to the increased contributions of the oscillating-ionic VB structures which maintain favorable electrostatic interactions; the [Sub─C+:H-+H:C-─Sub] and [Sub─C:-+H -H:C+─Sub] structures; Sub symbolizes general residues. This augmented contribution is complemented by simultaneously diminished-weights of the destabilizing pair of structures, [Sub─C+:H--H:C+─Sub] and [Sub─:C- H++H:C-─Sub]. The local charges are propagated to the entire ensemble of bonds/atoms by partially charging the Sub residues, thus bringing about the "gravitational-like" dependence of dispersion.

Weaker neuroligin 2 - neurexin 1β interaction tethers membranes and signal synaptogenesis through clustering.

Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules (SAMs) that are essential for the formation of functional synapses. Binding affinities vary by ∼ 1000 folds between arrays of NL and NRX subtypes, which contribute to chemical and spatial specificities. Current structures are obtained with truncated extracellular domains of NL and NRX and are limited to the higher-affinity NL1/4-NRX complexes. How NL-NRX interaction leads to functional synapses remains unknown. Here we report structures of full-length NL2 alone, and in complex with NRX1β in several conformations, which has the lowest affinity among major NL-NRX subtypes. We show how conformational flexibilities may help in adapting local membrane geometry, and reveal mechanisms underlying variations in NL-NRX affinities modulation. We further show that, despite lower affinity, NL2-NRX1β interaction alone is capable of tethering different lipid membranes in total reconstitution, and that NL2 and NRX1β cluster at inter-cellular junctions without the need of other synaptic components. In addition, NL2 combines with the master post-synaptic scaffolding protein gephyrin and clusters neurotransmitter receptors at cellular membrane. These findings suggest dual roles of NL2 - NRX1β interaction - both as mechanical tether, and as signaling receptors, to ensure correct spatial and chemical coordination between two cells to generate function synapses.

Improving the diffraction quality of heat-shock protein 47 crystals.

Heat-shock protein 47 (HSP47) is a potential target for inhibitors that ameliorate fibrosis by reducing collagen assembly. In an effort to develop a structure-based drug-design system, it was not possible to replicate a previous literature result (PDB entry 4au4) for apo dog HSP47; instead, crystal forms were obtained in which pairs of dog HSP47 molecules interacted through a noncleavable C-terminal His-tag to build up tetramers, all of which had multiple molecules of HSP47 in the asymmetric unit and none of which diffracted as wellas the literature precedent. To overcome these difficulties, a two-pronged approach was followed: (i) the His-tag was moved from the C-terminus to the N-terminus and was made cleavable, and (ii) Adnectin (derived from the tenth domain of human fibronectin type III) crystallization chaperones were developed. Both approaches provided well diffracting crystals, but the latter approach yielded crystal forms with only one or two HSP47 complexes per asymmetric unit, which made model building less onerous.

The crystal structures determination and Hirshfeld surface analysis of N-(4-bromo-3-methoxyphenyl)- and N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}- derivatives of N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}benzenesulfonamide

Two new phenylsulfonylindole derivatives, namely, N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}-N-(4-bromo-3-methoxyphenyl)benzenesulfonamide, C28H22Br2N2O5S2, (I), and N,N-bis{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}benzenesulfonamide, C36H27Br2N3O6S3, (II), reveal the impact of intramolecular π–π interactions of the indole moieties as a factor not only governing the conformation of N,N-bis(1H-indol-2-yl)methyl)amines, but also significantly influencing the crystal patterns. For I, the crystal packing is dominated by C—H...π and π–π bonding, with a particular significance of mutual indole–indole interactions. In the case of II, the molecules adopt short intramolecular π–π interactions between two nearly parallel indole ring systems [with the centroids of their pyrrole rings separated by 3.267 (2) Å] accompanied by a set of forced Br...O contacts. This provides suppression of similar interactions between the molecules, while the importance of weak C—H...O hydrogen bonding to the packing naturally increases. Short contacts of the latter type [C...O = 3.389 (6) Å] assemble pairs of molecules into centrosymmetric dimers with a cyclic R 2 2(13) ring motif. These findings are consistent with the results of a Hirshfeld surface analysis and together they suggest a tool for modulating the supramolecular behavior of phenylsulfonylated indoles.

