The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation

ChemPhysChem, Journal Year: 2024, Volume and Issue: 25(14)

Published: May 16, 2024

Abstract The enhancement of the peptide bond order by a resonance in lone pair N and π‐bond CO is analyzed. A decomposition terms localized molecular orbitals developed applied to bond. combination two rotations hybrid proposed improve boundary treatment fragment orbital method. approach bonds, it found crucial retain π variational space both fragments across boundary. interaction energies between conventional amino acid residues Trp‐cage (1L2Y) are discussed.

Language: Английский

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Nanoscale chemical reaction exploration with a quantum magnifying glass

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 22, 2024

Abstract Nanoscopic systems exhibit diverse molecular substructures by which they facilitate specific functions. Theoretical models of them, aim at describing, understanding, and predicting these capabilities, are difficult to build. Viable quantum-classical hybrid come with challenges regarding atomistic structure construction quantum region selection. Moreover, if their dynamics mapped onto a state-to-state mechanism such as chemical reaction network, its exhaustive exploration will be impossible due the combinatorial explosion space. Here, we introduce “quantum magnifying glass” that allows one interactively manipulate nanoscale structures level. The glass seamlessly combines autonomous model parametrization, ultra-fast mechanical calculations, automated exploration. It represents an approach investigate complex sequences in physically consistent manner unprecedented effortlessness real time. We demonstrate features for reactions bio-macromolecules metal-organic frameworks, highlight general applicability.

Language: Английский

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Neural Network Potential with Multiresolution Approach Enables Accurate Prediction of Reaction Free Energies in Solution

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

We present the design and implementation of a novel neural network potential (NNP) its combination with an electrostatic embedding scheme, commonly used within context hybrid quantum-mechanical/molecular-mechanical (QM/MM) simulations. Substitution computationally expensive QM Hamiltonian by NNP same accuracy largely reduces computational cost enables efficient sampling in prospective MD simulations, main limitation faced traditional QM/MM setups. The model relies on recently introduced anisotropic message passing (AMP) formalism to compute atomic interactions encode symmetries found systems. AMP is shown be highly terms both data costs can readily scaled sample systems involving more than 350 solute 40,000 solvent atoms for hundreds nanoseconds using umbrella sampling. Most deviations predictions from underlying DFT ground truth lie chemical (4.184 kJ mol–1). performance broad applicability our approach are showcased calculating free-energy surface alanine dipeptide, preferred ligation states nickel phosphine complexes, dissociation free energies charged pyridine quinoline dimers. Results this ML/MM show excellent agreement experimental reach most cases. In contrast, calculated static calculations paired implicit models or simulations cheaper semiempirical methods up ten times higher deviation sometimes even fail reproduce qualitative trends.

Language: Английский

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Fractional charging of electronically open molecules: An explicit projection operator approach

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(9)

Published: March 7, 2025

We introduce an approach to describe fractional charging of molecules interacting non-covalently with their environment. The formalism is based on dividing the full orbital space into orbitals localized molecule and This enables a separation electronic Hamiltonian terms referencing only molecule, environment, or interaction terms. are divided particle-conserving interactions particle-non-conserving (particle-breaking) interactions. dominant may be included using standard embedding schemes. particle-breaking responsible for inducing charging, we show that local provides convenient framework different types perturbative treatments. In basis, generate basis many-electron states composite system, in which specific molecular charge label each state. used construct projection operator acting Liouville-von Neumann equation system yield reduced density matrix molecule. diagonal elements represent populations determine charging. projected starting point two treatments: damped response theory Redfield theory. introduces energy broadening states. Phenomenological also introduced equation. illustrate presented by considering benzene physisorbed finite graphene sheet as toy model.

Language: Английский

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JOYCE3.0: A General Protocol for the Specific Parametrization of Accurate Intramolecular Quantum Mechanically Derived Force Fields

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

While the intrinsically multiscale nature of most advanced materials necessitates use cost-effective computational models based on classical physics, a reliable description structure and dynamics their components often requires quantum-mechanical treatment. In this work, we present JOYCE3.0, software package for parametrization accurate, quantum-mechanically derived force fields (QMD-FFs). Since its original release, code has been extensively automated expanded, with all novel implementations thoroughly discussed. To illustrate general applicability, QMD-FFs are parametrized seven benchmark cases, encompassing molecules diverse structures properties. These range from exotic stiff scaffolds, flexible polymeric chains, polyenes biological interest to transition-metal complexes. On one hand, JOYCE3.0 FFs consistently outperform available general-purpose descriptions, achieving excellent agreement higher-level theoretical methods or experimental validation data. other remarkable accuracy found in molecular extends electronic excited states, enabling integration into multilevel protocols aimed at reliably predicting selected properties spectral line shapes optoelectronic materials. The high quality results─spanning structures, condensed-phase properties, spectroscopic features─in combination enhanced interface popular codes engines, as well applicability chemically species, strongly suggests that could play pivotal role rational design functionalized heterogeneous systems.

