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Journals Journal of Chemical Theory and...

Journal of Chemical Theory and Computation

https://read.qxmd.com/read/38538531/calculations-of-absolute-free-energies-enthalpies-and-entropies-for-drug-binding
#1
JOURNAL ARTICLE
Christopher M Summa, Dillon P Langford, Sam H Dinshaw, Jennifer Webb, Steven W Rick
Computer simulation methods can aid in the rational design of drugs aimed at a specific target, typically a protein. The affinity of a drug for its target is given by the free energy of binding. Binding can be further characterized by the enthalpy and entropy changes in the process. Methods exist to determine exact free energies, enthalpies, and entropies that are dependent only on the quality of the potential model and adequate sampling of conformational degrees of freedom. Entropy and enthalpy are roughly an order of magnitude more difficult to calculate than the free energy...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38537131/analyzing-lipid-membrane-defects-via-a-coarse-grained-to-triangulated-surface-map-the-role-of-lipid-order-and-local-curvature-in-molecular-binding
#2
JOURNAL ARTICLE
Rianne W I van der Pol, Bregje W Brinkmann, G J Agur Sevink
Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature. We have applied our protocol to investigate the role of local curvature and varying lipid packing on the defect constant π...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38536965/nonadiabatic-conical-intersection-dynamics-in-the-local-diabatic-representation-with-strang-splitting-and-fourier-basis
#3
JOURNAL ARTICLE
Bing Gu
We develop and implement an exact conical intersection nonadiabatic wave packet dynamics method that combines the local diabatic representation, Strang splitting for the total molecular propagator, and discrete variable representation with uniform grids. By employing the local diabatic representation, this method captures all nonadiabatic effects, including nonadiabatic transitions, electronic coherences, and geometric phase. Moreover, it is free of singularities in the first and second derivative couplings and does not require the electronic wave function to be continuous with respect to the nuclear coordinates...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38536144/free-energy-density-of-a-fluid-and-its-role-in-solvation-and-binding
#4
JOURNAL ARTICLE
Michael K Gilson, Tom Kurtzman
The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. <u>First</u>, we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, f ( R ), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, f bulk , near a solute but should asymptotically approach f bulk with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38531828/first-principles-models-of-polymorphism-of-pharmaceuticals-maximizing-the-accuracy-to-cost-ratio
#5
JOURNAL ARTICLE
Jan Ludík, Veronika Kostková, Štefan Kocian, Petr Touš, Vojtěch Štejfa, Ctirad Červinka
Accuracy and sophistication of in silico models of structure, internal dynamics, and cohesion of molecular materials at finite temperatures increase over time. Applicability limits of ab initio polymorph ranking that would be feasible at reasonable costs currently represent crystals of moderately sized molecules (less than 20 nonhydrogen atoms) and simple unit cells (containing rather only one symmetry-irreducible molecule). Extending the applicability range of the underlying first-principles methods to larger systems with a real-life significance, and enabling to perform such computations in a high-throughput regime represent additional challenges to be tackled in computational chemistry...
March 26, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38530869/toward-post-hartree-fock-accuracy-for-protein-ligand-affinities-using-the-molecules-in-molecules-fragmentation-based-method
#6
JOURNAL ARTICLE
Ankur K Gupta, Sarah Maier, Bishnu Thapa, Krishnan Raghavachari
The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation...
March 26, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38527958/reweighting-from-molecular-mechanics-force-fields-to-the-ani-2x-neural-network-potential
#7
JOURNAL ARTICLE
Sara Tkaczyk, Johannes Karwounopoulos, Andreas Schöller, H Lee Woodcock, Thierry Langer, Stefan Boresch, Marcus Wieder
To achieve chemical accuracy in free energy calculations, it is necessary to accurately describe the system's potential energy surface and efficiently sample configurations from its Boltzmann distribution. While neural network potentials (NNPs) have shown significantly higher accuracy than classical molecular mechanics (MM) force fields, they have a limited range of applicability and are considerably slower than MM potentials, often by orders of magnitude. To address this challenge, Rufa et al. [Rufa et al...