Thionation of conjugated porphyrin with enhanced photodynamic and photothermal effects for cancer therapy

Phototherapy has emerged as a promising modality for cancer treatment in recent years, owing to its precise temporal control and minimally invasive nature. Here, two new organic porphyrin molecules, denoted as ONP and SNP, were designed and synthesized with an acceptor–donor–acceptor (A-D-A) architecture. The donor–acceptor (D-A) pairs in molecules facilitated the intermolecular charge transfer (ICT), thereby amplifying near-infrared (NIR) absorbance and promoting nonradiative heat generation. Notably, the substitution of oxygen atoms with sulfur in naphthalimides (NI) led to significant change of their photophysical and photochemical properties. Specifically, the sulfur atoms exhibited pronounced spin–orbit coupling (SOC) effect, leading to efficient photoinduced intersystem crossing (ISC) processes, thus facilitating the generation of reactive oxygen species (ROS). Upon self-assembly, the formed nanomaterials (ONP NPs and SNP NPs) exhibited spherical morphology with average size about 150 nm. The biocompatibility and photocytotoxicity of nanoparticles against Hepa1-6 cells were evaluated using the CCK-8 assay. Additionally, the synergistic effects (photodynamic therapy and photothermal therapy) of SNP NPs were confirmed through diverse in vitro experiment under 690 nm laser irradiation. The generation of intracellular ROS by SNP NPs was confirmed with DCFH-DA as probe. This study provides an ingenious strategy for developing organic nanomaterials with high treatment efficiency through synergistic photodynamic/photothermal effects.

Optimization of carrier transfer kinetics of BiOIO3 using TFA·/TFA- reversible redox pairs of TFA molecules as co-catalysts for efficient photoelectrochemical water splitting system

Co-catalyst loading on photoelectrodes is considered to be an effective way to accelerate charge transfer. However, the bonding between most of the co-catalysts and photoelectrodes tends to be weak, which severely limits the role of co-catalysts in the catalytic system. Based on the above problems, we introduced trifluoroacetic acid (TFA) as a homogeneous molecular co-catalyst in the layered BiOIO3 catalytic system for the first time. The BiOIO3-TFA photoelectrode exhibited excellent photoelectrochemical performance under light and applied bias voltage. The photocurrent density reached up to 0.228 μA cm−2, which was 2.11 times higher than that before modification, while the overpotential was negatively shifted by 183 mV. The results showed that the photogenerated electron-hole pairs in BiOIO3 are excited and transferred to the TFA causing the CO double bond to break to form a TFA radical (TFA·), which is then reduced to TFA-. This cyclic redox reaction accompanied by fast hole transfer can greatly reduce the recombination behavior during carrier transport. This work demonstrates a new form of co-catalyst for photoelectrochemical water splitting. Highly water-soluble molecules and TFA·/TFA- reversible reactions have considerable potential for the development of new co-catalysts. It also provides ideas for the establishment of new, efficient catalytic systems for inhibiting carrier recombination.

Study of molecular interaction between benzaldehyde and methanol using microwave dielectric relaxation spectroscopy and radial distribution function

A microwave dielectric relaxation study was conducted for mixtures of benzaldehyde (BZ) and methanol (MeOH) over a frequency range of 200 MHz to 20 GHz at seven different temperatures, ranging from 293.15 K to 323.15 K. The dielectric relaxation parameters, obtained through a fitting process, were used to examine their dependence on concentration and temperature. Thermodynamic parameters, such as Gibbs free energy (ΔG), molar enthalpy of activation (ΔH), and molar entropy of activation (ΔS), were evaluated using the temperature dependence of the dipolar relaxation time. The study provided valuable insights into the molecular interactions and dynamic behavior of the components in the binary mixture system. Additionally, a molecular dynamics (MD) simulation study was conducted on the binary mixture of BZ and MeOH to determine the Radial Distribution Function (RDF) and coordination number for different pairs of molecules and atoms, which revealed information about the binding and arrangement of the local structure.

