Solvation Free Energies in Subsystem Density Functional Theory

Journal of Chemical Theory and Computation, Journal Year: 2022, Volume and Issue: 18(2), P. 723 - 740

Published: Jan. 5, 2022

For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for explicit quantum mechanical solute-solvent and solvent-solvent interactions based on subsystem density functional theory continuum solvation schemes. Since molecules may compromise scalability model transferability predicted effect, aim to retain both, different solutes as well solvents. The key is consistent decomposition solute solvent. performance DFT increasing numbers subsystems. We investigate molecular dynamics stationary point sampling configurations compare resulting (Gibbs) free energies experiment theoretical methods. can show that with our reaction barriers accurately reproduced compared experimental data.

Language: Английский

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Quantum Chemical Microsolvation by Automated Water Placement

Molecules, Journal Year: 2021, Volume and Issue: 26(6), P. 1793 - 1793

Published: March 23, 2021

We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on free energy solvation thermodynamics derived from molecular dynamics (MD) simulations and grid inhomogeneous theory (GIST). This protocol enabled us rigorously define number, position, orientation determine their interaction with solute physical quantities. The generated solute-solvent clusters served as an input for subsequent investigations. showcased applicability, scope, limitations this computational number small molecules, including urea, 2-aminobenzothiazole, (+)-

Language: Английский

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PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

Journal of Chemical Information and Modeling, Journal Year: 2023, Volume and Issue: 63(17), P. 5400 - 5407

Published: Aug. 22, 2023

We introduce PyConSolv, a freely available Python package that automates the generation of conformers metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using streamlined workflow interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for any solvent. Input requirements are minimal; only geometry structure desired solvent xyz (XMOL) format needed. The can also account charged systems, by including arbitrary counterions simulation. A bonded model parametrization performed automatically, utilizing AmberTools, ORCA, Multiwfn software packages. provides selection preparametrized solvents use show applicability our on number (transition-metal-containing) systems. provided open source free charge.

Language: Английский

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Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy

Physical Chemistry Chemical Physics, Journal Year: 2021, Volume and Issue: 23(32), P. 17079 - 17096

Published: Jan. 1, 2021

A general “four-pillar strategy” (theory, simulation, machine learning and augemented reality/virtual reality) to integrate computational experimental spectroscopy.

Language: Английский

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Revisiting conformations of methyl lactate in water and methanol

The Journal of Chemical Physics, Journal Year: 2021, Volume and Issue: 155(2)

Published: July 13, 2021

The recently developed efficient protocols to implicit [Grimme et al., J. Phys. Chem. A 125, 4039–4054 (2021)] and explicit quantum mechanical modeling of non-rigid molecules in solution [Katsyuba B 124, 6664–6670 (2020)] are applied methyl lactate (ML). Building upon this work, a new combination scheme is proposed incorporate solvation effects for the computation infrared (IR) absorption spectra. Herein, Boltzmann populations calculated implicitly solvated single conformers used weight IR spectra explicitly clusters with size typically ten solvent molecules, i.e., accounting first shell. It found that water methanol, most abundant ML structurally modified relative gas phase, where major form ML1, which syn conformation –OH moiety stabilized by OH⋯O=C intramolecular hydrogen bond (HB). In solution, transforms gauche because HB disrupted intermolecular HBs hydroxyl carbonyl groups. Similar changes induced gas-solution transition observed minor conformers, ML2 and/or ML3, characterized OH⋯OCH3 phase. abundance ML1 shown decrease from ∼96% ∼51% ∼92% methanol. strongly influences frequencies, intensities, normal modes, resulting qualitatively different compared Some liquid-state conformational markers fingerprint region revealed.

