We present a Monte Carlo approach for performing titration simulations in the canonical ensemble. The standard constant pH (cpH) simulation methods are intrinsically grand canonical, allowing us to study the protonation state of molecules only as a function of pH in the reservoir. Due to the Donnan potential between a system and an (implicit) reservoir of a semi-grand canonical simulation, the pH of the reservoir can be significantly different from that of an isolated system, for an identical protonation state. The new titration method avoids this difficulty by using the canonical reactive Monte Carlo algorithm to calculate the protonation state of macromolecules as a function of the total number of protons present inside the simulation cell. The pH of an equilibrated system is then calculated using a new surface insertion Widom algorithm, which bypasses the difficulties associated with the bulk Widom particle insertion for intermediate and high pH values. To properly treat the long range Coulomb force, we use the Ewald summation method, showing the importance of the Bethe potential for calculating the pH of canonical systems.
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http://dx.doi.org/10.1039/d3cp04607a | DOI Listing |
J Mol Model
January 2025
School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Haidian District, Ding No.11 Xueyuan Road, Beijing, 100083, People's Republic of China.
Context: Understanding the structural characteristics of coal at the molecular level is fundamental for its effective utilization. To explore the molecular structure characteristic, the long-flame coal from Daliuta (DLT), coking coal from Yaoqiao (YQ), and anthracite from Taixi (TX) were investigated using various techniques such as elemental analysis, Fourier transform infrared spectroscopy, solid-state C nuclear magnetic resonance spectroscopy, and X-ray photoelectron spectroscopy. Based on the structural parameters, the coal molecular model was constructed and optimized.
View Article and Find Full Text PDFMol Pharm
January 2025
Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.
Lumefantrine (LMF) is a low-solubility antimalarial drug that cures acute, uncomplicated malaria. It exerts its pharmacological effects against erythrocytic stages of spp. and prevents malaria pathogens from producing nucleic acid and protein, thereby eliminating the parasites.
View Article and Find Full Text PDFDalton Trans
January 2025
Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan.
The Ru(IV,IV), Ru(III,IV), and Ru(III,III) complexes with the doubly oxido- and/or hydroxido-bridged diamond core {Ru(μ-O(H))}, bridged by an η:η:μ-type bidentate sulfato ligand, [{Ru(L)}(μ-O)(μ-OSO)] ( = 1: [III,IV]; = 2: [IV,IV]), [{Ru(L)}(μ-O)(μ-OH)(μ-OSO)] ([III,IV_1H]), and [{Ru(L)}(μ-OH)(μ-OSO)] ([III,III_2H]) (L = ethylbis(2-pyridylmethyl)amine), were synthesised as ClO-salts, and their crystal and electronic structures investigated. The corresponding hydrogencarbonato-bridged Ru(III,III) complex, [{Ru(L)}(μ-OH)(μ-OCOH)] ([III,III(HCO3)_2H]), was also prepared and its crystallographic and electronic structures compared to those of the sulfato-bridged system, [III,III_2H]. All the sulfato-bridged complexes isolated were confirmed in the Pourbaix diagram, wherein the redox potential was plotted as a function of pH.
View Article and Find Full Text PDFDalton Trans
January 2025
Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
The electrochemical proton reactivity of transition metal complexes has received intensive attention in catalyst research. The proton-coupled electron transfer (PCET) process, influenced by the coordination geometry, determines the catalytic reaction mechanisms. Additionally, the p value of a proton source, as an external factor, plays a crucial role in regulating the proton transfer step.
View Article and Find Full Text PDFNano Lett
January 2025
Interdisciplinary Graduate Program in Materials Science, Vanderbilt University, Nashville, Tennessee 37235, United States.
Permeance-selectivity trade-offs are inherent to polymeric membranes. In fuel cells, thinner proton exchange membranes (PEMs) could enable higher proton conductance and increased power density with lower area-specific resistance (ASR), smaller ohmic losses, and lower ionomer cost. However, reducing thickness is accompanied by an increase in undesired species crossover harming performance and long-term efficiency.
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