Crystal structure of perfluorononanoic acid, C9HF17O2

The crystal structure of perfluorononanoic acid (PFNA) was solved via parallel tempering using synchrotron powder diffraction data obtained from the Brockhouse X-ray Diffraction and Scattering (BXDS) Wiggler Lower Energy (WLE) beamline at the Canadian Light Source. PFNA crystallizes in monoclinic space group P21/c (#14) with lattice parameters a = 26.172(1) Å, b = 5.6345(2) Å, c = 10.9501(4) Å, and β = 98.752(2)°. The crystal structure is composed of dimers, with pairs of PFNA molecules connected by hydrogen bonds via the carboxylic acid functional groups. The Rietveld-refined structure was compared to a density functional theory-optimized structure, and the root-mean-square Cartesian difference was larger than normally observed for correct powder structures. The powder data likely exhibited evidence of disorder which was not successfully modeled.

Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation

Human ABC transporters ABCD1–3 are all localized on the peroxisomal membrane and participate in the β-oxidation of fatty acyl-CoAs, but they differ from each other in substrate specificity. The transport of branched-chain fatty acids from cytosol to peroxisome is specifically driven by ABCD3, dysfunction of which causes severe liver diseases such as hepatosplenomegaly. Here we report two cryogenic electron microscopy (cryo-EM) structures of ABCD3 bound to phytanoyl-CoA and ATP at resolutions of 2.9 Å and 3.2 Å, respectively. A pair of phytanoyl-CoA molecules were observed in ABCD3, each binding to one transmembrane domain (TMD), which is distinct from our previously reported structure of ABCD1, where each fatty acyl-CoA molecule strongly crosslinks two TMDs. Upon ATP binding, ABCD3 exhibits a conformation that is open towards the peroxisomal matrix, leaving two extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity. Structural analysis combined with substrate-stimulated ATPase activity assays indicated that the present structures might represent two states of ABCD3 in the transport cycle. These findings advance our understanding of fatty acid oxidation and the molecular pathology of related diseases.

Crystal structure and Hirshfeld surface analysis of 1-[6-bromo-2-(3-bromo-phen-yl)-1,2,3,4-tetra-hydro-quinolin-4-yl]pyrrolidin-2-one.

This study presents the synthesis, characterization and Hirshfeld surface analysis of 1-[6-bromo-2-(3-bromo-phen-yl)-1,2,3,4-tetra-hydro-quinolin-4-yl]pyrrolidin-2-one, C19H18Br2N2O. In the title compound, the pyrrolidine ring adopts a distorted envelope configuration. In the crystal, mol-ecules are linked by inter-molecular N-H⋯O, C-H⋯O and C-H⋯Br hydrogen bonds, forming a three-dimensional network. In addition, pairs of mol-ecules along the c axis are connected by C-H⋯π inter-actions. According to a Hirshfeld surface study, H⋯H (36.9%), Br⋯H/H⋯Br (28.2%) and C⋯H/H⋯C (24.3%) inter-actions are the most significant contributors to the crystal packing.

Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure.

We present a computational scheme for predicting the ligands that bind to a pocket of a known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations, and permutations of atoms, and has some degree of isometry with the space of conformations. We use these representations to train a nondeep machine learning algorithm to classify the binding between pockets and molecule pairs and show that this approach has a better generalization capability than existing methods.

Spatial localization of CD16a at the human NK cell ADCC lytic synapse.

Natural Killer (NK) cells utilize effector functions, including antibody-dependent cellular cytotoxicity (ADCC), for the clearance of viral infection and cellular malignancies. NK cell ADCC is mediated by Fc γ RIIIa (CD16a) binding to the fragment crystallizable (Fc) region of immunoglobulin G (IgG) within immune complexes on a target cell surface. While antibody-induced clustering of CD16a is thought to drive ADCC, the molecular basis for this activity has not been fully described. Here we use MINFLUX nanoscopy to map the spatial distribution of stoichiometrically labeled CD16a across the NK cell membrane, revealing the presence of pairs of CD16a molecules with intra-doublet distance of approximately 17 nm. NK cells activated on supported lipid bilayers by Trastuzumab results in an increase of synaptic regions with greater CD16a density. Our results provide the highest spatial resolution yet described for CD16a imaging, offering new insight into how CD16a organization within the immune synapse could influence ADCC activity. MINFLUX holds great promise to further unravel the molecular details driving CD16a-based activation of NK cells.