March 25, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38518257/systematic-incorporation-of-ionic-hard-core-size-into-the-debye-h%C3%A3-ckel-theory-via-the-cumulant-expansion-of-the-schwinger-dyson-equations
#8
JOURNAL ARTICLE
Sahin Buyukdagli
The Debye-Hückel (DH) formalism of bulk electrolytes equivalent to the Gaussian-level closure of the electrostatic Schwinger-Dyson identities without the interionic hard-core (HC) coupling is extended via the cumulant treatment of these equations augmented by HC interactions. By comparing the monovalent ion activity and pressure predictions of our cumulant-corrected DH (CCDH) theory with hypernetted-chain results and Monte Carlo simulations from the literature, we show that this rectification extends the accuracy of the DH formalism from submolar to molar salt concentrations...
March 22, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38518174/analytical-form-of-the-fluorescence-correlation-spectroscopy-autocorrelation-function-in-chemically-reactive-systems
#9
JOURNAL ARTICLE
Andrzej Poniewierski, Robert Hołyst
Fluorescence correlation spectroscopy (FCS) applied to chemically reactive systems provides information about chemical reaction equilibrium constants and diffusion coefficients of reactants. These physical quantities are determined from the FCS-measured autocorrelation function, G ( t ), as a function of time, t . In most of the studied cases, the analytical form of G ( t ) is well-known for reactions that are much faster than the diffusion time of reactants across the focal volume probed by FCS or when they are much slower than the diffusion time...
March 22, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38516954/valency-of-ligand-receptor-binding-from-pair-potentials
#10
JOURNAL ARTICLE
William Morton, Robert Vácha, Stefano Angioletti-Uberti
Coarse grained molecular dynamics simulations have been crucial for investigating the dynamics of nanoparticle uptake by cell membranes via ligand-receptor interactions. These models have enabled researchers to evaluate the effects of nanoparticle size, shape, and ligand distribution on cellular uptake. However, when pair potentials are used to represent ligand-receptor interactions, the number of receptors interacting with one ligand, valency, may vary. We demonstrate that the curvature of a nanoparticle, strength of ligand-receptor interactions, and ligand or receptor concentration change the valency, ranging from 3...
March 22, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38513261/improved-cps-and-cbs-extrapolation-of-pno-ccsd-t-energies-the-mobh35-and-isol24-data-sets
#11
JOURNAL ARTICLE
Kesha Sorathia, Damyan Frantzov, David P Tew
Computation of heats of reaction of large molecules is now feasible using the domain-based pair natural orbital (PNO)-coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] theory. However, to obtain agreement within 1 kcal/mol of experiment, it is necessary to eliminate basis set incompleteness error, which comprises both the AO basis set error and the PNO truncation error. Our investigation into the convergence to the canonical limit of PNO-CCSD(T) energies with the PNO truncation threshold <mml:math xmlns:mml="https://www...
March 21, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38513192/locating-transition-states-by-variational-reaction-path-optimization-with-an-energy-derivative-free-objective-function
#12
JOURNAL ARTICLE
Shin-Ichi Koda, Shinji Saito
Locating transition states is essential for understanding molecular reactions. We propose a double-ended transition state search method by revisiting a variational reaction path optimization method known as the MaxFlux method. Although its original purpose is to add temperature effects to reaction paths, we conversely let the temperature approach zero to obtain an asymptotically exact minimum energy path and its corresponding transition state in variational formalism with an energy-derivative-free objective function...
March 21, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38507252/constant-ph-simulations-with-the-polarizable-atomic-multipole-amoeba-force-field
#13
JOURNAL ARTICLE
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Accurately predicting protein behavior across diverse pH environments remains a significant challenge in biomolecular simulations. Existing constant-pH molecular dynamics (CpHMD) algorithms are limited to fixed-charge force fields, hindering their application to biomolecular systems described by permanent atomic multipoles or induced dipoles. This work overcomes these limitations by introducing the first polarizable CpHMD algorithm in the context of the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field...
