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1.
J Org Chem ; 87(7): 4649-4653, 2022 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-35200013

RESUMEN

To improve the rigidity of spirobisindane, it was intramolecularly locked by forming eight-membered rings via sulfur and phosphorus atoms to produce an interlocked polycyclic structure under mild conditions in good yields. By carefully analyzing the crystal structures, we noticed that the angle between the two benzene rings in the locked version is significantly smaller than that of the typical spirobisindane structure. Molecular modeling indicated that locking the spiro center can remarkably enhance the rigidity.


Asunto(s)
Carbono , Fósforo , Cristalografía por Rayos X , Modelos Moleculares , Fósforo/química , Azufre
2.
ChemistryOpen ; 11(5): e202200049, 2022 May.
Artículo en Inglés | MEDLINE | ID: mdl-35543217

RESUMEN

Protonation of 1,3,5-tricyano- and 1,3,5-triaminobenzene was achieved in various superacidic media, resulting in the formation of the respective trinitrilium and triammonium species. Furthermore, the respective N-methyl nitrilium species was synthesized by methylation. Characterization was performed by NMR and vibrational spectroscopy, followed by single-crystal X-ray diffraction analyses of selected species. Fourfold protonation of the amine, which would have led to the triammonium arenium species, could not be achieved. Quantum chemical calculations are employed to enable full vibrational assignment as well to quantify charge localization.


Asunto(s)
Teoría Cuántica , Vibración , Cristalografía por Rayos X , Espectroscopía de Resonancia Magnética/métodos , Modelos Moleculares
3.
J Mol Model ; 28(6): 162, 2022 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-35597858

RESUMEN

The present work reports the theoretical investigation of Co(II), Ni(II), and Zn(II) complexes containing Schiff bases (used as ligands) derived from the reaction of 2-hydroxy-1-naphthaldehyde with N-(2-aminoethyl) pyrazoles. The spectral analyses were carried out using infrared, Raman, and UV-Vis spectroscopy. Vibrational analyses were performed in order to investigate the mechanisms involving metal-ligand and intra-ligand vibrations and indicated the possibility of charge transfer related to the transitions n[Formula: see text]* and [Formula: see text]*. Structure optimizations and normal coordinate force field calculations were performed via the density functional theory (DFT) method at the HSE06/6-311G(d,p)/LanL2DZ level. A thorough analysis was also conducted regarding the nonlinear optical (NLO) properties and the natural bond orbital (NBO) of the complexes. The results show that these complexes have prospective application as materials for NLO. Furthermore, the NBO analysis confirms the coordination between the lone pair (LP) electrons of the donor atoms (O and N) and the metal acceptors. Finally, studies were conducted regarding the electronic properties of the complexes; among the properties investigated included the frontier molecular orbitals (FMO) and the molecular electrostatic potential (MEP), allowing to determine the energy gap and charge distribution.


Asunto(s)
Iminas , Vibración , Electrónica , Ligandos , Modelos Moleculares , Pirazoles , Teoría Cuántica , Espectrofotometría Ultravioleta , Espectroscopía Infrarroja por Transformada de Fourier , Espectrometría Raman , Zinc
4.
Acta Crystallogr D Struct Biol ; 78(Pt 5): 553-559, 2022 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-35503204

RESUMEN

Crystallographers have an array of search-model options for structure solution by molecular replacement (MR). The well established options of homologous experimental structures and regular secondary-structure elements or motifs are increasingly supplemented by computational modelling. Such modelling may be carried out locally or may use pre-calculated predictions retrieved from databases such as the EBI AlphaFold database. MrParse is a new pipeline to help to streamline the decision process in MR by consolidating bioinformatic predictions in one place. When reflection data are provided, MrParse can rank any experimental homologues found using eLLG, which indicates the likelihood that a given search model will work in MR. Inbuilt displays of predicted secondary structure, coiled-coil and transmembrane regions further inform the choice of MR protocol. MrParse can also identify and rank homologues in the EBI AlphaFold database, a function that will also interest other structural biologists and bioinformaticians.


Asunto(s)
Proteínas , Bases de Datos de Proteínas , Modelos Moleculares , Dominios Proteicos , Estructura Secundaria de Proteína , Proteínas/química
5.
Chem Rev ; 122(9): 7987-7989, 2022 May 11.
Artículo en Inglés | MEDLINE | ID: mdl-35538860
6.
Nat Commun ; 13(1): 2416, 2022 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-35504909

RESUMEN

A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits1. Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.


Asunto(s)
ADN Viral , Integrasas , Animales , Dominio Catalítico , ADN Viral/metabolismo , Humanos , Integrasas/metabolismo , Lentivirus/genética , Lentivirus/metabolismo , Modelos Moleculares , Retroviridae/genética , Ovinos/genética
7.
Plant Signal Behav ; 17(1): 2062555, 2022 12 31.
Artículo en Inglés | MEDLINE | ID: mdl-35510715

RESUMEN

The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.