Language: Английский

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Energy decomposition analysis method with the DFT-in-xTB embedding strategy for intermolecular interactions in large systems

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(12)

Published: March 24, 2025

In this work, an energy decomposition analysis (EDA) method, termed DM-EDA(EB), is introduced to explore intermolecular interactions in large systems by employing a DFT-in-xTB embedding scheme. DM-EDA(EB) integrates density matrix-based EDA (DM-EDA) with the GFNn-xTB method decompose total interaction into electrostatic, exchange–repulsion, polarization, and correlation terms. Test cases demonstrate that can accurately analyze energies computational efficiency comparable GFNn-xTB. Notably, using appropriate partition strategy, able provide quantificational knowledge of individual assemblies.

Language: Английский

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On-Surface Synthesis and Cryogenic Exfoliation of Sterically Frustrated Atropisomers

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

On-surface synthesis provides exceptional control over nanostructure and material composition, enabling the creation of molecular compounds that are difficult or impossible to obtain with other methods. In this work, we demonstrate possibility synthesizing atropisomeric molecules made chains polyaromatic hydrocarbon units via on-surface synthesis. Scanning probe microscopy reveals adsorbed on Au(111) surfaces adopt a planar structure, adjacent monomeric aligning either in parallel antiparallel configurations, influencing alignment molecule surface. Cryo-force spectroscopy peeling experiments show metastable conformers can be mechanically stabilized during lifting-redeposition process polymer from process, periodic drops frequency shift observed, corresponding monomer detachment-readsorption. Interestingly, periodicity is independent parallel/antiparallel configuration but counterintuitively smaller than size. Molecular dynamics simulations relate effective reduction unit length tethering effect between chain This, turn, allowed us test validate Silva's analytical phenomenological power law model for peeling. Our findings not only provide method studying elusive class 1 also offer deeper insight into phenomenon at nanoscale.

Language: Английский

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The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems

Journal of Computational Chemistry, Journal Year: 2025, Volume and Issue: 46(11)

Published: April 19, 2025

Molecular properties in combined quantum mechanics and molecular (QM/MM) simulations have been shown to be dependent on the size of mechanical (QM) region amount conformational sampling. Previous studies largely focused enzymatic systems, which made it difficult distinguish effects QM sampling from other factors including QM-MM boundary artifacts effects. This study uses difference-based adaptive solvation QM/MM method investigate tautomerization reactions alanine aspartate explicit solvent. The choice computationally tractable systems enables decoupling a direct comparison free energy surfaces with potential (PESs). results show that (1) is crucial properly account for thermal fluctuations along reaction pathways, (2) converge rapidly increasing size, whereas charge transfer requires slightly larger achieve convergence. These findings are expected guide future complex where methods applied.

Language: Английский

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Time-Dependent Particle-Breaking Hartree–Fock Model for Electronically Open Molecules

The Journal of Physical Chemistry A, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

We develop the time-dependent particle-breaking Hartree-Fock (TDPBHF) model to describe excited states and linear response properties of electronically open molecules. This work represents first step toward building a wave function-based theory framework for quantum systems equivalent that closed systems. In limit particle conservation, TDPBHF reduces standard theory. illustrate by computing valence absorption spectra frequency-dependent electric dipole polarizabilities set small- medium-sized organic The interactions are observed nonuniformly redshift excitation energies induce qualitative changes in profile. addition, mixing multiple excitations function is dampen divergence vicinity resonance energies.

Language: Английский

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PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(3)

Published: July 15, 2024

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program designed to treat short-range and long-range interactions through user-specified combinations electrostatic mechanical embedding procedures within periodic simulation domains, providing necessary interfaces external chemistry molecular dynamics software. To enable direct electrostatics in systems, we have derived implemented force terms our previously described QM/MM/PME approach [Pederson McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with software packages Psi4 OpenMM facilitated Python application programming (APIs). core library contains basic utilities running QM/MM simulations, plug-in entry-points are provided users implement custom energy/force calculation integration routines, an extensible architecture. user interacts primarily its API, allowing complex workflow development scripting, example, interfacing PLUMED free energy simulations. We provide benchmarks forces conservation alternative approaches. further demonstrate simple example use case water solute solvent system, which radial distribution functions computed from 100 ps simulations; this highlight how solvation structure sensitive different basis-set choices due under- or over-polarization QM molecule’s electron density.

Language: Английский

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