March 20, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38502776/pcmresp-a-method-for-polarizable-force-field-parameter-development-and-transferability-of-the-polarizable-gaussian-multipole-models-across-multiple-solvents
#14
JOURNAL ARTICLE
Yong Duan, Taoyu Niu, Junmei Wang, Piotr Cieplak, Ray Luo
The transferability of force field parameters is a crucial aspect of high-quality force fields. Previous investigations have affirmed the transferability of electrostatic parameters derived from polarizable Gaussian multipole models (pGMs) when applied to water oligomer clusters, polypeptides across various conformations, and different sequences. In this study, we introduce PCMRESP, a novel method for electrostatic parametrization in solution, intended for the development of polarizable force fields. We utilized this method to assess the transferability of three models: a fixed charge model and two variants of pGM models...
March 19, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38502102/aufbau-suppressed-coupled-cluster-theory-for-electronically-excited-states
#15
JOURNAL ARTICLE
Harrison Tuckman, Eric Neuscamman
We introduce an approach to improve single-reference coupled cluster theory in settings where the Aufbau determinant is absent from or plays only a small role in the true wave function. Using a de-excitation operator that can be efficiently hidden within a similarity transform, we create a coupled cluster wave function in which de-excitations work to suppress the Aufbau determinant and produce wave functions dominated by other determinants. Thanks to an invertible and fully exponential form, the approach is systematically improvable, size consistent, size extensive, and, interestingly, size intensive in a granular way that should make the adoption of some ground state techniques, such as local correlation, relatively straightforward...
March 19, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38501645/kinetic-ensemble-of-tau-protein-through-the-markov-state-model-and-deep-learning-analysis
#16
JOURNAL ARTICLE
Yongna Yuan, Xuqi Mao, Xiaohang Pan, Ruisheng Zhang, Wei Su
The ordered assembly of Tau protein into filaments characterizes Alzheimer's and other neurodegenerative diseases, and thus, stabilization of Tau protein is a promising avenue for tauopathies therapy. To dissect the underlying aggregation mechanisms on Tau, we employ a set of molecular simulations and the Markov state model to determine the kinetics of ensemble of K18. K18 is the microtubule-binding domain of Tau protein and plays a vital role in the microtubule assembly, recycling processes, and amyloid fibril formation...
March 19, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38499981/high-throughput-computational-screening-of-solid-binding-peptides
#17
JOURNAL ARTICLE
Xin Qi, Jim Pfaendtner
Inspired by biomineralization, a naturally occurring, protein-facilitated process, solid-binding peptides (SBPs) have gained much attention for their potential to fabricate various shaped nanocrystals and hierarchical nanostructures. The advantage of SBPs over other traditionally used synthetic polymers or short ligands is their tunable interaction with the solid material surface via carefully programmed sequence and being solution-dependent simultaneously. However, designing a sequence with targeted binding affinity or selectivity often involves intensive processes such as phage display, and only a limited number of sequences can be identified...
March 18, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38498914/competition-between-stacking-and-divalent-cation-mediated-electrostatic-interactions-determines-the-conformations-of-short-dna-sequences
#18
JOURNAL ARTICLE
Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T Nguyen, D Thirumalai
Interplay between divalent cations (Mg2+ and Ca2+ ) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30 , with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments...
March 18, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38498904/enhanced-twist-averaging-technique-for-magnetic-metals-applications-using-quantum-monte-carlo
#19
JOURNAL ARTICLE
Abdulgani Annaberdiyev, Panchapakesan Ganesh, Jaron T Krogel
We propose an improved twist-averaging (TA) scheme for quantum Monte Carlo methods that use converged Kohn-Sham or Hartree-Fock orbitals as the reference. This TA technique is tailored to sample the Brillouin zone of magnetic metals, although it naturally extends to nonmagnetic (NM) conducting systems. The proposed scheme aims to reproduce the reference magnetization and achieves charge neutrality by construction, thus avoiding the large energy fluctuations and the postprocessing needed to correct the energies...
March 18, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38497488/systematic-qm-mm-study-for-predicting-31-p-nmr-chemical-shifts-of-adenosine-nucleotides-in-solution-and-stages-of-atp-hydrolysis-in-a-protein-environment
#20
JOURNAL ARTICLE
Judit Katalin Szántó, Johannes C B Dietschreit, Mikhail Shein, Anne K Schütz, Christian Ochsenfeld
NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential...
March 18, 2024: Journal of Chemical Theory and Computation
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