Asunto(s)
Carboxiliasas , Acilcoenzima A , Carboxiliasas/genética , Carboxiliasas/metabolismo , Modelos Moleculares , Oxalatos/metabolismo , Ácido Oxálico , Filogenia
8.
J Chem Inf Model ; 62(10): 2538-2549, 2022 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-35511068

RESUMEN

Dynamic allostery refers to one important class of allosteric regulation that does not involve noticeable conformational changes upon effector binding. In recent years, many "quasi"-dynamic allosteric proteins have been found to only experience subtle conformational changes during allosteric regulation. However, as enthalpic and entropic contributions are coupled to each other and even tiny conformational changes could bring in noticeable free energy changes, a quantitative description is essential to understand the contribution of pure dynamic allostery. Here, by developing a unified anisotropic elastic network model (uANM) considering both side-chain information and ligand heavy atoms, we quantitatively estimated the contribution of pure dynamic allostery in a dataset of known allosteric proteins by excluding the conformational changes upon ligand binding. We found that the contribution of pure dynamic allostery is generally small (much weaker than previously expected) and robustly exhibits an allosteric activation effect, which exponentially decays with the distance between the substrate and the allosteric ligand. We further constructed toy models to study the determinant factors of dynamic allostery in monomeric and oligomeric proteins using the uANM. Analysis of the toy models revealed that a short distance, a small angle between the two ligands, strong protein-ligand interactions, and weak protein internal interactions lead to strong dynamic allostery. Our study provides a quantitative estimation of pure dynamic allostery and facilitates the understanding of dynamic-allostery-controlled biological processes and the design of allosteric drugs and proteins.


Asunto(s)
Proteínas , Regulación Alostérica , Ligandos , Modelos Moleculares , Proteínas/química , Termodinámica
9.
Adv Protein Chem Struct Biol ; 130: 59-83, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35534116

RESUMEN

Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.


Asunto(s)
Aminoácidos , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Modelos Moleculares , Conformación Proteica , Especificidad por Sustrato
10.
J Chem Inf Model ; 62(10): 2269-2279, 2022 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-35544331

RESUMEN

A persistent goal for de novo drug design is to generate novel chemical compounds with desirable properties in a labor-, time-, and cost-efficient manner. Deep generative models provide alternative routes to this goal. Numerous model architectures and optimization strategies have been explored in recent years, most of which have been developed to generate two-dimensional molecular structures. Some generative models aiming at three-dimensional (3D) molecule generation have also been proposed, gaining attention for their unique advantages and potential to directly design drug-like molecules in a target-conditioning manner. This review highlights current developments in 3D molecular generative models combined with deep learning and discusses future directions for de novo drug design.


Asunto(s)
Diseño de Fármacos , Modelos Moleculares , Estructura Molecular
11.
Nature ; 605(7908): 166-171, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35477757

RESUMEN

DNA wraps around the histone octamer to form nucleosomes1, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions2,3. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases.


Asunto(s)
Histonas , Nucleosomas , Adenosina Trifosfato/metabolismo , Cromatina/genética , Ensamble y Desensamble de Cromatina , Proteínas Cromosómicas no Histona/metabolismo , Microscopía por Crioelectrón , ADN/metabolismo , ADN Helicasas/metabolismo , Histonas/metabolismo , Proteínas de Homeodominio , Humanos , Modelos Moleculares , Proteínas de Neoplasias , Proteínas Nucleares/metabolismo , Factores de Transcripción/metabolismo
12.
Molecules ; 27(7)2022 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-35408606

RESUMEN

To search for new suitable Pd precursors for MOCVD/ALD processes, the extended series of fluorinated palladium complexes [Pd(CH3CXCHCO(R))2] with ß-diketone [tfa-1,1,1-trifluoro-2,4-pentanedionato (1); pfpa-5,5,6,6,6-pentafluoro-2,4-hexanedionato (3); hfba-5,5,6,6,7,7,7-heptafluoro-2,4-heptanedionato (5)] and ß-iminoketone [i-tfa-1,1,1-trifluoro-2-imino-4-pentanonato (2); i-pfpa-5,5,6,6,6-pentafluoro-2-imino-4-hexanonato (4); i-hfba-5,5,6,6,7,7,7-heptafluoro-2-imino-4-heptanonato (6)] ligands were synthesized with 70-80% yields and characterized by a set of experimental (SXRD, XRD, IR, NMR spectroscopy, TG) and theoretical (DFT, Hirshfeld surface analysis) methods. Solutions of Pd ß-diketonates contained both cis and trans isomers, while only trans isomers were detected in the solutions of Pd ß-iminoketonates. The molecules 2-6 and new polymorphs of complexes 3 and 5 were arranged preferentially in stacks, and the distance between molecules in the stack generally increased with elongation of the fluorine chain in ligands. The H…F contacts were the main ones involved in the formation of packages of molecules 1-2, and C…F, F…F, NH…F contacts appeared in the structures of complexes 4-6. The stability of complexes and their polymorphs in the crystal phases were estimated from DFT calculations. The TG data showed that the volatility differences between Pd ß-iminoketonates and Pd ß-diketonates were minimized with the elongation of the fluorine chain in the ligands.


