Article
Chemistry, Physical
Erdal Mutlu, Ajay Panyala, Nitin Gawande, Abhishek Bagusetty, Jeffrey Glabe, Jinsung Kim, Karol Kowalski, Nicholas P. Bauman, Bo Peng, Himadri Pathak, Jiri Brabec, Sriram Krishnamoorthy
Summary: This paper presents the TAMM framework for productive and scalable development of computational chemistry methods. By decoupling computation specifications from execution, TAMM allows domain scientists to focus on algorithmic requirements while optimizing performance on various computing systems. The modular structure of TAMM supports different hardware architectures and incorporates new algorithmic advances.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Juncheng Harry Zhang, Timothy C. Ricard, Cody Haycraft, Srinivasan S. Iyengar
Summary: The weighted-graph approach presented in this paper offers an adaptive method to calculate contributions from many-body approximations in highly fluxional chemical systems for post-Hartree-Fock ab initio molecular dynamics. By dynamically combining graphs and considering a range of neighboring graphical representations during dynamics, the approach improves dynamic trajectories using lower-order many-body interaction terms. This method outperforms traditional approaches in terms of accuracy and cost-effectiveness when computing dynamical properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Onur Caylak, Bjorn Baumeier
Summary: The study focuses on gas-phase geometry optimization of molecules in excited states using many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation. The results show good agreement with higher-order wave function methods for structural parameters, indicating the efficiency of the GW-BSE method in providing accurate excitation energies and geometries.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Chemistry, Multidisciplinary
Justus A. Calvin, Chong Peng, Varun Rishi, Ashutosh Kumar, Edward F. Valeev
Summary: This review examines the deployment of many-body quantum chemistry methods on high-performance computing platforms, specifically focusing on accurate methods like the coupled-cluster method. Before discussing relevant literature, it analyzes the current and future HPC landscape and the computational characteristics of many-body methods that pose challenges to their implementation on HPC systems.
Article
Chemistry, Physical
Kristina M. Herman, Sotiris S. Xantheas
Summary: We have introduced a new formulation of the many-body expansion (MBE) that connects gas-phase clusters to infinite solids via a hierarchical procedure. The validity of the method has been demonstrated for periodic systems by comparing computed lattice energies up to the 4-body in the MBE with those obtained using periodic boundary conditions and an Ewald summation for the 7 ice polymorphs. This development allows for the quantification of many-body contributions to the lattice energy of various ice polymorphs, which range from 7 to 24% of the total lattice energies.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Kristina M. Herman, Sotiris S. Xantheas
Summary: We present a new formulation of the many-body expansion (MBE) for periodic systems and apply it to 7 ice polymorphs. The method is validated by comparing the lattice energies computed using the MBE with those obtained using periodic boundary conditions and Ewald summation. This development enables the quantification of many-body contributions to the lattice energy of ice polymorphs and provides insights into their solid-state properties.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Computer Science, Interdisciplinary Applications
P. Arthuis, A. Tichai, J. Ripoche, T. Duguet
Summary: The second version of the code ADG automates the generation and evaluation of valid off-diagonal Bogoliubov many-body perturbation theory diagrams. It can handle Hamiltonians with both two-body and three-body interactions, and utilizes algebraic Feynman's rules and diagrammatic rules for evaluation. The program has been optimized for efficiency and moved to Python3, while still supporting Python2.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Fabien Bruneval, Nike Dattani, Michiel J. van Setten