Evaluation of reinforcement learning in transformer-based molecular design

Designing compounds with a range of desirable properties is a fundamental challenge in drug discovery. In pre-clinical early drug discovery, novel compounds are often designed based on an already existing promising starting compound through structural modifications for further property optimization. Recently, transformer-based deep learning models have been explored for the task of molecular optimization by training on pairs of similar molecules. This provides a starting point for generating similar molecules to a given input molecule, but has limited flexibility regarding user-defined property profiles. Here, we evaluate the effect of reinforcement learning on transformer-based molecular generative models. The generative model can be considered as a pre-trained model with knowledge of the chemical space close to an input compound, while reinforcement learning can be viewed as a tuning phase, steering the model towards chemical space with user-specific desirable properties. The evaluation of two distinct tasks—molecular optimization and scaffold discovery—suggest that reinforcement learning could guide the transformer-based generative model towards the generation of more compounds of interest. Additionally, the impact of pre-trained models, learning steps and learning rates are investigated.Scientific contributionOur study investigates the effect of reinforcement learning on a transformer-based generative model initially trained for generating molecules similar to starting molecules. The reinforcement learning framework is applied to facilitate multiparameter optimisation of starting molecules. This approach allows for more flexibility for optimizing user-specific property profiles and helps finding more ideas of interest.

Direct Enantiomer Differentiation of Drugs and Drug-Like Compounds via Noncovalent Copper-Amino Acid Complexation and Ion Mobility-Mass Spectrometry.

Drug enantiomers can possess vastly different pharmacological properties, yet they are identical in their chemical composition and structural connectivity. Thus, resolving enantiomers poses a great challenge in the field of separation science. Enantiomer separations necessitate interaction of the analyte with a chiral environment─in mass spectrometry-based analysis, a common approach is through a three-point interaction with a chiral selector commonly introduced during sample preparation. In select cases, the structural difference imparted through noncovalent complexation results in enantiomer-specific structural differences, facilitating measurement using a structurally selective analytical technique such as ion mobility-mass spectrometry (IM-MS). In this work, we investigate the direct IM-MS differentiation of chiral drug compounds using mononuclear copper complexes incorporating an amino acid chiral selector. A panel of 20 chiral drugs and drug-like compounds were investigated for separation, and four l-amino acids (l-histidine, l-tryptophan, l-proline, and l-tyrosine) were evaluated as chiral selectors (CS) to provide the chiral environment necessary for differentiation. Enantiomer differentiation was achieved for four chiral molecule pairs (R/S-thalidomide, R/S-baclofen, R/S-metoprolol, and d/l-panthenol) with two-peak resolution (Rp-p) values ranging from 0.7 (>10% valley) to 1.5 (baseline separation). Calibration curves relating IM peak areas to enantiomeric concentrations enabled enantiomeric excess quantitation of racemic thalidomide and metoprolol with residuals of 5.7 and 2.5%, respectively. Theoretical models suggest that CuII and l-histidine complexation around the analyte chiral center is important for gas-phase stereoselectivity. This study demonstrates the potential of combining enantioselective noncovalent copper complexation with structurally selective IM-MS for differentiating chiral drugs and drug-like compounds.

Probe Absorption Spectroscopy As a Tool to Study the Excited States in a Cooperative System of Two Organic Molecules

The applicability of the method for measuring the probe absorption and gain spectra in a system of quantum emitters excited by a resonant driving field for studying cooperative photoluminescence is considered. The gain and attenuation of a probe signal in the system of two quantum emitters with the dipole–dipole interaction have been calculated for the conditions of observing the cooperative photoluminescence of a pair of impurity molecules described in the literature and close to them. The resulting dependences demonstrate the structure of excited collective molecular states, which can be used to reconstruct the positions of molecules in a matrix and to determine the difference in their photophysical properties. Thus, the probe absorption and gain spectra can be used to analyze the photoluminescence of quantum-entangled particles and to transform light signals.