Language: Английский

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Disentangling the complex network of non-covalent interactions in fenchone hydrates via rotational spectroscopy and quantum chemistry

Physical Chemistry Chemical Physics, Journal Year: 2021, Volume and Issue: 23(36), P. 20686 - 20694

Published: Jan. 1, 2021

We report on the microwave spectra of water adducts fenchone. In particular, we were able to observe spectral signatures three trihydrates

Language: Английский

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Solvation Free Energies from Machine Learning Molecular Dynamics

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: 20(11), P. 4820 - 4823

Published: May 21, 2024

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations a hybrid model. is first re-expressed within quasi-chemical theory solvation. Then, allow for longer simulation times than original and thus improve convergence statistical averages at fraction computational cost, machine-learned (ML) energy function trained on FP forces used in MD simulations. ML workflow (≈200 ps) are adjusted converge predicted chemical accuracy 0.04 eV. successfully benchmarked same set alkaline alkaline-earth ions.

Language: Английский

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Single-ion solvation free energy: A new cluster–continuum approach based on the cluster expansion method

Physical Chemistry Chemical Physics, Journal Year: 2021, Volume and Issue: 23(47), P. 26902 - 26910

Published: Jan. 1, 2021

Accurate calculation of the solvation free energy single ions remains an important goal, involving development in dielectric continuum models, and statistical mechanics with explicit solvent hybrid discrete-continuum methods. In last case, many research studies involve a quasi-chemical approach using monomer cycle or cluster to calculate ions. this work, different cluster-continuum based on expansion method was tested for 16 cations 32 anions aqueous solution. The SMD model used part three water molecules were introduced region solute highest interaction energy. Harmonic frequency calculations molecular dynamics sampling configurations are not required. An empirical γN parameter another is introduced. produces substantial improvement mean absolute deviation 2.3 kcal mol-1 2.9 anions. analysis correlation between theoretical experimental data linear regression line slope 1.09 1.01 good results approximated suggest that could be further improved by including more configurations.

Language: Английский

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Exploring borderline S_N1–S_N2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

RSC Advances, Journal Year: 2024, Volume and Issue: 14(7), P. 4692 - 4701

Published: Jan. 1, 2024

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly solvolysis often exhibit borderline pathway. A molecular-level understanding these processes fundamental developing more efficient transformations. Typically, quantum-chemical simulations solvent medium combine explicit implicit solvation methods. The configuration molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations generating initial configurations, bottom-up methods involve user-dependent protocols to add around substrate. Herein, we investigated mechanism hydrolysis substrate, isopropyl chloride (iPrCl), DFT-M06-2X/aug-cc-pVDZ level, employing + protocols. Top-down approaches were employed generate substrate-solvent complexes varying number (n = 1, 3, 5, 7, 9, 12) configurations H2O molecules. Our findings consistently reveal regardless approach, iPrCl follows loose-SN2-like with nucleophilic assistance. Increasing water cluster substrate most cases led reaction barriers ΔH‡ ≈ 21 kcal mol-1, nine from MC sufficient describe reaction. More O'Ferrall-Jencks plot demonstrates an SN1-like character all transition state structures, showing clear merged profile. fragmentation activation strain analyses indicate energy are predominantly controlled by solvent-substrate interactions, supported leaving group stabilization assessed CHELPG atomic charges.

Language: Английский

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Navigating chemical reaction space with a steering wheel

arXiv (Cornell University), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 1, 2023

Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting networks are so vast that an all potentially accessible intermediates is computationally too demanding. This renders brute-force explorations unfeasible, while with completely pre-defined or hard-wired constraints, such as element-specific coordination numbers, not flexible enough for systems. Here, we introduce Steering Wheel guide otherwise unbiased automated exploration. The algorithm intuitive, generally applicable, and enables one focus on specific regions emerging network. It also allows guiding data generation in context mechanism exploration, catalyst design, other optimization challenges. demonstrated elucidation transition metal catalysts. We highlight how catalytic cycles reproducible way. objectives fully adjustable, allowing harness both structure-specific (accurate) calculations well broad high-throughput screening possible intermediates.

Language: Английский

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