Summary: This study systematically evaluates the quality of several perturbation theories against high-level quantum chemistry methods, finding GW to be the most accurate approximation for ionization potentials. Attempts to improve upon GW by adding more diagrams were mostly unsuccessful, with only the inclusion of a GW density-matrix showing positive impact. Additionally, using an improved hybrid functional for the non-interacting Green's function further enhanced the accuracy of the simplest GW approximation.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Thibault Pariat, Maxime Munch, Martyna Durko-Maciag, Jaroslaw Mysliwiec, Pascal Retailleau, Pauline M. Verite, Denis Jacquemin, Julien Massue, Gilles Ulrich
Summary: HBX fluorophores are well-known for their synthetic versatility, photostability, and strong solid-state fluorescence. However, their performance is heavily quenched in solution due to efficient non-radiative pathways. In this study, a simple structural modification of the heteroring in HBX dyes led to significant changes in emission color, dual emission engineering, and fluorescent quantum yield, showing promising abilities as bright dual-state emitters in both solution and solid state.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Woojin Park, Jun Shen, Seunghoon Lee, Piotr Piecuch, Michael Filatov, Cheol Ho Choi
Summary: The study investigated the internal conversion (IC) between the two lowest singlet excited states of s-trans-butadiene and s-trans-hexatriene using a series of methodologies. It was found that some multireference methods and TDDFT approach had issues in describing the 1(1)B(u)(+)/2(1)A(g)(-) crossing, while multistate many-body perturbation theory methods could accurately reproduce the curve crossing. This is promising for nonadiabatic molecular dynamics simulations in larger systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Nanoscience & Nanotechnology
Vrindaa Somjit, Bilge Yildiz
Summary: Identifying the structure of the Al2O3/Al interface is crucial for enhancing its performance in various applications. This study utilizes ab initio grand canonical Monte Carlo to explore the composition and configuration space of the interface, revealing its atomically sharp and layer-by-layer propagation nature. The insights obtained contribute to the design and engineering of Al2O3/Al-based corrosion coatings, controllable transistor technologies, and noise-free superconducting qubits.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Alexey Akimov
Summary: This study computationally investigates the dynamics of electron-hole recombination in pristine and defect-containing monolayer black phosphorus, utilizing advanced methods for handling excited states dynamics. The optoelectronic properties and nonadiabatic dynamics of ground state recovery in these materials are characterized comprehensively using linear-response time-dependent density functional theory and various trajectory surface hopping methodologies with decoherence correction schemes.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Giampaolo Marcolin, Elisabetta Collini
Summary: By characterizing fucoxanthin with 2DES, researchers can reveal its ultrafast relaxation dynamics and focus on the photophysical properties of the intramolecular charge-transfer state. These results are significant for unraveling the dynamics of the electronic state manifold of carotenoids.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Carlos H. Borca, Zachary L. Glick, Derek P. Metcalf, Lori A. Burns, C. David Sherrill
Summary: The use of many-body expansion (MBE) method, combining CCSD(T)/CBS for closest dimers and trimers and MP2 for more distant ones, shows promising results in efficiently calculating lattice energies in organic crystals. The effectiveness of MP2(+ATM) as a replacement for CCSD(T)/CBS is demonstrated. The CCSD(T)/CBS best estimate of the lattice energy at 0 K is -54.01 kJ mol(-1).
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Hassan Ahmoum, Guojian Li, Yongjun Piao, Shiying Liu, Ralph Gebauer, Mourad Boughrara, Mohd Sukor Su'ait, Mohamed Kerouad, Qiang Wang
Summary: This study investigates the structural, electronic, and magnetic properties of Ni-doped ZnO nanoparticles synthesized using the sol-gel method. Results show that Ni-doped ZnO exhibits ferromagnetic and antiferromagnetic properties within certain Ni concentrations, making it a potential candidate as a diluted magnetic semiconductor.