Insights into the electronic structure and interaction energies of 4-ethoxy-N-(4-ethoxy-2-hydoxybenzylidene)benzohydrazide

The molecule 4-ethoxy-N-(4-ethoxy-2-hydroxybenzylidene)benzohydrazide (4EHB) is characterized by a rigid aroylhydrazone core, acting as a mesogenic unit, and a flexible chain at its terminal end. The aroylhydrazone core comprises two aromatic rings linked by connecting groups, resulting in moderate size and elongation of the molecule. Variations in the positions and orientations of elongated molecules give rise to different mesogenic phases such as Nematic, Smectic, and Hexatic Smectic. The mesogenic behavior of aroylhydrazone-based materials is governed by various non-covalent interactions. In this study, molecular geometry optimization, analysis of HOMO-LUMO orbitals, and MEP surfaces of individual and pairs of 4EHB molecules were conducted using the Density functional B3LYP technique with the basis set 6-31G**. Intermolecular interaction energies between pairs of 4EHB molecules are evaluated using the technique M06-2X/6-311G** in stacking, terminal, and side-to-side (in-plane) configurations. Basis set superposition error (BSSE) is corrected using counterpoise method and interaction energy(I.E.) is decomposed in different components using SAPT0 method at level 6-311G**, which provided insights into the mesogenic behavior of the system.

Design of Photonic Molecule-Based Multiway Beam Splitter/Coupler with Variable Division Ratio

An optical beam splitter is used for dividing an input optical beam into several separate beams with a specific power ratio. Usually, conventional optical beam splitters have bulky dimensions (many optical wavelengths) and a fixed dividing ratio, which significantly limit the design of new miniaturized optical devices and integrated optical circuits. We propose and investigate in detail a novel physical concept of a highly miniaturized (up to two working wavelengths) planar optical resonant splitter/coupler with a switching element comprising a photonic molecule (PM) pair dispersing input optical fluxes in multiple directions with a tailored power ratio. The structural design of the proposed splitter is based on a silicon-on-insulator (SOI) platform and composed of high-quality resonators in the form of electromagnetically coupled submicron-sized microcylinders. The control on the power division ratio and the selection of optical beam directions is realized by tuning the photonic splitter structure to the corresponding resonance of the PM supermode. Compared to known analogs, the proposed design is easy and cheap in fabrication. Because of its tiny dimensions, it is suitable for integration into a “System-on-a-chip” platform and can dynamically change the beam power division ratio by input wave-phase manipulation.

Forecasting the molecular interactions: A hypergraph-based neural network for molecular relational learning

Molecular relational learning refers to forecasting the interaction performance between pairs of molecules. Graph neural networks (GNNs) enables the effective modeling of chemical molecules by transferring them as abstract structures of graph, thus considering node-level interactions instead of atom’s. However, the abilities of modeling and predicting of classical GNN methods is restricted by edges’ redundancy and insufficient process of interaction modeling in a pair of molecular graphs. Therefore, based on the novel hypergraph convolutional neural network and bi-view cross interaction message passing and updating, we propose a hypergraph-based neural network method named IE-HGNN (Internal-External Bi-view Hypergraph Neural Network). We evaluate our method on two real-world molecular datasets, i.e., LEP and ZhangDDI, demonstrating IE-HGNN achieves excellent performance for both macro and micro molecules, while maintaining high training efficiency. We believe that this study introduces a novel approach for exploring the field of molecular relational learning and interaction prediction.

RNA modifications in physiology and pathology: Progressing towards application in clinical settings

The potential to modify individual nucleotides through chemical means in order to impact the electrostatic charge, hydrophobic properties, and base pairing of RNA molecules is harnessed in the medical application of stable synthetic RNAs like mRNA vaccines and synthetic small RNA molecules. These modifications are used to either increase or decrease the production of therapeutic proteins. Additionally, naturally occurring biochemical alterations of nucleotides play a role in regulating RNA metabolism and function, thereby modulating essential cellular processes. Research elucidating the mechanisms through which RNA modifications govern fundamental cellular functions in multicellular organisms has enhanced our comprehension of how irregular RNA modification profiles can lead to human diseases. Collectively, these fundamental scientific findings have unveiled the molecular and cellular functions of RNA modifications, offering new opportunities for therapeutic intervention and paving the way for a variety of innovative clinical strategies.