Optimization of colloidal nanoparticle synthesis techniques requires an understanding of underlying particle growth mechanisms. Nonclassical growth mechanisms are particularly important as they affect nanoparticle size and shape distributions, which in turn influence functional properties. For example, preferential attachment of nanoparticles is known to lead to the formation of mesocrystals, although the formation mechanism is currently not well-understood. Here we employ in situ liquid cell scanning transmission electron microscopy and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally observed preference for end-to-end attachment of silver nanorods is a result of weaker solvation forces occurring at rod ends. SMD reveals that when the side of a nanorod approaches another rod, perturbation in the surface-bound water at the nanorod surface creates significant energy barriers to attachment. Additionally, rod morphology (i.e., facet shape) effects can explain the majority of the side attachment effects that are observed experimentally.
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http://dx.doi.org/10.1021/acsnano.5b06632 | DOI Listing |
J Chem Inf Model
January 2025
Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.
The near neutral p of histidine is commonly exploited to engineer pH-sensitive biomolecules. For example, histidine mutations introduced in the complementarity-determining region (CDR) of therapeutic antibodies can enhance selectivity for antigens in the acidic microenvironment of solid tumors or increase dissociation rates in the acidic early endosomes of cells. While solvent-exposed histidines typically have a p near 6.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States.
The separation and structural identification of glycans are of great bioanalytical importance. To obtain a good understanding of the structural flexibility of glycans, replica exchange molecular dynamics (REMD) simulations were used based on AMBER force field calculations to create ensembles of glycan structures. Nonpolar surface area (NPSA) calculations based on continuum solvation (CS) models (Dhakal, R.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Center for Advanced Materials Research, Beijing Normal University at Zhuhai, Zhuhai, 519087, China.
Understanding the molecular mechanism of inhibitor binding to prostate-specific membrane antigen (PSMA) is of fundamental importance for designing targeted drugs for prostate cancer. Here we designed a series of PSMA-targeting inhibitors with distinct molecular structures, which were synthesized and characterized using both experimental and computational approaches. Microsecond molecular dynamics simulations revealed the structural and thermodynamic details of PSMA-inhibitor interactions.
View Article and Find Full Text PDFJ 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 Chem Phys
January 2025
Department of Chemistry - Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden.
Isonitrile-derivatized amino acids are emerging as highly effective infrared (IR) probes for investigating the structures and dynamics of hydrogen (H)-bonds. These probes enable the quantification of chemical exchange processes in solute-solvent complexes via two-dimensional IR spectroscopy and hold significant promise for site-specific dynamic studies within proteins. Despite their potential, theoretical models that elucidate the solvatochromism of isonitriles remain underdeveloped.
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