JOURNAL OF ALLOYS AND COMPOUNDS
(2021)
Article
Chemistry, Multidisciplinary
Giovanna M. A. Rogati, Chiara Capecci, Enza Fazio, Scolastica Serroni, Fausto Puntoriero, Sebastiano Campagna, Leonardo Guidoni
Summary: The structure of a decanuclear dendrimer based on Ru(II) polypyridine subunits, suitable for artificial photosynthesis as a light-harvesting species, has been investigated through computer modeling. Molecular dynamics and quantum mechanics simulations were used to study the stability of possible isomers of each monomer, revealing a prevalence of MER isomerism in the central core. Additionally, the self-aggregation of the dendrimer and the distribution of counterions around the complexes were investigated using Molecular Dynamics in both implicit and explicit acetonitrile solution, suggesting a self-aggregation mechanism for the dendrimers.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Leonardo Ratini, Chiara Capecci, Francesco Benfenati, Leonardo Guidoni
Summary: The study introduces a modified VQE method named WAHTOR, which adapts the form of the molecular Hamiltonian to the circuit ansatz through an optimization procedure, making it more flexible. The method has been successfully applied to simulations of small molecules, demonstrating advantages over traditional VQE methods, being less dependent on circuit topology and less likely to be trapped in high-energy local minima.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Physics, Multidisciplinary
Bosong Sun, Wenjin Zhao, Tauno Palomaki, Zaiyao Fei, Elliott Runburg, Paul Malinowski, Xiong Huang, John Cenker, Yong-Tao Cui, Jiun-Haw Chu, Xiaodong Xu, S. Samaneh Ataei, Daniele Varsano, Maurizia Palummo, Elisa Molinari, Massimo Rontani, David H. Cobden
Summary: Evidence shows that monolayer WTe2 contains excitons formed by electrons and holes bound by Coulomb attraction, exhibiting V-shaped dependence on electrostatic doping and step in chemical potential at the neutral point upon cooling. Strong electronic interactions allow excitons to form and condense at high temperature, showing strong correlations over a wide temperature range.
Article
Chemistry, Physical
S. Vacondio, D. Varsano, A. Ruini, A. Ferretti
Summary: We investigate the performance of beyond-GW approaches in many-body perturbation theory and find that the GW+SOSEX self-energy is a viable scheme to go beyond GW in finite systems, even in the atomic limit. The GW method also shows comparable performance if a hybrid starting point is used. Additionally, the 2B self-energy on top of Hartree-Fock yields promising results, suggesting that the full time-dependent Hartree-Fock vertex may be another viable beyond-GW scheme for finite systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Angela Montanaro, Francesca Giusti, Matteo Zanfrognini, Paola Di Pietro, Filippo Glerean, Giacomo Jarc, Enrico Maria Rigoni, Shahla Y. Mathengattil, Daniele Varsano, Massimo Rontani, Andrea Perucchi, Elisa Molinari, Daniele Fausti
Summary: The authors investigate the optical response of bulk black phosphorus to mid-infrared pulses, and find that while above-gap excitation leads to a broadband light-induced transparency, sub-gap pulses drive an anomalous response, peaked at the single-layer exciton resonance.
NATURE COMMUNICATIONS
(2022)
Article
Materials Science, Multidisciplinary
Miki Bonacci, Matteo Zanfrognini, Elisa Molinari, Alice Ruini, Marilia J. Caldas, Andrea Ferretti, Daniele Varsano
Summary: In this paper, the electronic and dielectric properties of C3N are described, with a focus on the momentum-resolved exciton band structure. It is found that excitonic states can be activated for finite transferred momenta, and an indirect exciton with lower energy than the direct optical gap is observed. The quasi-linear excitonic dispersion near Gamma is also found, which is related to the indirect band gap and the dark nature of the excitons in C3N.
PHYSICAL REVIEW MATERIALS
(2022)
Article
Materials Science, Multidisciplinary
Dario A. Leon, Andrea Ferretti, Daniele Varsano, Elisa Molinari, Claudia Cardoso
Summary: We used density functional theory to study the effects of oxygen adsorption on the structural and electronic properties of Gr/Co(0001) and Gr/Co/Ir(111) interfaces. Oxygen intercalation effectively decreased the electronic interaction, restoring the typical Dirac cone of pristine graphene. The interplay between the O distribution and the continuous change of the graphene-Co registry can be used to tune graphene corrugation and electronic properties.
