Publications related to Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

Related publications (32)

Solvation Free Energies from Machine Learning Molecular Dynamics

Nicola Marzari, Nicéphore Arthur François Bonnet

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] to calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations of a hybrid solvation model. The approa ...

Amer Chemical Soc2024

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger, Sophia Kathryn Johnson

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

EPFL2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

Paolo Pegolo

We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...

Amer Chemical Soc2024

Thermal transport of glasses via machine learning driven simulations

Federico Grasselli, Paolo Pegolo

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

Frontiers Media Sa2024

A diversity-driven discovery of potential nanoporous materials for energy-related applications

Sauradeep Majumdar

The design and discovery of potential novel materials is critical for the advancement of climate change mitigation technologies. In this respect, metal-organic frameworks (MOFs) have received considerable attention over the last two decades. The combinatio ...

EPFL2024

Thermal conductivity of Li 3 PS 4 solid electrolytes with ab initio accuracy

Michele Ceriotti, Federico Grasselli, Davide Tisi, Lorenzo Gigli

The vast amount of computational studies on electrical conduction in solid-state electrolytes is not mirrored by comparable efforts addressing thermal conduction, which has been scarcely investigated despite its relevance to thermal management and (over)he ...

Amer Physical Soc2024

Role of Carbonyl Compounds for N-Nitrosamine Formation during Nitrosation: Kinetics and Mechanisms

Yishuai Pan, Urs von Gunten, Florian Frédéric Vincent Breider

N-Nitrosamines are potential human carcinogens frequently detected in natural and engineered aquatic systems. This study sheds light on the role of carbonyl compounds in the formation of N-nitrosamines by nitrosation of five secondary amines via different ...

2024

High-order geometric integrators for the variational Gaussian wavepacket dynamics and application to vibronic spectra at finite temperature

Roya Moghaddasi Fereidani

Molecular quantum dynamics simulations are essential for understanding many fundamental phenomena in physics and chemistry. They often require solving the time-dependent Schrödinger equation for molecular nuclei, which is challenging even for medium-sized ...

EPFL2024

Applications of the thawed Gaussian approximation to electronic spectroscopy

Eriks Kletnieks

The exploration of electronically excited states and the study of diverse photochemical and photophysical processes are the main goals of molecular electronic spectroscopy. Exact quantum-mechanical simulation of such experiments is, however, beyond current ...

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Martin Peter Bircher, Justin Villard

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Hybrid organic/metal-oxide shells on semiconductor nanocrystals via colloidal atomic layer deposition

Ona Segura Lecina

The escalating energy demand and the imperative necessity to reduce the carbon footprint require transformative approaches to energy conversion. Materials chemistry plays a pivotal role in addressing these global challenges by developing novel materials fo ...

EPFL2024

Computational Studies on the Stability of Organic-Inorganic Hybrid Halide Lead Perovskites

Mathias Dankl

Perovskite-based solar cells are currently the most rapidly advancing photovoltaic technology but concerns about their long-term stability are still impeding full-scale commercialization. This thesis provides computational insights into some of the stabili ...

EPFL2024

Live-cell imaging powered by computation

Suliana Manley

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...

Nature Portfolio2024

Second harmonic scattering of nanoparticles: A journey into the electrical double layer

Bingxin Chu

In aqueous solutions, a charged surface causes the redistribution of nearby ions. The ion layers formed are known as the electrical double layer (EDL), and are widespread in many systems involving electrochemistry, colloidal science, biomedicine, and energ ...

EPFL2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

Francesco Aquilante

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments sp ...

Washington2023

Advancing first principle-based molecular dynamics of biological systems with machine learning

François Louis Mouvet

Molecular dynamics (MD) simulations have emerged as a transformative approach to analyse molecular systems at the atomic level, offering valuable insights into complex biological processes. Many biological phenomena can only accurately be described by inco ...

EPFL2023