Asunto(s)
Flúor , Paladio , Cristalografía por Rayos X , Ligandos , Modelos Moleculares , Paladio/química
13.
Phys Chem Chem Phys ; 24(16): 9051-9081, 2022 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-35389399

RESUMEN

Important contemporary biological and materials problems often depend on interactions that span orders of magnitude differences in spatial and temporal dimensions. This Tutorial Review attempts to provide an introduction to such fascinating problems through a series of case studies, aimed at beginning researchers, graduate students, postdocs and more senior colleagues who are changing direction to focus on multiscale aspects of their research. The choice of specific examples is highly personal, with examples either chosen from our own work or outstanding multiscale efforts from the literature. I start with various embedding schemes, as exemplified by polarizable continuum models, 3-D RISM, molecular DFT and frozen-density embedding. Next, QM/MM (quantum mechanical/molecular mechanical) techniques are the workhorse of pm-to-nm/ps-to-ns simulations; examples are drawn from enzymes and from nanocatalysis for oil-sands upgrading. Using polarizable force-fields in the QM/MM framework represents a burgeoning subfield; with examples from ion channels and electron dynamics in molecules subject to strong external fields, probing the atto-second dynamics of the electrons with RT-TDDFT (real-time - time-dependent density functional theory) eventually coupled with nuclear motion through the Ehrenfest approximation. This is followed by a section on coarse graining, bridging dimensions from atoms to cells. The penultimate chapter gives a quick overview of multiscale approaches that extend into the meso- and macro-scales, building on atomistic and coarse-grained techniques to enter the world of materials engineering, on the one hand, and cell biology, on the other. A final chapter gives just a glimpse of the burgeoning impact of machine learning on the structure-dynamics front. I aim to capture the excitement of contemporary leading-edge breakthroughs in the description of physico-chemical systems and processes in complex environments, with only enough historical content to provide context and aid the next generation of methodological development. While I aim also for a clear description of the essence of methodological breakthroughs, equations are kept to a minimum and detailed formalism and implementation details are left to the references. My approach is very selective (case studies) rather than exhaustive. I think that these case studies should provide fodder to build as complete a reference tree on multiscale modelling as the reader may wish, through forward and backward citation analysis. I hope that my choices of cases will excite interest in newcomers and help to fuel the growth of multiscale modelling in general.


Asunto(s)
Electrónica , Electrones , Humanos , Modelos Moleculares , Simulación de Dinámica Molecular
14.
Bioorg Chem ; 123: 105763, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35366581

RESUMEN

The SPRY domain-containing SOCS box protein-2 (SPSB2) plays a critical role in the degradation of inducible nitric oxide synthase (iNOS) in macrophages. In this study, we have conjugated a peptide inhibitor of the iNOS-SPSB2 interaction with a cell-penetrating peptide (CPP) for delivery into macrophages, and confirmed its binding to SPSB2. We have assessed the uptake of a fluorophore-tagged analogue by RAW 264.7 and immortalised bone marrow derived macrophage (iBMDM) cell lines, and shown that the CPP-peptide conjugate enhanced NO production. The findings of this study will be useful in further refinement of CPP-peptide conjugates as leads in the development of new antibiotics that target the host innate immune response.


Asunto(s)
Péptidos de Penetración Celular , Óxido Nítrico , Péptidos de Penetración Celular/farmacología , Macrófagos/metabolismo , Modelos Moleculares , Óxido Nítrico Sintasa de Tipo II/metabolismo
15.
J Med Chem ; 65(8): 6070-6087, 2022 04 28.
Artículo en Inglés | MEDLINE | ID: mdl-35417652

RESUMEN

Targeting the kinases MNK1 and MNK2 has emerged as a valuable strategy in oncology. However, most of the advanced inhibitors are acting in an adenosine triphosphate (ATP)-competitive mode, precluding the evaluation of different binding modes in preclinical settings. Using rational design, we identified and validated the 4,6-diaryl-pyrazolo[3,4-b]pyridin-3-amine scaffold as the core for MNK inhibitors. Signaling pathway analysis confirmed a direct effect of the hit compound EB1 on MNKs, and in line with the reported function of these kinases, EB1 only affects the growth of tumor but not normal cells. Molecular modeling revealed the binding of EB1 to the inactive conformation of MNK1 and the interaction with the specific DFD motif. This novel mode of action appears to be superior to the ATP-competitive inhibitors, which render the protein in a pseudo-active state. Overcoming this paradoxical activation of MNKs by EB1 represents therefore a promising starting point for the development of a novel generation of MNK inhibitors.