PHYSICAL REVIEW MATERIALS
(2022)
Article
Plant Sciences
Mario Frezzini, Anna Scortica, Matteo Capone, Daniele Narzi, Manuel Benedetti, Francesco Angelucci, Benedetta Mattei, Leonardo Guidoni
Summary: OGOX1 is an enzyme that oxidizes pectin fragments (OGs) and releases H2O2, thereby reducing the activity of OGs. Molecular dynamics simulations and enzyme kinetics studies have revealed the molecular determinants of OGOX1 that are responsible for binding OGs of different lengths. The results suggest that the binding between OGOX1 and OG5 is the most stable, with salt-bridge interactions stabilizing the optimal conformation of OG5 for efficient oxidation by the enzyme.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Paul Greife, Matthias Schoenborn, Matteo Capone, Ricardo Assuncao, Daniele Narzi, Leonardo Guidoni, Holger Dau
Summary: Photosynthesis stores solar energy in chemical form, which supports life on Earth. The splitting of water at the manganese cluster of photosystem II during photosynthesis has resulted in an oxygen-rich atmosphere. This study reveals the crucial stage of oxygen formation in photosynthesis and its mechanistic role.
Article
Chemistry, Physical
Alberto Guandalini, Pino D'Amico, Andrea Ferretti, Daniele Varsano
Summary: Many-body perturbation theory methods, such as the G(0)W(0) approximation, are accurate in predicting quasiparticle properties of materials, but for 2D semiconductors, calculating the QP band structure requires dense BZ sampling. This work shows a method that combines Monte Carlo integration with interpolation to achieve better convergence of QP corrections for 2D semiconductors.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Chemistry, Physical
Gianluca Parisse, Daniele Narzi, Benny Danilo Belviso, Vito Capriati, Rocco Caliandro, Massimo Trotta, Leonardo Guidoni
Summary: Deep eutectic solvents (DESs) are versatile solvents that can be manipulated to improve the performance of biomolecules. A recent study has investigated the effects of hydrated DESs on protein dynamics using molecular dynamics simulations. The results show that DESs can restrict protein motion and increase the overall structural rigidity. Furthermore, specific interactions between DES components and protein residues have been identified, suggesting the potential for protein crystallization in the presence of hydrated DESs.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Materials Science, Multidisciplinary
Matteo Zanfrognini, Nicola Spallanzani, Miki Bonacci, Elisa Molinari, Alice Ruini, Marilia J. Caldas, Andrea Ferretti, Daniele Varsano
Summary: In recent years, the application of mechanical stress has become a widespread experimental method to tune the electronic and optical properties of two-dimensional materials. In this work, we investigate the impact of uniaxial tensile strain along zigzag and armchair directions on the excitonic properties of graphene-like C3N. We develop a tight-binding Bethe-Salpeter equation framework based on a Wannier-function description of the frontier bands of the system and use it to compute both dark and bright excitons of C3N for different applied strain configurations.
Article
Chemistry, Physical
Daniele Narzi, Leonardo Guidoni
Summary: This study used classical Molecular Dynamics simulations to characterize the structural and dynamic features of apo PSII, revealing that not all residues acting as Mn ligands are pre-organized prior to Mn4Ca formation and previous local conformational changes are required to bind the first Mn ion.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Giovanna M. A. Rogati, Chiara Capecci, Enza Fazio, Scolastica Serroni, Fausto Puntoriero, Sebastiano Campagna, Leonardo Guidoni
Summary: The study investigated a decanuclear photo- and redox-active dendrimer based on Ru(II) polypyridine subunits using computer modelling. It was found that the stability of the dendrimer is governed by the steric constrains originated by the multimetallic assembly rather than the stability of the individual monomers. Additionally, molecular dynamics analysis showed a self-aggregation mechanism of Ru10. The results provide new insights for the design and development of light-harvesting multicomponent species for artificial photosynthesis.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Materials Science, Multidisciplinary
Giacomo Sesti, Daniele Varsano, Elisa Molinari, Massimo Rontani
Summary: The screening of Coulomb interaction plays a crucial role in controlling many-body physics in carbon nanotubes. Different types of tubes exhibit different effects of the Coulomb interaction, which can be evaluated by computing the dielectric function. The standard effective-mass model may underestimate the interaction strength at long wavelengths and miss important interactions.
