Publications related to Spartan (chemistry software)

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

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

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

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

NMR Crystallography in the Big Data Era: New Methods and Applications Powered by Machine Learning

Manuel Cordova

Structure determination of materials is key to understanding their physical properties. While single-crystal X-ray diffraction is the gold standard for structures displaying long-range order, many materials of interest are polycrystalline and/or disordered ...

EPFL2023

Multiphysics model for assessing photoelectrochemical phenomena under concentrated irradiation

Sophia Haussener, Isaac Thomas Holmes-Gentle, Franky Esteban Bedoya Lora

A multiphysics model was developed for a photoelectrochemical (PEC) cell at the device level to simulate water splitting operating under concentrated irradiation (between 50 to 600 kW m−2). The 2D model couples charge, heat, mass, photon, and momentum tran ...

2023

Magnon-phonon interactions enhance the gap at the Dirac point in the spin-wave spectra of CrI3 two-dimensional magnets

Iurii Timrov

Recent neutron-diffraction experiments in honeycomb CrI3 quasi-2D ferromagnets have evinced the existence of a gap at the Dirac point in their spin-wave spectra. The existence of this gap has been attributed to strong in-plane Dzyaloshinskii-Moriya or Kita ...

2023

turboMagnon - A code for the simulation of spin-wave spectra using the Liouville-Lanczos approach to time-dependent density-functional perturbation theory

Iurii Timrov

We introduce turboMagnon, an implementation of the Liouville-Lanczos approach to linearized time-dependent density-functional theory, designed to simulate spin-wave spectra in solid-state materials. The code is based on the noncollinear spin-polarized fram ...

ELSEVIER2022

Structure determination of an amorphous drug through large-scale NMR predictions

David Lyndon Emsley, Pierrick Berruyer, Albert Hofstetter, Manuel Cordova, Federico Maria Paruzzo, Bruno Simões de Almeida, Martins Balodis

Knowledge of the structure of amorphous solids can direct, for example, the optimization of pharmaceutical formulations, but atomic-level structure determination in amorphous molecular solids has so far not been possible. Solid-state nuclear magnetic reson ...

Nature Research2021

Machine learning for metallurgy II. A neural-network potential for magnesium

William Curtin, Binglun Yin, Eleanor Yi Kei Mak

Interatomic potentials are essential for studying fundamental mechanisms of deformation and failure in metals and alloys because the relevant defects (dislocations, cracks, etc.) are far above the scales accessible to first-principles studies. Existing pot ...

2020

Accuracy of Molecular Simulation-Based Predictions of k(off) Values: A Metadynamics Study

Ursula Röthlisberger, Simone Meloni, Viacheslav Bolnykh, Michele Parrinello, Paolo Carloni

The k(off) values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-i ...

AMER CHEMICAL SOC2020

Efficient Treatment of Correlation Energies at the Basis-Set Limit by Monte Carlo Summation of Continuum States

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The calculation of electron correlation is vital for the description of atomistic phenomena in physics, chemistry, and biology. However, accurate wavefunction-based methods exhibit steep scaling and often sluggish convergence with respect to the basis set ...

AMER CHEMICAL SOC2020

Theoretical Investigation of the Electronic Structure and Magnetic Properties of Oxo-Bridged Uranyl(V) Dinuclear and Trinuclear Complexes

Marinella Mazzanti

The uranyl(V) complexes UO2(dbm)(2)K(18C6) (dbm = dibenzoylmethanate) and UO2(L)(L = 2-(4-tolyl)-1,3-bis(quinolyl)malondiiminate), exhibiting diamond-shaped U2O2 and triangular-shaped U3O3 cores respectively with 5f(1)-5f(1 )and 5f(1)-5f(1)-5f(1) ...

2019

Microhydration of Dibenzo-18-Crown-6 Complexes with K+, Rb+, and Cs+ Investigated by Cold UV and IR Spectroscopy in the Gas Phase

Thomas Rizzo, Yoshiya Inokuchi

In this Article, we examine the hydration structure of dibenzo-18-crown-6 (DB18C6) complexes with K+, Rb+, and Cs+ ion in the gas phase. We measure well-resolved UV photodissociation (UVPD) spectra of K+·DB18C6·(H2O)n, Rb+·DB18C6·(H2O)n, and Cs+·DB18C6·(H2 ...

2018

Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev, Robert Benny Gerber

The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed th ...

2018

Cold ion spectroscopy for structural identifications of biomolecules

Oleg Boyarkine

Over the last decade, the spectroscopy of cryogenically cold ions iso- lated in the gas phase has been developed as a new tool for structural elucidations of biological molecules. Cooling allows for vibrational resolution in UV and IR spectra of small to m ...

2018

High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev

Histidine remained the last aromatic amino acid for which the intrinsic spectroscopic properties and structures were obscure. We measured the UV and IR spectra of protonated histidine, isolated in the gas phase, using photofragmentation cold ion spectrosco ...

Wiley-Blackwell2017

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Sara Bonella, Mohammadhassan Valadan

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime ...

2017

A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy

Natalia Nagornova, Oleg Boyarkine, Robert Benny Gerber

The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic le ...

American Chemical Society2017

Columnar self-assembly of N,N ',N ''-trihexylbenzene-1,3,5-tricarboxamides investigated by means of NMR spectroscopy and computational methods in solution and the solid state

Diego Carnevale, Mathieu Baudin

The columnar self-assembly resulting from units of N, N', N"-trihexylbenzene-1,3,5-tricarboxamide is investigated in solution and the solid state by means of NMR spectroscopy. A parallel computational study utilizing both semiempirical and DFT methods allo ...

Royal Soc Chemistry2017

Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks

Berend Smit, Daniele Ongari, Davide Tiana

The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore bee ...

American Chemical Society2017

Targeted design of alpha-MnO2 based catalysts for oxygen reduction

Michael Markus Busch

The paper focuses on theoretical and experimental aspects of an oxide surface optimization for oxygen reduction reaction (ORR). Various doped alpha-MnO2 based electrocatalysts were prepared by microwave-assisted hydrothermal synthesis and electrochemically ...

Pergamon-Elsevier Science Ltd2016