Asunto(s)
Péptidos y Proteínas de Señalización Intracelular , Adenosina Trifosfato , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Modelos Moleculares , Transducción de Señal
16.
Nat Commun ; 13(1): 1977, 2022 Apr 13.
Artículo en Inglés | MEDLINE | ID: mdl-35418573

RESUMEN

The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.


Asunto(s)
Proteínas del Complejo del Centro de Reacción Fotosintética , Rhodobacter sphaeroides , Proteínas Bacterianas/metabolismo , Benzoquinonas , Microscopía por Crioelectrón , Complejos de Proteína Captadores de Luz/metabolismo , Modelos Moleculares , Péptidos/química , Fotosíntesis , Proteínas del Complejo del Centro de Reacción Fotosintética/metabolismo , Rhodobacter sphaeroides/metabolismo
17.
Acta Crystallogr C Struct Chem ; 78(Pt 4): 240-249, 2022 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-35380127

RESUMEN

Seven solvates of the angiotensin II receptor blocker agent olmesartan (C24H26N6O3), namely, the methanol (C24H26N6O3·CH4O), ethanol (C24H26N6O3·C2H6O), isopropanol (C24H26N6O3·C3H8O), isobutanol (C24H26N6O3·C4H10O), 2-ethoxyethanol (C24H26N6O3·C4H10O2), chloroform (C24H26N6O3·CHCl3) and acetonitrile (C24H26N6O3·C2H3N) solvates, were successfully obtained. The crystal structures were determined using the single-crystal X-ray diffraction technique and the structural features are described, each solvate containing one molecule of olmesartan and one of solvent in the asymmetric unit. The samples were also analyzed by powder X-ray diffraction. Total lattice energies and binding energies between the olmesartan and solvent molecules were evaluated, which can be partitioned into electrostatic, polarization, dispersion and repulsion components. Hirshfeld and fingerprint plot analysis was performed to highlight the intermolecular contacts. Hydrogen bonding and supramolecular arrangements were comparatively studied for the seven solvates.


Asunto(s)
Tetrazoles , Cristalografía por Rayos X , Enlace de Hidrógeno , Imidazoles , Modelos Moleculares
18.
Nat Commun ; 13(1): 1904, 2022 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-35393413

RESUMEN

Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 ß-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 ß-polypeptides, indicating a critical role for protein-U in controlling the number of αß-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex.


Asunto(s)
Rhodobacter sphaeroides , Proteínas Bacterianas/metabolismo , Complejos de Proteína Captadores de Luz/metabolismo , Modelos Moleculares , Péptidos/química , Fotosíntesis , Rhodobacter sphaeroides/metabolismo
19.
Nat Commun ; 13(1): 2162, 2022 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-35443756

RESUMEN

Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which intrinsic dynamics is hard to elucidate. Here we report coarse-grained molecular simulations that allow studying supramolecular polymers at the thermodynamic equilibrium, explicitly showing the complex nature of these systems, which are composed of exquisitely dynamic molecular entities. Detailed studies of molecular exchange provide insights into key factors controlling how assemblies communicate with each other, defining the equilibrium dynamics of the system. Using minimalistic and finer chemically relevant molecular models, we observe that a rich concerted complexity is intrinsic in such self-assembling systems. This offers a new dynamic and probabilistic (rather than structural) picture of supramolecular polymer systems, where the travelling molecular species continuously shape the assemblies that statistically emerge at the equilibrium.


Asunto(s)
Comunicación , Polímeros , Modelos Moleculares , Polímeros/química
20.
Int J Mol Sci ; 23(8)2022 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-35457005

RESUMEN

In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt coordination complexes where divalent Ch atoms (Se/Te) were used as ligands. Interestingly, the coordination to the metal center enhanced the σ-hole donor ability of the Ch atom, which participates in ChBs with neighboring units present in the X-ray crystal structure, therefore dictating the solid state architecture. The X-ray analyses were complemented with a computational study (PBE0-D3/def2-TZVP level of theory), which shed light into the strength and directionality of the ChBs studied herein. Owing to the new possibilities that metal coordination offers to enhance or modulate the σ-hole donor ability of Chs, we believe that the findings presented herein are of remarkable importance for supramolecular chemists as well as for those scientists working in the field of solid state chemistry.


Asunto(s)
Metales , Ligandos , Modelos Moleculares
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