The assembly of molecular networks into structures such as random tilings and glasses has recently been demonstrated for a number of two-dimensional systems. These structures are dynamically arrested on experimental time scales, so the critical regime in their formation is that of initial growth. Here, we identify a transition from energetic to entropic stabilization in the nucleation and growth of a molecular rhombus tiling. Calculations based on a lattice-gas model show that clustering of topological defects and the formation of faceted boundaries followed by a slow relaxation to equilibrium occur under conditions of energetic stabilization. We also identify an entropically stabilized regime in which the system grows directly into an equilibrium configuration without the need for further relaxation. Our results provide a methodology for identifying equilibrium and nonequilibrium randomness in the growth of molecular tilings, and we demonstrate that equilibrium spatial statistics are compatible with exponentially slow dynamical behavior.
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http://dx.doi.org/10.1103/PhysRevE.82.041109 | DOI Listing |
J Mol Model
January 2025
Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, 48128, USA.
Context: Riboflavin (RF), also known as B2 vitamin, is the precursor to flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), two co-enzymes involved in many electron transport processes. Interactions of the isoalloxazine ring, common to all three compounds, are of great interest due to their biological function in flavoproteins and relevance in the transport by the carrier protein leading to development of drug delivery strategies and non-invasive diagnostics techniques. Based on protein crystallographic data, a computational investigation of the interactions in the complexes between lumiflavin, a model compound, and aromatic amino acids, tyrosine and tryptophan, was pursued with the goal of characterizing noncovalent interactions.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.
Nonheme iron enzymes utilize = 2 iron(IV)-oxo intermediates as oxidants in biological oxygenations. In contrast, corresponding synthetic nonheme Fe═O complexes characterized to date favor the = 1 ground state that generally shows much poorer oxidative reactivity than their = 2 counterparts. However, one intriguing exception found by Nam a decade ago is the = 1 [Fe(O)(MeNTB)] complex (MeNTB = [tris((-methyl-benzimidazol-2-yl)methyl)amine], ) with a hydrogen atom transfer (HAT) reactivity that is 70% that of the = 2 [Fe(O)(TQA)] complex (TQA = tris(2-quinolylmethyl)amine, ).
View Article and Find Full Text PDFInt J Mol Sci
November 2024
Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), Rua Cristóvão Colombo, 2265, São José do Rio Preto 15054-000, SP, Brazil.
The respiratory syncytial virus (RSV) matrix protein plays key roles in the virus life cycle and is essential for budding, as it stimulates the optimal membrane curvature necessary for the emergence of viral particles. Resveratrol, a polyphenol (3,4',5-trihydroxy-trans-stilbene) produced by plants, exhibits pharmacological effects, including anti-inflammatory and antiviral activities. In this study, resveratrol was tested in HEp-2 (Epidermoid carcinoma of the larynx cell) cells for its post-infection effects, and recombinant M protein was produced to characterize the biophysical mechanisms underlying this interaction.
View Article and Find Full Text PDFAdv Sci (Weinh)
December 2024
State Key Laboratory of Luminescent Materials and Devices and Guangdong Provincial Key Laboratory of Fiber Laser Materials and Applied Techniques, School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, China.
The entropy mediated temperature-structure evolution has attracted significant interest, which is used for the development of functional alloys and ceramics. But such strategy has not yet been demonstrated for development of non-metallic glasses. Herein, the successful application of the entropy engineering concept to non-metallic glass to manipulate its in situ crystallization process is demonstrated.
View Article and Find Full Text PDFThe LOV2 domain is commonly harnessed as a source of light-based regulation in engineered optogenetic switches. In prior work, we used LOV2 to create a light-regulated Dihydrofolate Reductase (DHFR) enzyme and showed that structurally disperse mutations in DHFR were able to tune the allosteric response to light. However, it remained unclear how light allosterically activates DHFR, and how disperse mutations modulate the allosteric effect.
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